Starting phenix.real_space_refine on Wed Feb 14 09:21:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uun_20883/02_2024/6uun_20883.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 64 5.16 5 C 5693 2.51 5 N 1580 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 274": "NH1" <-> "NH2" Residue "R TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 314": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8980 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 627 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 260 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2565 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 232 Time building chain proxies: 5.21, per 1000 atoms: 0.58 Number of scatterers: 8980 At special positions: 0 Unit cell: (84.66, 95.45, 160.19, 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 64 16.00 O 1643 8.00 N 1580 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 41.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.668A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.905A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.572A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.542A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.508A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.638A pdb=" N ILE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 155 Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 156 through 167 removed outlier: 3.610A pdb=" N LEU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.593A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 23 through 34 removed outlier: 4.326A pdb=" N GLN P 32 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.708A pdb=" N ASP R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 167 removed outlier: 3.955A pdb=" N ASN R 128 " --> pdb=" O TYR R 124 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS R 132 " --> pdb=" O ASN R 128 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.515A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR R 227 " --> pdb=" O MET R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 Processing helix chain 'R' and resid 263 through 279 removed outlier: 3.570A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 290 through 294 Processing helix chain 'R' and resid 296 through 321 Processing helix chain 'R' and resid 333 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 400 removed outlier: 4.056A pdb=" N ASN R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.110A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.757A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.056A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.517A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.544A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AB4, first strand: chain 'R' and resid 82 through 87 removed outlier: 4.095A pdb=" N THR R 82 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS R 105 " --> pdb=" O THR R 82 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1287 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: 2.65 Time building geometry restraints manager: 3.69 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: 2765 1.34 - 1.45: 1409 1.45 - 1.57: 4896 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9154 Sorted by residual: bond pdb=" N VAL R 198 " pdb=" CA VAL R 198 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.67e+00 bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N VAL R 135 " pdb=" CA VAL R 135 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 100.17 - 107.00: 219 107.00 - 113.83: 5137 113.83 - 120.66: 3885 120.66 - 127.49: 3115 127.49 - 134.32: 83 Bond angle restraints: 12439 Sorted by residual: angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 