Starting phenix.real_space_refine on Thu Feb 13 01:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868.map" model { file = "/net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dde_7868/02_2025/6dde_7868_neut.cif" } resolution = 3.5 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= 0.027 sd= 0.613 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 60 5.16 5 C 5416 2.51 5 N 1457 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8489 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2097 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.64 Number of scatterers: 8489 At special positions: 0 Unit cell: (100.88, 118.56, 112.32, 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 60 16.00 O 1556 8.00 N 1457 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.70 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied TRANS " DAL D 2 " - " TYR D 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 35.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.834A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.989A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.191A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.648A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.723A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.529A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.710A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.109A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.307A pdb=" N ALA R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 120 removed outlier: 3.589A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 125 removed outlier: 4.160A pdb=" N GLN R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 120 through 125' Processing helix chain 'R' and resid 126 through 128 No H-bonds generated for 'chain 'R' and resid 126 through 128' Processing helix chain 'R' and resid 136 through 171 removed outlier: 4.077A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 3.758A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 205 removed outlier: 3.764A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 227 through 241 removed outlier: 3.662A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 232 " --> pdb=" O TRP R 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 removed outlier: 4.180A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 294 Processing helix chain 'R' and resid 294 through 306 removed outlier: 3.764A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 301 " --> pdb=" O HIS R 297 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.686A pdb=" N SER R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix removed outlier: 3.837A pdb=" N PHE R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.082A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.082A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.823A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.636A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.529A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.690A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.809A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.563A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.569A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.937A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.653A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.653A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.538A pdb=" N ARG E 148 " --> pdb=" O THR E 129 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.728A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1110 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: 2.36 Time building geometry restraints manager: 2.61 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: 2712 1.34 - 1.46: 2067 1.46 - 1.58: 3798 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 8664 Sorted by residual: bond pdb=" C THR E 138 " pdb=" N PRO E 139 " ideal model delta sigma weight residual 1.332 1.375 -0.044 1.34e-02 5.57e+03 1.06e+01 bond pdb=" O ETA D 5 " pdb=" CB ETA D 5 " ideal model delta sigma weight residual 1.413 1.459 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.16e+00 bond pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CG LEU A 227 " pdb=" CD2 LEU A 227 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.31e+00 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11086 1.97 - 3.94: 577 3.94 - 5.92: 63 5.92 - 7.89: 27 7.89 - 9.86: 13 Bond angle restraints: 11766 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 111.91 106.14 5.77 8.90e-01 1.26e+00 4.20e+01 angle pdb=" CA ARG E 206 " pdb=" CB ARG E 206 " pdb=" CG ARG E 206 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" N