Starting phenix.real_space_refine on Fri Dec 8 17:04:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/12_2023/8hbd_34619_neut.pdb" } resolution = 2.99 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= 0.001 sd= 0.026 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 63 5.16 5 C 5635 2.51 5 N 1481 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1717 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2540 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1726 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 123 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2293 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 5.18, per 1000 atoms: 0.59 Number of scatterers: 8803 At special positions: 0 Unit cell: (107.12, 112.32, 130, 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 63 16.00 O 1624 8.00 N 1481 7.00 C 5635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.05 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.520A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.587A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.107A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.365A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.881A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.660A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.970A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'L' and resid 10 through 18 removed outlier: 4.143A pdb=" N PHE L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 129 removed outlier: 3.982A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN R 104 " --> pdb=" O PHE R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 Processing helix chain 'R' and resid 154 through 165 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.610A pdb=" N LEU R 192 " --> pdb=" O THR R 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS R 193 " --> pdb=" O VAL R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 233 removed outlier: 3.576A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP R 226 " --> pdb=" O ILE R 222 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 237 Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 272 through 280 removed outlier: 3.594A pdb=" N PHE R 280 " --> pdb=" O TRP R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 removed outlier: 4.362A pdb=" N ALA R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS R 298 " --> pdb=" O THR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 349 removed outlier: 4.000A pdb=" N LYS R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 321 " --> pdb=" O GLN R 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU R 328 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Proline residue: R 338 - end of helix removed outlier: 3.933A pdb=" N ARG R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 344 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 345 " --> pdb=" O LEU R 341 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS R 346 " --> pdb=" O SER R 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 380 removed outlier: 3.892A pdb=" N PHE R 363 " --> pdb=" O GLU R 359 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 389 removed outlier: 3.723A pdb=" N ILE R 384 " --> pdb=" O CYS R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 399 removed outlier: 4.075A pdb=" N CYS R 396 " --> pdb=" O ARG R 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.921A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.589A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.154A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 7.014A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.202A 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: 6.751A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.909A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.819A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.551A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.904A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.538A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.659A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'R' and resid 240 through 246 removed outlier: 3.683A pdb=" N ASP R 241 " --> pdb=" O LEU R 256 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU R 256 " --> pdb=" O ASP R 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET R 245 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU R 252 " --> pdb=" O MET R 245 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1143 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: 2.60 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1528 1.32 - 1.45: 2385 1.45 - 1.57: 4983 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 8984 Sorted by residual: bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.23e-02 6.61e+03 8.69e+00 bond pdb=" C PRO R 178 " pdb=" O PRO R 178 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.30e-02 5.92e+03 7.43e+00 bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.77e+00 bond pdb=" N PRO R 178 " pdb=" CA PRO R 178 " ideal model delta sigma weight residual 1.469 1.439 0.030 1.28e-02 6.10e+03 5.35e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.94: 210 106.94 - 113.75: 4981 113.75 - 120.57: 3624 120.57 - 127.38: 3295 127.38 - 134.19: 93 Bond angle restraints: 12203 Sorted by residual: angle pdb=" N GLN A 52 " pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 112.04 102.46 9.58 1.44e+00 4.82e-01 4.43e+01 angle pdb=" N TRP R 206 " pdb=" CA TRP R 206 " pdb=" C TRP R 206 " ideal model delta sigma weight residual 113.20 104.38 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" N ARG R 343 " pdb=" CA ARG R 343 " pdb=" C ARG R 343 " ideal model delta sigma weight residual 114.75 108.35 6.40 1.26e+00 6.30e-01 2.58e+01 angle pdb=" N ILE R 209 " pdb=" CA ILE R 209 " pdb=" C ILE R 209 " ideal model delta sigma weight residual 109.34 118.89 -9.55 2.08e+00 2.31e-01 2.11e+01 angle pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 113.61 106.75 6.86 1.50e+00 4.44e-01 2.09e+01 ... (remaining 12198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4556 17.51 - 35.01: 545 35.01 - 52.52: 156 52.52 - 70.03: 24 70.03 - 87.53: 7 Dihedral angle restraints: 5288 sinusoidal: 1929 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 