112.72 105.06 7.66 1.14e+00 7.69e-01 4.51e+01 angle pdb=" C LEU E 156 " pdb=" N ILE E 157 " pdb=" CA ILE E 157 " ideal model delta sigma weight residual 120.33 123.99 -3.66 8.00e-01 1.56e+00 2.09e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.01 107.74 5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CA ASN R 281 " pdb=" C ASN R 281 " pdb=" O ASN R 281 " ideal model delta sigma weight residual 121.54 117.06 4.48 1.16e+00 7.43e-01 1.49e+01 angle pdb=" N CYS R 282 " pdb=" CA CYS R 282 " pdb=" C CYS R 282 " ideal model delta sigma weight residual 113.56 108.68 4.88 1.39e+00 5.18e-01 1.23e+01 ... (remaining 12434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5073 17.66 - 35.32: 292 35.32 - 52.97: 51 52.97 - 70.63: 13 70.63 - 88.29: 5 Dihedral angle restraints: 5434 sinusoidal: 1935 harmonic: 3499 Sorted by residual: dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -139.41 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.77 -49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS P 16 " pdb=" SG CYS P 16 " pdb=" SG CYS P 21 " pdb=" CB CYS P 21 " ideal model delta sinusoidal sigma weight residual -86.00 -43.45 -42.55 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 5431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1102 0.055 - 0.111: 258 0.111 - 0.166: 54 0.166 - 0.221: 18 0.221 - 0.277: 6 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1435 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C THR R 196 " -0.025 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO G 55 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG B 52 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1423 2.76 - 3.30: 8778 3.30 - 3.83: 14872 3.83 - 4.37: 18007 4.37 - 4.90: 30630 Nonbonded interactions: 73710 Sorted by model distance: nonbonded pdb=" O ASN R 398 " pdb=" ND2 ASN R 398 " model vdw 2.226 2.520 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.270 2.440 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.275 2.520 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.282 2.520 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.283 2.520 ... (remaining 73705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.010 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: 5.660 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 27.110 Find NCS groups from input model: 0.270 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9154 Z= 0.351 Angle : 0.729 7.657 12439 Z= 0.515 Chirality : 0.055 0.277 1438 Planarity : 0.003 0.036 1597 Dihedral : 11.918 88.291 3135 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.45 % Allowed : 4.20 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.59 (0.23), residues: 1176 helix: 0.35 (0.25), residues: 433 sheet: -1.39 (0.32), residues: 223 loop : -2.11 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR P 31 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7834 (mt0) cc_final: 0.7143 (tp-100) REVERT: A 34 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7979 (ttmm) REVERT: A 274 ASP cc_start: 0.7228 (t0) cc_final: 0.6908 (t70) REVERT: B 111 TYR cc_start: 0.8834 (m-80) cc_final: 0.8547 (m-80) REVERT: B 124 TYR cc_start: 0.8821 (m-80) cc_final: 0.8550 (m-80) REVERT: B 325 MET cc_start: 0.8077 (tpp) cc_final: 0.7685 (tpt) REVERT: E 167 ARG cc_start: 0.4151 (mpt180) cc_final: 0.3350 (mmm-85) REVERT: G 42 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6530 (mm-30) REVERT: N 80 TYR cc_start: 0.8083 (m-80) cc_final: 0.7666 (m-80) REVERT: N 87 LYS cc_start: 0.7990 (mttp) cc_final: 0.7278 (mtpm) REVERT: R 134 LYS cc_start: 0.6307 (ttpt) cc_final: 0.6106 (mmtt) REVERT: R 139 LEU cc_start: 0.6457 (mm) cc_final: 0.6232 (mm) REVERT: R 213 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6256 (mttt) REVERT: R 332 MET cc_start: 0.6557 (mmp) cc_final: 0.6302 (pmm) REVERT: R 381 SER cc_start: 0.7836 (t) cc_final: 0.7489 (m) outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 1.2753 time to fit residues: 251.0594 Evaluate side-chains 135 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 31 GLN A 35 GLN A 213 GLN A 218 ASN A 262 GLN A 377 ASN A 390 GLN B 6 GLN B 32 GLN B 175 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 39 GLN N 74 ASN N 120 GLN P 24 GLN R 172 GLN R 179 ASN R 281 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9154 Z= 0.288 Angle : 0.565 6.836 12439 Z= 0.301 Chirality : 0.044 0.153 1438 Planarity : 0.004 0.040 1597 Dihedral : 4.700 57.676 1290 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.41 % Allowed : 12.39 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1176 helix: 1.29 (0.25), residues: 454 sheet: -1.22 (0.32), residues: 222 loop : -1.72 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE N 108 TYR 0.016 0.001 TYR R 278 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7761 (mt0) cc_final: 0.7028 (tp-100) REVERT: A 34 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7848 (ttmm) REVERT: A 274 ASP cc_start: 0.7458 (t0) cc_final: 0.7163 (t70) REVERT: B 124 TYR cc_start: 0.8825 (m-80) cc_final: 0.8551 (m-80) REVERT: B 127 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8396 (mmtm) REVERT: B 195 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7565 (p0) REVERT: B 325 MET cc_start: 0.7972 (tpp) cc_final: 0.7586 (tpt) REVERT: E 167 ARG cc_start: 0.4462 (mpt180) cc_final: 0.3604 (mmm-85) REVERT: N 65 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8004 (ttpt) REVERT: N 80 TYR cc_start: 0.8115 (m-80) cc_final: 0.7783 (m-80) REVERT: R 134 LYS cc_start: 0.6086 (ttpt) cc_final: 0.5853 (mmtt) REVERT: R 139 LEU cc_start: 0.6647 (mm) cc_final: 0.6346 (mm) REVERT: R 182 PHE cc_start: 0.6735 (t80) cc_final: 0.6152 (t80) REVERT: R 213 LYS cc_start: 0.6677 (mtmt) cc_final: 0.6262 (mttt) REVERT: R 253 MET cc_start: 0.7687 (ttt) cc_final: 0.7339 (ttp) REVERT: R 269 ILE cc_start: 0.7454 (mm) cc_final: 0.7246 (mp) REVERT: R 381 SER cc_start: 0.7631 (t) cc_final: 0.7207 (m) outliers start: 30 outliers final: 10 residues processed: 149 average time/residue: 1.5480 time to fit residues: 245.2958 Evaluate side-chains 140 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN R 219 HIS R 281 ASN R 370 HIS R 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9154 Z= 0.167 Angle : 0.482 6.452 12439 Z= 0.257 Chirality : 0.041 0.145 1438 Planarity : 0.003 0.039 1597 Dihedral : 4.479 59.303 1290 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.18 % Allowed : 14.09 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.20 (0.24), residues: 1176 helix: 1.61 (0.25), residues: 460 sheet: -1.01 (0.32), residues: 221 loop : -1.39 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 PHE 0.014 0.001 PHE R 228 TYR 0.009 0.001 TYR R 278 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 31 GLN cc_start: 0.7709 (mt0) cc_final: 0.7050 (tp-100) REVERT: A 34 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7785 (ttmt) REVERT: A 266 LEU cc_start: 0.8520 (tp) cc_final: 0.8181 (tp) REVERT: A 274 ASP cc_start: 0.7336 (t0) cc_final: 0.7050 (t70) REVERT: B 124 TYR cc_start: 0.8789 (m-80) cc_final: 0.8504 (m-80) REVERT: B 127 LYS cc_start: 0.8671 (mmpt) cc_final: 0.8321 (mmtp) REVERT: B 186 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: B 325 MET cc_start: 0.7927 (tpp) cc_final: 0.7457 (tpt) REVERT: E 167 ARG cc_start: 0.4521 (mpt180) cc_final: 0.3644 (mmm-85) REVERT: N 5 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6886 (tp40) REVERT: N 65 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: N 73 