GLY B 131 " pdb=" CA GLY B 131 " pdb=" C GLY B 131 " ideal model delta sigma weight residual 111.45 116.63 -5.18 1.23e+00 6.61e-01 1.77e+01 angle pdb=" N THR E 116 " pdb=" CA THR E 116 " pdb=" C THR E 116 " ideal model delta sigma weight residual 109.24 102.47 6.77 1.63e+00 3.76e-01 1.73e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 ... (remaining 11761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 4770 15.14 - 30.28: 253 30.28 - 45.41: 69 45.41 - 60.55: 9 60.55 - 75.69: 4 Dihedral angle restraints: 5105 sinusoidal: 1846 harmonic: 3259 Sorted by residual: dihedral pdb=" CA LEU B 30 " pdb=" C LEU B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 5102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 931 0.051 - 0.102: 312 0.102 - 0.153: 90 0.153 - 0.204: 24 0.204 - 0.255: 5 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1359 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 61 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ALA E 61 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA E 61 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP E 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" CG TRP B 63 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO C 49 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.034 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1755 2.77 - 3.31: 7700 3.31 - 3.84: 14166 3.84 - 4.37: 15799 4.37 - 4.90: 27949 Nonbonded interactions: 67369 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" O LYS A 277 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.251 3.040 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.290 3.040 ... (remaining 67364 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 group one per residue 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: 0.870 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.006 0.078 8664 Z= 0.409 Angle : 1.026 9.858 11766 Z= 0.569 Chirality : 0.059 0.255 1362 Planarity : 0.006 0.062 1484 Dihedral : 10.869 75.688 2991 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 0.46 % Allowed : 6.00 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.56 (0.21), residues: 1103 helix: -2.51 (0.20), residues: 348 sheet: -2.14 (0.29), residues: 256 loop : -2.22 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 63 HIS 0.011 0.003 HIS E 155 PHE 0.028 0.003 PHE B 241 TYR 0.030 0.003 TYR E 163 ARG 0.018 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 362 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 309 ASP cc_start: 0.7384 (t0) cc_final: 0.7153 (t0) REVERT: A 341 ASP cc_start: 0.8439 (t70) cc_final: 0.8170 (t0) REVERT: B 86 THR cc_start: 0.8060 (p) cc_final: 0.7552 (p) REVERT: B 163 ASP cc_start: 0.7499 (p0) cc_final: 0.7240 (p0) REVERT: B 221 THR cc_start: 0.8150 (m) cc_final: 0.7823 (m) REVERT: B 339 TRP cc_start: 0.8617 (m100) cc_final: 0.8210 (m100) REVERT: E 7 SER cc_start: 0.8095 (p) cc_final: 0.7554 (t) REVERT: E 130 GLN cc_start: 0.6596 (tp40) cc_final: 0.6065 (mt0) REVERT: R 112 LEU cc_start: 0.9102 (tp) cc_final: 0.8888 (tt) REVERT: R 145 SER cc_start: 0.8369 (t) cc_final: 0.7708 (m) REVERT: R 228 TRP cc_start: 0.7285 (t-100) cc_final: 0.7051 (t-100) REVERT: R 261 SER cc_start: 0.8665 (m) cc_final: 0.8283 (t) REVERT: R 263 ARG cc_start: 0.8061 (tmt90) cc_final: 0.7791 (tpt90) REVERT: R 270 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 4 outliers final: 1 residues processed: 365 average time/residue: 0.2465 time to fit residues: 118.3263 Evaluate side-chains 234 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 347 ASN B 110 ASN B 295 ASN E 130 GLN E 171 GLN E 174 GLN E 182 ASN R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN R 150 ASN R 230 ASN R 297 HIS R 328 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142446 restraints weight = 12948.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147288 restraints weight = 6704.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150406 restraints weight = 4233.199| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8664 Z= 0.224 Angle : 0.674 10.575 11766 Z= 0.347 Chirality : 0.044 0.203 1362 Planarity : 0.004 0.041 1484 Dihedral : 5.581 67.874 1214 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.04 % Allowed : 17.