139.64 -46.64 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" C ARG R 208 " pdb=" N ARG R 208 " pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA LEU B 14 " pdb=" C LEU B 14 " pdb=" N LYS B 15 " pdb=" CA LYS B 15 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1251 0.062 - 0.125: 146 0.125 - 0.187: 16 0.187 - 0.249: 4 0.249 - 0.311: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ARG R 208 " pdb=" N ARG R 208 " pdb=" C ARG R 208 " pdb=" CB ARG R 208 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL R 177 " pdb=" CA VAL R 177 " pdb=" CG1 VAL R 177 " pdb=" CG2 VAL R 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 52 " pdb=" N GLN A 52 " pdb=" C GLN A 52 " pdb=" CB GLN A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1416 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 313 " -0.038 2.00e-02 2.50e+03 7.40e-02 5.47e+01 pdb=" C ASN B 313 " 0.128 2.00e-02 2.50e+03 pdb=" O ASN B 313 " -0.048 2.00e-02 2.50e+03 pdb=" N ARG B 314 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 307 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C PHE A 307 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 307 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU A 308 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 180 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C PHE B 180 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 181 " 0.023 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 68 2.51 - 3.11: 6276 3.11 - 3.70: 13791 3.70 - 4.30: 19315 4.30 - 4.90: 31914 Nonbonded interactions: 71364 Sorted by model distance: nonbonded pdb=" CE1 TYR A 296 " pdb=" OE1 GLU A 297 " model vdw 1.912 3.340 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.034 2.440 nonbonded pdb=" OE1 GLU A 289 " pdb=" OH TYR A 302 " model vdw 2.212 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.232 2.440 ... (remaining 71359 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: 1.870 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: 4.050 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.100 Find NCS groups from input model: 0.260 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.003 0.048 8984 Z= 0.194 Angle : 0.709 9.582 12203 Z= 0.408 Chirality : 0.044 0.311 1419 Planarity : 0.004 0.074 1536 Dihedral : 16.471 87.532 3110 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 29.55 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.26), residues: 1134 helix: 0.26 (0.27), residues: 397 sheet: 1.16 (0.32), residues: 281 loop : -0.42 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE A 336 TYR 0.011 0.001 TYR H 175 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 252 average time/residue: 0.9422 time to fit residues: 257.3173 Evaluate side-chains 232 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.4931 time to fit residues: 2.9813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 102 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 331 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8984 Z= 0.216 Angle : 0.564 8.856 12203 Z= 0.293 Chirality : 0.041 0.196 1419 Planarity : 0.004 0.037 1536 Dihedral : 3.916 20.823 1235 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.89 % Allowed : 25.85 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.26), residues: 1134 helix: 0.59 (0.27), residues: 401 sheet: 1.03 (0.32), residues: 276 loop : -0.26 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 111 HIS 0.004 0.001 HIS G 44 PHE 0.026 0.002 PHE A 336 TYR 0.013 0.001 TYR R 102 ARG 0.008 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 268 time to evaluate : 0.965 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 295 average time/residue: 0.8020 time to fit residues: 259.9226 Evaluate side-chains 284 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 8 residues processed: 15 average time/residue: 0.4189 time to fit residues: 8.6305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 17 GLN B 125 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8984 Z= 0.167 Angle : 0.553 9.608 12203 Z= 0.280 Chirality : 0.040 0.174 1419 Planarity : 0.004 0.059 1536 Dihedral : 3.875 20.096 1235 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.56 % Allowed : 29.01 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1134 helix: 0.62 (0.27), residues: 402 sheet: 1.01 (0.31), residues: 272 loop : -0.19 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 111 HIS 0.003 0.001 HIS R 314 PHE 0.020 0.001 PHE L 14 TYR 0.031 0.001 TYR H 190 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 301 average time/residue: 0.8722 time to fit residues: 286.1247 Evaluate side-chains 279 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 9 residues processed: 13 average time/residue: 0.3047 time to fit residues: 6.2958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 125 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 194 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8984 Z= 0.233 Angle : 0.591 9.124 12203 Z= 0.300 Chirality : 0.042 0.169 1419 Planarity : 0.004 0.054 1536 Dihedral : 4.129 21.540 1235 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.56 % Allowed : 29.88 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.26), residues: 1134 helix: 0.63 (0.27), residues: 403 sheet: 0.81 (0.31), residues: 286 loop : -0.20 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 111 HIS 0.003 0.001 HIS R 314 PHE 0.024 0.002 PHE L 14 TYR 0.029 0.002 TYR R 102 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 28 residues processed: 325 average time/residue: 0.7498 time to fit residues: 268.4694 Evaluate side-chains 301 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 273 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.3485 time to fit residues: 4.3784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 125 ASN B 220 GLN B 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8984 Z= 0.227 Angle : 0.603 9.533 12203 Z= 0.303 Chirality : 0.043 0.206 1419 Planarity : 0.004 0.054 1536 Dihedral : 4.276 23.890 1235 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.78 % Allowed : 33.04 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.25), residues: 1134 helix: 0.64 (0.27), residues: 397 sheet: 0.91 (0.31), residues: 