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6714 (t0) REVERT: N 80 TYR cc_start: 0.8067 (m-80) cc_final: 0.7662 (m-80) REVERT: N 89 GLU cc_start: 0.6888 (pt0) cc_final: 0.6483 (pp20) REVERT: N 105 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7447 (ttp-110) REVERT: R 127 CYS cc_start: 0.4923 (OUTLIER) cc_final: 0.4144 (p) REVERT: R 134 LYS cc_start: 0.6132 (ttpt) cc_final: 0.5919 (mmtt) REVERT: R 182 PHE cc_start: 0.6779 (t80) cc_final: 0.6206 (t80) REVERT: R 213 LYS cc_start: 0.6693 (mtmt) cc_final: 0.6290 (mttt) REVERT: R 253 MET cc_start: 0.7622 (ttt) cc_final: 0.7278 (ttp) REVERT: R 370 HIS cc_start: 0.6384 (m-70) cc_final: 0.6017 (m90) REVERT: R 381 SER cc_start: 0.7560 (t) cc_final: 0.7130 (m) outliers start: 28 outliers final: 8 residues processed: 148 average time/residue: 1.2727 time to fit residues: 200.5019 Evaluate side-chains 144 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 0.0570 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9154 Z= 0.222 Angle : 0.509 6.497 12439 Z= 0.270 Chirality : 0.042 0.144 1438 Planarity : 0.003 0.038 1597 Dihedral : 4.556 59.742 1290 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 15.34 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.05 (0.25), residues: 1176 helix: 1.72 (0.25), residues: 460 sheet: -0.96 (0.32), residues: 217 loop : -1.26 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR B 105 ARG 0.002 0.000 ARG R 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7430 (mmmm) cc_final: 0.7207 (mmmm) REVERT: A 21 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 31 GLN cc_start: 0.7773 (mt0) cc_final: 0.7106 (tp-100) REVERT: A 34 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7745 (ttmt) REVERT: A 266 LEU cc_start: 0.8538 (tp) cc_final: 0.8220 (tp) REVERT: A 274 ASP cc_start: 0.7452 (t0) cc_final: 0.7161 (t70) REVERT: B 127 LYS cc_start: 0.8663 (mmpt) cc_final: 0.8425 (mmtm) REVERT: B 186 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: B 325 MET cc_start: 0.8073 (tpp) cc_final: 0.7611 (tpt) REVERT: E 167 ARG cc_start: 0.4564 (mpt180) cc_final: 0.3656 (mmm-85) REVERT: G 46 LYS cc_start: 0.8291 (pmtt) cc_final: 0.8082 (pmtt) REVERT: N 5 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7138 (tm-30) REVERT: N 65 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7908 (ttpt) REVERT: N 73 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6692 (t0) REVERT: N 80 TYR cc_start: 0.8105 (m-80) cc_final: 0.7757 (m-80) REVERT: N 89 GLU cc_start: 0.6938 (pt0) cc_final: 0.6561 (pp20) REVERT: N 105 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7496 (ttp-110) REVERT: R 127 CYS cc_start: 0.4494 (OUTLIER) cc_final: 0.3946 (p) REVERT: R 134 LYS cc_start: 0.6205 (ttpt) cc_final: 0.5971 (mmtt) REVERT: R 213 LYS cc_start: 0.6784 (mtmt) cc_final: 0.6326 (mttt) REVERT: R 251 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6742 (t-170) REVERT: R 253 MET cc_start: 0.7615 (ttt) cc_final: 0.7145 (ttp) REVERT: R 277 TYR cc_start: 0.6616 (m-80) cc_final: 0.6411 (m-10) REVERT: R 370 HIS cc_start: 0.6365 (m-70) cc_final: 0.5997 (m90) REVERT: R 381 SER cc_start: 0.7553 (t) cc_final: 0.7090 (m) outliers start: 35 outliers final: 16 residues processed: 150 average time/residue: 1.2728 time to fit residues: 203.8457 Evaluate side-chains 151 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9154 Z= 0.187 Angle : 0.489 6.647 12439 Z= 0.261 Chirality : 0.041 0.145 1438 Planarity : 0.003 0.035 1597 Dihedral : 4.450 59.387 1290 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.43 % Allowed : 14.89 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.12 (0.25), residues: 1176 helix: 1.82 (0.25), residues: 460 sheet: -0.82 (0.32), residues: 215 loop : -1.16 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 