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.05 (0.24), residues: 1103 helix: -0.60 (0.27), residues: 351 sheet: -1.68 (0.31), residues: 239 loop : -1.65 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE R 241 TYR 0.019 0.002 TYR R 75 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 51 LYS cc_start: 0.8610 (ttmp) cc_final: 0.8191 (tmmt) REVERT: A 216 GLU cc_start: 0.7863 (pt0) cc_final: 0.7616 (pp20) REVERT: A 254 CYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7637 (m) REVERT: A 302 TYR cc_start: 0.8185 (t80) cc_final: 0.7958 (t80) REVERT: A 341 ASP cc_start: 0.8710 (t70) cc_final: 0.8474 (t0) REVERT: B 82 TRP cc_start: 0.8953 (m100) cc_final: 0.8728 (m100) REVERT: B 86 THR cc_start: 0.8451 (p) cc_final: 0.8246 (p) REVERT: B 117 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7334 (tt) REVERT: B 163 ASP cc_start: 0.7875 (p0) cc_final: 0.7651 (p0) REVERT: B 280 LYS cc_start: 0.8148 (tmmt) cc_final: 0.7905 (tttt) REVERT: B 339 TRP cc_start: 0.8781 (m100) cc_final: 0.8223 (m-10) REVERT: E 115 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8317 (p) REVERT: E 130 GLN cc_start: 0.6484 (tp-100) cc_final: 0.5744 (mt0) REVERT: R 106 TYR cc_start: 0.9037 (m-80) cc_final: 0.8665 (m-10) REVERT: R 123 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7030 (t80) REVERT: R 161 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (tpp) REVERT: R 165 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8204 (mtt90) REVERT: R 185 LYS cc_start: 0.8622 (ttmp) cc_final: 0.8057 (tptt) REVERT: R 228 TRP cc_start: 0.7481 (t-100) cc_final: 0.7147 (t-100) REVERT: R 263 ARG cc_start: 0.8274 (tmt90) cc_final: 0.7848 (tmt170) REVERT: R 270 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7864 (tm-30) REVERT: R 298 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7167 (pt) REVERT: R 336 TYR cc_start: 0.7122 (m-10) cc_final: 0.6858 (m-80) outliers start: 35 outliers final: 18 residues processed: 278 average time/residue: 0.2348 time to fit residues: 85.6075 Evaluate side-chains 248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 161 MET Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 92 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 75 GLN E 130 GLN ** R 109 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 = 0.4191 r_free = 0.4191 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143553 restraints weight = 13094.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.148367 restraints weight = 6668.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.151456 restraints weight = 4193.528| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8664 Z= 0.188 Angle : 0.656 8.769 11766 Z= 0.334 Chirality : 0.043 0.193 1362 Planarity : 0.004 0.040 1484 Dihedral : 5.299 71.363 1214 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.50 % Allowed : 20.09 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.45 (0.25), residues: 1103 helix: 0.10 (0.28), residues: 355 sheet: -1.40 (0.31), residues: 237 loop : -1.44 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.001 PHE R 241 TYR 0.025 0.002 TYR R 75 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 228 SER cc_start: 0.7886 (p) cc_final: 0.7300 (m) REVERT: A 341 ASP cc_start: 0.8688 (t70) cc_final: 0.8473 (t0) REVERT: A 347 ASN cc_start: 0.9268 (m-40) cc_final: 0.8856 (m-40) REVERT: B 117 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7230 (tt) REVERT: B 170 ASP cc_start: 0.6996 (t0) cc_final: 0.6698 (t0) REVERT: B 212 ASP cc_start: 0.7141 (p0) cc_final: 0.6930 (m-30) REVERT: B 308 LEU cc_start: 0.8257 (mp) cc_final: 0.7969 (mp) REVERT: B 339 TRP cc_start: 0.8762 (m100) cc_final: 0.8167 (m-10) REVERT: R 106 TYR cc_start: 0.9031 (m-80) cc_final: 0.8436 (m-10) REVERT: R 161 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: R 164 ASP cc_start: 0.8611 (t70) cc_final: 0.8340 (t70) REVERT: R 170 CYS cc_start: 0.7394 (t) cc_final: 0.7157 (t) REVERT: R 185 LYS cc_start: 0.8555 (ttmp) cc_final: 0.8035 (tptt) REVERT: R 228 TRP cc_start: 0.7507 (t-100) cc_final: 0.7146 (t-100) REVERT: R 233 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7754 (ttpt) REVERT: R 263 ARG cc_start: 0.8205 (tmt90) cc_final: 0.7794 (tmt170) REVERT: R 270 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7924 (tm-30) REVERT: R 277 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.7928 (tmm-80) REVERT: R 298 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7092 (pt) REVERT: R 336 TYR cc_start: 0.7210 (m-10) cc_final: 0.6931 (m-10) outliers start: 39 outliers final: 22 residues processed: 276 average time/residue: 0.2351 time to fit residues: 85.5460 Evaluate side-chains 247 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 161 MET Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 109 optimal weight: 0.0570 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 156 GLN B 230 ASN E 82 GLN E 130 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144664 restraints weight = 13254.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149567 restraints weight = 6718.