278 loop : -0.41 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.004 0.001 HIS R 314 PHE 0.015 0.001 PHE A 189 TYR 0.035 0.002 TYR H 190 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 288 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 32 residues processed: 322 average time/residue: 0.8532 time to fit residues: 299.9208 Evaluate side-chains 303 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 271 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 10 average time/residue: 0.3921 time to fit residues: 5.9563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8984 Z= 0.222 Angle : 0.617 10.078 12203 Z= 0.310 Chirality : 0.043 0.193 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.298 23.315 1235 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 7.09 % Allowed : 31.84 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.25), residues: 1134 helix: 0.62 (0.27), residues: 401 sheet: 0.84 (0.30), residues: 276 loop : -0.42 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 111 HIS 0.005 0.001 HIS B 54 PHE 0.031 0.002 PHE A 336 TYR 0.024 0.002 TYR R 102 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 281 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 36 residues processed: 320 average time/residue: 0.7670 time to fit residues: 269.8068 Evaluate side-chains 317 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 25 residues processed: 12 average time/residue: 0.3228 time to fit residues: 6.0202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8984 Z= 0.273 Angle : 0.666 10.418 12203 Z= 0.335 Chirality : 0.044 0.235 1419 Planarity : 0.004 0.056 1536 Dihedral : 4.550 26.910 1235 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.23 % Allowed : 33.70 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.26), residues: 1134 helix: 0.56 (0.27), residues: 404 sheet: 0.76 (0.30), residues: 284 loop : -0.43 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.026 0.002 PHE L 14 TYR 0.037 0.002 TYR H 190 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 288 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 318 average time/residue: 0.7903 time to fit residues: 276.8845 Evaluate side-chains 315 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 288 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 10 average time/residue: 0.2732 time to fit residues: 4.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8984 Z= 0.195 Angle : 0.652 10.571 12203 Z= 0.324 Chirality : 0.043 0.256 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.367 24.433 1235 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.47 % Allowed : 36.21 % Favored : 59.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.25), residues: 1134 helix: 0.68 (0.27), residues: 399 sheet: 0.72 (0.31), residues: 266 loop : -0.61 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 111 HIS 0.007 0.001 HIS B 54 PHE 0.026 0.002 PHE A 336 TYR 0.020 0.002 TYR R 102 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 28 residues processed: 332 average time/residue: 0.8072 time to fit residues: 293.4115 Evaluate side-chains 318 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.6325 time to fit residues: 8.3059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8984 Z= 0.230 Angle : 0.652 10.385 12203 Z= 0.327 Chirality : 0.043 0.250 1419 Planarity : 0.004 0.063 1536 Dihedral : 4.429 24.474 1235 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.60 % Allowed : 37.40 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.25), residues: 1134 helix: 0.72 (0.27), residues: 398 sheet: 0.73 (0.31), residues: 267 loop : -0.63 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 111 HIS 0.006 0.001 HIS B 54 PHE 0.037 0.002 PHE L 14 TYR 0.035 0.002 TYR H 190 ARG 0.012 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 27 residues processed: 311 average time/residue: 0.7476 time to fit residues: 256.3563 Evaluate side-chains 320 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 293 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.4961 time to fit residues: 5.3109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 112 optimal weight: 0.0370 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 125 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8984 Z= 0.172 Angle : 0.640 10.367 12203 Z= 0.322 Chirality : 0.042 0.276 1419 Planarity : 0.004 0.054 1536 Dihedral : 4.315 23.354 1235 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.84 % Allowed : 39.37 % Favored : 57.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.25), residues: 1134 helix: 0.79 (0.28), residues: 398 sheet: 0.66 (0.30), residues: 269 loop : -0.73 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 111 HIS 0.005 0.001 HIS B 54 PHE 0.032 0.002 PHE R 179 TYR 0.030 0.002 TYR H 190 ARG 0.013 0.001 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 299 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 321 average time/residue: 0.7978 time to fit residues: 280.3931 Evaluate side-chains 312 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 291 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 1.1185 time to fit residues: 6.1304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 24 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 125 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 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 = 0.3764 r_free = 0.3764 target = 0.124908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113971 restraints weight = 14164.914| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.16 r_work: 0.3507 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8984 Z= 0.180 Angle : 0.646 10.159 12203 Z= 0.324 Chirality : 0.042 0.260 1419 Planarity : 0.004 0.055 1536 Dihedral : 4.284 22.830 1235 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.62 % Allowed : 40.46 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1134 helix: 0.85 (0.28), residues: 397 sheet: 0.54 (0.30), residues: 273 loop : -0.67 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 111 HIS 0.005 0.001 HIS B 54 PHE 0.037 0.002 PHE L 14 TYR 0.019 0.002 TYR R 102 ARG 0.012 0.001 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4516.29 seconds wall clock time: 80 minutes 24.34 seconds (4824.34 seconds total)