PHE 0.014 0.001 PHE R 228 TYR 0.011 0.001 TYR R 278 ARG 0.002 0.000 ARG R 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7118 (mmmm) REVERT: A 21 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 31 GLN cc_start: 0.7719 (mt0) cc_final: 0.7032 (tp-100) REVERT: A 34 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7752 (ttmt) REVERT: A 266 LEU cc_start: 0.8492 (tp) cc_final: 0.8170 (tp) REVERT: A 274 ASP cc_start: 0.7404 (t0) cc_final: 0.7125 (t70) REVERT: B 127 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8429 (mmtm) REVERT: B 186 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: B 195 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7524 (p0) REVERT: B 325 MET cc_start: 0.8028 (tpp) cc_final: 0.7572 (tpt) REVERT: E 167 ARG cc_start: 0.4557 (mpt180) cc_final: 0.3607 (mmm-85) REVERT: G 46 LYS cc_start: 0.8288 (pmtt) cc_final: 0.8047 (pmtt) REVERT: N 65 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7839 (ttpt) REVERT: N 73 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6711 (t0) REVERT: N 80 TYR cc_start: 0.8141 (m-80) cc_final: 0.7801 (m-80) REVERT: N 89 GLU cc_start: 0.6914 (pt0) cc_final: 0.6561 (pp20) REVERT: N 105 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7457 (ttp-110) REVERT: R 127 CYS cc_start: 0.4472 (OUTLIER) cc_final: 0.3928 (p) REVERT: R 134 LYS cc_start: 0.6197 (ttpt) cc_final: 0.5954 (mmtt) REVERT: R 213 LYS cc_start: 0.6772 (mtmt) cc_final: 0.6288 (mttt) REVERT: R 253 MET cc_start: 0.7562 (ttt) cc_final: 0.7218 (ttp) REVERT: R 277 TYR cc_start: 0.6616 (m-80) cc_final: 0.6398 (m-10) REVERT: R 370 HIS cc_start: 0.6367 (m-70) cc_final: 0.5965 (m90) REVERT: R 381 SER cc_start: 0.7491 (t) cc_final: 0.7042 (m) outliers start: 39 outliers final: 20 residues processed: 153 average time/residue: 1.2339 time to fit residues: 201.2839 Evaluate side-chains 154 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9154 Z= 0.181 Angle : 0.487 6.761 12439 Z= 0.259 Chirality : 0.041 0.146 1438 Planarity : 0.003 0.033 1597 Dihedral : 4.382 59.140 1290 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.20 % Allowed : 15.91 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.27 (0.25), residues: 1176 helix: 1.94 (0.25), residues: 460 sheet: -0.76 (0.32), residues: 214 loop : -1.05 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 PHE 0.013 0.001 PHE R 228 TYR 0.011 0.001 TYR B 105 ARG 0.001 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.072 Fit side-chains REVERT: A 17 LYS cc_start: 0.7312 (mmmm) cc_final: 0.7075 (mmmm) REVERT: A 21 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: A 31 GLN cc_start: 0.7755 (mt0) cc_final: 0.7086 (tp-100) REVERT: A 34 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7727 (ttmt) REVERT: A 266 LEU cc_start: 0.8494 (tp) cc_final: 0.8174 (tp) REVERT: A 274 ASP cc_start: 0.7424 (t0) cc_final: 0.7147 (t70) REVERT: A 333 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.3399 (ttt180) REVERT: B 127 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8426 (mmtm) REVERT: B 186 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: B 195 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 325 MET cc_start: 0.7989 (tpp) cc_final: 0.7546 (tpt) REVERT: E 151 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4701 (mt) REVERT: E 167 ARG cc_start: 0.4511 (mpt180) cc_final: 0.3599 (mmm-85) REVERT: G 46 LYS cc_start: 0.8297 (pmtt) cc_final: 0.8051 (pmtt) REVERT: N 65 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: N 73 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6781 (t0) REVERT: N 80 TYR cc_start: 0.8142 (m-80) cc_final: 0.7808 (m-80) REVERT: N 89 GLU cc_start: 0.6844 (pt0) cc_final: 0.6562 (pp20) REVERT: N 99 CYS cc_start: 0.7048 (m) cc_final: 0.6815 (t) REVERT: N 105 