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152675 restraints weight = 4190.701| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8664 Z= 0.213 Angle : 0.661 8.186 11766 Z= 0.331 Chirality : 0.044 0.275 1362 Planarity : 0.004 0.038 1484 Dihedral : 5.137 70.991 1214 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.50 % Allowed : 22.52 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.19 (0.25), residues: 1103 helix: 0.61 (0.29), residues: 345 sheet: -1.30 (0.31), residues: 243 loop : -1.47 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 133 HIS 0.004 0.001 HIS R 319 PHE 0.015 0.001 PHE R 241 TYR 0.031 0.002 TYR E 178 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 51 LYS cc_start: 0.8737 (ttmp) cc_final: 0.8257 (tmmt) REVERT: A 197 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8178 (mtpp) REVERT: A 228 SER cc_start: 0.7856 (p) cc_final: 0.7371 (m) REVERT: A 253 ILE cc_start: 0.8746 (tt) cc_final: 0.8489 (mm) REVERT: A 341 ASP cc_start: 0.8678 (t70) cc_final: 0.8446 (t0) REVERT: A 347 ASN cc_start: 0.9272 (m-40) cc_final: 0.8890 (m-40) REVERT: B 117 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 170 ASP cc_start: 0.7167 (t0) cc_final: 0.6948 (t0) REVERT: B 308 LEU cc_start: 0.8395 (mp) cc_final: 0.7925 (mp) REVERT: B 339 TRP cc_start: 0.8825 (m100) cc_final: 0.8260 (m-10) REVERT: R 161 MET cc_start: 0.8700 (tpp) cc_final: 0.8138 (tpp) REVERT: R 164 ASP cc_start: 0.8620 (t70) cc_final: 0.8332 (t70) REVERT: R 165 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7749 (mtt90) REVERT: R 185 LYS cc_start: 0.8644 (ttmp) cc_final: 0.8162 (tptp) REVERT: R 211 ARG cc_start: 0.6288 (mtt90) cc_final: 0.6016 (mtt180) REVERT: R 228 TRP cc_start: 0.7482 (t-100) cc_final: 0.7151 (t-100) REVERT: R 263 ARG cc_start: 0.8216 (tmt90) cc_final: 0.7833 (tmt170) REVERT: R 277 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.8183 (tmm-80) REVERT: R 336 TYR cc_start: 0.7255 (m-10) cc_final: 0.6926 (m-10) outliers start: 39 outliers final: 28 residues processed: 269 average time/residue: 0.2336 time to fit residues: 82.9900 Evaluate side-chains 255 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 156 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142841 restraints weight = 13117.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147382 restraints weight = 7098.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150258 restraints weight = 4565.664| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8664 Z= 0.235 Angle : 0.671 9.539 11766 Z= 0.336 Chirality : 0.044 0.306 1362 Planarity : 0.004 0.037 1484 Dihedral : 5.100 71.230 1214 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.54 % Allowed : 22.98 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1103 helix: 0.77 (0.29), residues: 348 sheet: -1.29 (0.31), residues: 254 loop : -1.41 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 133 HIS 0.005 0.001 HIS R 319 PHE 0.015 0.001 PHE R 241 TYR 0.025 0.002 TYR E 178 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 51 LYS cc_start: 0.8800 (ttmp) cc_final: 0.8285 (tmmt) REVERT: A 197 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8137 (mtpp) REVERT: A 216 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: A 334 PHE cc_start: 0.8865 (t80) cc_final: 0.8608 (t80) REVERT: A 341 ASP cc_start: 0.8734 (t70) cc_final: 0.8473 (t0) REVERT: A 347 ASN cc_start: 0.9349 (m-40) cc_final: 0.8996 (m-40) REVERT: B 59 TYR cc_start: 0.8863 (m-80) cc_final: 0.8585 (m-80) REVERT: B 117 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 170 ASP cc_start: 0.7372 (t0) cc_final: 0.7088 (t0) REVERT: B 339 TRP cc_start: 0.8911 (m100) cc_final: 0.8300 (m-10) REVERT: C 13 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8082 (mtm110) REVERT: E 207 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6559 (tt) REVERT: R 161 MET cc_start: 0.8756 (tpp) cc_final: 0.8225 (tpp) REVERT: R 164 ASP cc_start: 0.8676 (t70) cc_final: 0.8372 (t70) REVERT: R 165 ARG cc_start: 0.8461 (mtt90) cc_final: 0.7781 (mtt90) REVERT: R 185 LYS cc_start: 0.8722 (ttmp) cc_final: 0.8195 (tptp) REVERT: R 228 TRP cc_start: 0.7571 (t-100) cc_final: 0.7249 (t-100) REVERT: R 233 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7769 (ttmt) REVERT: R 263 ARG cc_start: 0.8231 (tmt90) cc_final: 0.7819 (tmt170) REVERT: R 270 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7451 (tm-30) REVERT: R 277 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.8181 (tmm-80) REVERT: R 336 TYR cc_start: 0.7201 (m-10) cc_final: 0.6814 (m-10) outliers start: 48 outliers final: 33 residues processed: 258 average time/residue: 0.2287 time to fit residues: 77.9918 Evaluate side-chains 247 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 156 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.178904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.153389 restraints weight = 12773.