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7443 (ttp-110) REVERT: R 127 CYS cc_start: 0.4239 (OUTLIER) cc_final: 0.3684 (p) REVERT: R 134 LYS cc_start: 0.6188 (ttpt) cc_final: 0.5936 (mmtt) REVERT: R 213 LYS cc_start: 0.6825 (mtmt) cc_final: 0.6352 (mttt) REVERT: R 253 MET cc_start: 0.7551 (ttt) cc_final: 0.7209 (ttp) REVERT: R 370 HIS cc_start: 0.6343 (m-70) cc_final: 0.5978 (m90) REVERT: R 381 SER cc_start: 0.7497 (t) cc_final: 0.7046 (m) outliers start: 37 outliers final: 20 residues processed: 154 average time/residue: 1.2309 time to fit residues: 202.1814 Evaluate side-chains 157 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.0270 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9154 Z= 0.133 Angle : 0.467 6.684 12439 Z= 0.247 Chirality : 0.040 0.148 1438 Planarity : 0.003 0.032 1597 Dihedral : 4.223 58.736 1290 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.64 % Allowed : 17.39 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.58 (0.25), residues: 1176 helix: 2.18 (0.25), residues: 452 sheet: -0.50 (0.33), residues: 210 loop : -0.87 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS R 270 PHE 0.013 0.001 PHE R 228 TYR 0.010 0.001 TYR R 278 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.038 Fit side-chains REVERT: A 17 LYS cc_start: 0.7275 (mmmm) cc_final: 0.7074 (mmmm) REVERT: A 21 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 31 GLN cc_start: 0.7667 (mt0) cc_final: 0.7012 (tp-100) REVERT: A 34 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7614 (tttt) REVERT: A 274 ASP cc_start: 0.7347 (t0) cc_final: 0.7072 (t70) REVERT: A 333 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.3387 (ttt180) REVERT: B 127 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8348 (mmtp) REVERT: B 137 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7680 (mmt-90) REVERT: B 186 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: B 195 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 325 MET cc_start: 0.7966 (tpp) cc_final: 0.7515 (tpt) REVERT: E 151 ILE cc_start: 0.4998 (OUTLIER) cc_final: 0.4748 (mt) REVERT: E 167 ARG cc_start: 0.4380 (mpt180) cc_final: 0.3514 (mmm-85) REVERT: G 46 LYS cc_start: 0.8274 (pmtt) cc_final: 0.8020 (pmtt) REVERT: N 65 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: N 73 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6778 (t0) REVERT: N 80 TYR cc_start: 0.8051 (m-80) cc_final: 0.7720 (m-80) REVERT: N 89 GLU cc_start: 0.6851 (pt0) cc_final: 0.6606 (pp20) REVERT: N 105 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7198 (ttp-110) REVERT: R 127 CYS cc_start: 0.4129 (OUTLIER) cc_final: 0.3597 (p) REVERT: R 134 LYS cc_start: 0.6178 (ttpt) cc_final: 0.5941 (mmtt) REVERT: R 202 GLN cc_start: 0.5987 (tp40) cc_final: 0.5500 (mm-40) REVERT: R 213 LYS cc_start: 0.6859 (mtmt) cc_final: 0.6393 (mttt) REVERT: R 253 MET cc_start: 0.7557 (ttt) cc_final: 0.7209 (ttp) REVERT: R 370 HIS cc_start: 0.6334 (m-70) cc_final: 0.6013 (OUTLIER) REVERT: R 373 MET cc_start: 0.6818 (ttp) cc_final: 0.6437 (ttp) REVERT: R 381 SER cc_start: 0.7426 (t) cc_final: 0.7002 (m) outliers start: 32 outliers final: 16 residues processed: 158 average time/residue: 1.2400 time to fit residues: 208.6278 Evaluate side-chains 152 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 175 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9154 Z= 0.370 Angle : 0.598 6.791 12439 Z= 0.317 Chirality : 0.045 0.143 1438 Planarity : 0.004 0.032 1597 Dihedral : 4.770 59.659 1290 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.98 % Allowed : 18.18 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.25 (0.25), residues: 1176 helix: 1.90 (0.25), residues: 456 sheet: -0.90 (0.32), residues: 217 loop : -0.95 