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157728 restraints weight = 7135.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.160362 restraints weight = 4028.901| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8664 Z= 0.176 Angle : 0.653 11.175 11766 Z= 0.324 Chirality : 0.043 0.270 1362 Planarity : 0.004 0.036 1484 Dihedral : 4.993 72.876 1214 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.73 % Allowed : 23.79 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.87 (0.26), residues: 1103 helix: 1.06 (0.30), residues: 346 sheet: -1.32 (0.31), residues: 256 loop : -1.30 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 133 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.001 PHE R 241 TYR 0.021 0.002 TYR E 178 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 51 LYS cc_start: 0.8852 (ttmp) cc_final: 0.8278 (tmmt) REVERT: A 216 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8177 (pp20) REVERT: A 228 SER cc_start: 0.7652 (p) cc_final: 0.7051 (m) REVERT: A 242 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7411 (mtp180) REVERT: A 245 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8301 (pt0) REVERT: A 334 PHE cc_start: 0.8892 (t80) cc_final: 0.8567 (t80) REVERT: A 347 ASN cc_start: 0.9300 (m-40) cc_final: 0.8888 (m-40) REVERT: B 59 TYR cc_start: 0.8801 (m-80) cc_final: 0.8427 (m-80) REVERT: B 117 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7110 (tt) REVERT: B 172 GLU cc_start: 0.7826 (mp0) cc_final: 0.7626 (mp0) REVERT: B 280 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8219 (tttt) REVERT: B 339 TRP cc_start: 0.8963 (m100) cc_final: 0.8234 (m-10) REVERT: C 32 LYS cc_start: 0.8357 (mppt) cc_final: 0.8111 (mptt) REVERT: E 71 SER cc_start: 0.8035 (p) cc_final: 0.7650 (t) REVERT: E 207 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6608 (tt) REVERT: R 78 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8637 (t) REVERT: R 141 LYS cc_start: 0.6141 (pttp) cc_final: 0.5550 (tttt) REVERT: R 161 MET cc_start: 0.8647 (tpp) cc_final: 0.8288 (tpp) REVERT: R 164 ASP cc_start: 0.8673 (t70) cc_final: 0.7925 (t70) REVERT: R 179 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8277 (ptm160) REVERT: R 185 LYS cc_start: 0.8656 (ttmp) cc_final: 0.8148 (tptp) REVERT: R 228 TRP cc_start: 0.7538 (t-100) cc_final: 0.7214 (t-100) REVERT: R 233 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7922 (ttmt) REVERT: R 263 ARG cc_start: 0.8205 (tmt90) cc_final: 0.7783 (tmt170) REVERT: R 277 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: R 336 TYR cc_start: 0.7272 (m-10) cc_final: 0.6937 (m-10) outliers start: 41 outliers final: 26 residues processed: 246 average time/residue: 0.2299 time to fit residues: 75.0801 Evaluate side-chains 236 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.2274 > 50: distance: 5 - 10: 18.957 distance: 10 - 11: 13.477 distance: 11 - 12: 16.111 distance: 11 - 14: 9.720 distance: 12 - 13: 20.856 distance: 12 - 16: 5.003 distance: 14 - 15: 9.411 distance: 16 - 17: 13.226 distance: 17 - 18: 12.113 distance: 17 - 20: 12.533 distance: 18 - 19: 24.171 distance: 18 - 22: 27.007 distance: 20 - 21: 22.511 distance: 22 - 23: 25.155 distance: 22 - 115: 23.726 distance: 23 - 24: 17.243 distance: 23 - 26: 8.701 distance: 24 - 25: 10.026 distance: 24 - 29: 17.855 distance: 25 - 127: 32.333 distance: 26 - 27: 21.895 distance: 26 - 28: 22.695 distance: 29 - 30: 11.324 distance: 29 - 35: 30.698 distance: 30 - 31: 10.658 distance: 30 - 33: 4.029 distance: 31 - 32: 7.651 distance: 31 - 36: 10.725 distance: 33 - 34: 15.982 distance: 34 - 35: 20.967 distance: 36 - 37: 9.179 distance: 37 - 38: 17.662 distance: 37 - 40: 17.893 distance: 38 - 39: 27.470 distance: 38 - 43: 22.373 distance: 40 - 41: 15.280 distance: 40 - 42: 27.443 distance: 43 - 44: 11.538 distance: 44 - 45: 8.579 distance: 44 - 47: 25.994 distance: 45 - 46: 15.532 distance: 45 - 50: 12.999 distance: 47 - 48: 24.946 distance: 47 - 49: 16.808 distance: 50 - 51: 21.407 distance: 50 - 56: 31.100 distance: 51 - 52: 5.661 distance: 51 - 54: 11.809 distance: 52 - 53: 8.753 distance: 52 - 57: 13.808 distance: 54 - 55: 5.550 distance: 55 - 56: 50.756 distance: 57 - 58: 13.087 distance: 58 - 59: 14.761 distance: 59 - 60: 7.293 distance: 59 - 61: 11.426 distance: 61 - 62: 14.857 distance: 62 - 65: 23.237 distance: 63 - 64: 14.544 distance: 63 - 66: 7.777 distance: 66 - 67: 6.414 distance: 67 - 68: 11.012 distance: 67 - 70: 8.988 distance: 68 - 69: 13.595 distance: 68 - 72: 14.269 distance: 70 - 71: 25.495