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 99 HIS 0.006 0.001 HIS B 62 PHE 0.051 0.002 PHE A 222 TYR 0.019 0.002 TYR B 105 ARG 0.003 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 0.993 Fit side-chains REVERT: A 17 LYS cc_start: 0.7342 (mmmm) cc_final: 0.7044 (mmmm) REVERT: A 21 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: A 31 GLN cc_start: 0.7781 (mt0) cc_final: 0.7103 (tp-100) REVERT: A 34 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7797 (ttmt) REVERT: A 211 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7624 (mmmt) REVERT: A 266 LEU cc_start: 0.8458 (tp) cc_final: 0.8142 (tp) REVERT: A 274 ASP cc_start: 0.7547 (t0) cc_final: 0.7211 (t70) REVERT: A 333 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.3374 (ttt180) REVERT: B 127 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8431 (mmtm) REVERT: B 325 MET cc_start: 0.7970 (tpp) cc_final: 0.7559 (tpt) REVERT: E 151 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4886 (mt) REVERT: E 167 ARG cc_start: 0.4389 (mpt180) cc_final: 0.3486 (mmm-85) REVERT: N 65 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7899 (ttpt) REVERT: N 73 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6809 (t0) REVERT: N 80 TYR cc_start: 0.8198 (m-80) cc_final: 0.7963 (m-80) REVERT: N 89 GLU cc_start: 0.6908 (pt0) cc_final: 0.6595 (pp20) REVERT: N 105 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7281 (ttp-110) REVERT: R 127 CYS cc_start: 0.4072 (OUTLIER) cc_final: 0.3718 (p) REVERT: R 134 LYS cc_start: 0.6231 (ttpt) cc_final: 0.5967 (mmtt) REVERT: R 182 PHE cc_start: 0.6913 (t80) cc_final: 0.6365 (t80) REVERT: R 202 GLN cc_start: 0.6288 (tp40) cc_final: 0.5664 (mm-40) REVERT: R 253 MET cc_start: 0.7592 (ttt) cc_final: 0.7373 (ttt) REVERT: R 370 HIS cc_start: 0.6403 (m-70) cc_final: 0.6059 (m90) REVERT: R 381 SER cc_start: 0.7648 (t) cc_final: 0.7147 (m) outliers start: 35 outliers final: 22 residues processed: 152 average time/residue: 1.2985 time to fit residues: 209.7641 Evaluate side-chains 154 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9154 Z= 0.245 Angle : 0.535 6.941 12439 Z= 0.284 Chirality : 0.042 0.140 1438 Planarity : 0.003 0.031 1597 Dihedral : 4.644 59.137 1290 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.52 % Allowed : 18.64 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.33 (0.25), residues: 1176 helix: 1.93 (0.25), residues: 461 sheet: -0.86 (0.32), residues: 215 loop : -0.89 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 41 PHE 0.018 0.001 PHE A 222 TYR 0.014 0.001 TYR B 105 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7406 (mmmm) cc_final: 0.7140 (mmmm) REVERT: A 21 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: A 31 GLN cc_start: 0.7762 (mt0) cc_final: 0.7082 (tp-100) REVERT: A 34 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7758 (ttmt) REVERT: A 266 LEU cc_start: 0.8434 (tp) cc_final: 0.8103 (tp) REVERT: A 274 ASP cc_start: 0.7459 (t0) cc_final: 0.7141 (t70) REVERT: A 333 ARG cc_start: 0.5550 (OUTLIER) cc_final: 0.3412 (ttt180) REVERT: B 127 LYS cc_start: 0.8658 (mmpt) cc_final: 0.8406 (mmtm) REVERT: B 325 MET cc_start: 0.7903 (tpp) cc_final: 0.7440 (tpt) REVERT: E 151 ILE cc_start: 0.5111 (OUTLIER) cc_final: 0.4874 (mt) REVERT: E 167 ARG cc_start: 0.4333 (mpt180) cc_final: 0.3449 (mmm-85) REVERT: N 65 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7845 (ttpt) REVERT: N 73 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6762 (t0) REVERT: N 80 TYR cc_start: 0.8219 (m-80) cc_final: 0.7918 (m-80) REVERT: N 89 GLU cc_start: 0.6875 (pt0) cc_final: 0.6570 (pp20) REVERT: N 105 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.7283 (ttp-110) REVERT: R 127 CYS cc_start: 0.4065 (OUTLIER) cc_final: 0.3672 (p) REVERT: R 134 LYS cc_start: 0.6204 (ttpt) cc_final: 0.5960 (mmtt) REVERT: R 182 PHE cc_start: 0.6934 (t80) cc_final: 0.6424 (t80) REVERT: R 202 GLN cc_start: 0.6340 (tp40) cc_final: 0.5583 (mm-40) REVERT: R 213 LYS cc_start: 0.6730 (mtpt) cc_final: 0.6230 (mttt) REVERT: R 253 MET cc_start: 0.7559 (ttt) cc_final: 0.7343 (ttt) REVERT: R 370 HIS cc_start: 0.6359 (m-70) cc_final: 0.6006 (m90) REVERT: R 381 SER cc_start: 0.7602 (t) cc_final: 0.7111 (m) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 1.3264 time to fit residues: 201.7525 Evaluate side-chains 148 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9154 Z= 0.305 Angle : 0.557 7.157 12439 Z= 0.296 Chirality : 0.043 0.137 1438 Planarity : 0.004 0.030 1597 Dihedral : 4.729 59.282 1290 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.18 % Allowed : 18.75 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.25 (0.25), residues: 1176 helix: 1.88 (0.25), residues: 463 sheet: -0.95 (0.32), residues: 216 loop : -0.94 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE A 222 TYR 0.017 0.001 TYR B 105 ARG 0.002 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.072 Fit side-chains REVERT: A 17 LYS cc_start: 0.7487 (mmmm) cc_final: 0.7138 (mmmm) REVERT: A 21 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 31 GLN cc_start: 0.7767 (mt0) cc_final: 0.7094 (tp-100) REVERT: A 34 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7735 (ttmm) REVERT: A 266 LEU cc_start: 0.8446 (tp) cc_final: 0.8120 (tp) REVERT: A 274 ASP cc_start: 0.7496 (t0) cc_final: 0.7180 (t70) REVERT: A 333 ARG cc_start: 0.5487 (OUTLIER) cc_final: 0.3364 (ttt180) REVERT: B 127 LYS cc_start: 0.8649 (mmpt) cc_final: 0.8399 (mmtm) REVERT: B 325 MET cc_start: 0.7927 (tpp) cc_final: 0.7459 (tpt) REVERT: E 151 ILE cc_start: 0.5139 (OUTLIER) cc_final: 0.4904 (mt) REVERT: E 167 ARG cc_start: 0.4328 (mpt180) cc_final: 0.3439 (mmm-85) REVERT: N 73 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6768 (t0) REVERT: N 80 TYR cc_start: 0.8229 (m-80) cc_final: 0.7969 (m-80) REVERT: N 89 GLU cc_start: 0.6901 (pt0) cc_final: 0.6580 (pp20) REVERT: N 105 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7364 (ttp-110) REVERT: R 127 CYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3680 (p) REVERT: R 134 LYS cc_start: 0.6199 (ttpt) cc_final: 0.5928 (mmtt) REVERT: R 182 PHE cc_start: 0.6946 (t80) cc_final: 0.6420 (t80) REVERT: R 202 GLN cc_start: 0.6374 (tp40) cc_final: 0.5587 (mm-40) REVERT: R 213 LYS cc_start: 0.6743 (mtpt) cc_final: 0.6243 (mttt) REVERT: R 253 MET cc_start: 0.7543 (ttt) cc_final: 0.7331 (ttt) REVERT: R 370 HIS cc_start: 0.6346 (m-70) cc_final: 0.5991 (m90) REVERT: R 381 SER cc_start: 0.7612 (t) cc_final: 0.7122 (m) outliers start: 28 outliers final: 18 residues processed: 143 average time/residue: 1.2781 time to fit residues: 194.4674 Evaluate side-chains 144 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.178423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122082 restraints weight = 10342.027| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.91 r_work: 0.3266 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9154 Z= 0.189 Angle : 0.508 7.383 12439 Z= 0.270 Chirality : 0.041 0.143 1438 Planarity : 0.003 0.031 1597 Dihedral : 4.542 58.732 1290 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.95 % Allowed : 19.43 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.42 (0.25), residues: 1176 helix: 2.00 (0.25), residues: 464 sheet: -0.81 (0.32), residues: 214 loop : -0.87 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.014 0.001 HIS A 220 PHE 0.019 0.001 PHE A 222 TYR 0.011 0.001 TYR R 278 ARG 0.001 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.84 seconds wall clock time: 70 minutes 14.41 seconds (4214.41 seconds total)