Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:37:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/04_2023/7wv9_32850_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 26 atoms to isotropic. 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 66 5.16 5 C 5660 2.51 5 N 1508 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1732 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2583 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2306 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1740 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'7IC': 1, '9GF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.39, per 1000 atoms: 0.61 Number of scatterers: 8848 At special positions: 0 Unit cell: (130.05, 113.9, 109.65, 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 66 16.00 O 1614 8.00 N 1508 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " 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: 3.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 33.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.756A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.144A pdb=" N ALA A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.595A pdb=" N LYS A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.889A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.597A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 141 removed outlier: 4.134A pdb=" N ALA R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 149 Processing helix chain 'R' and resid 151 through 178 removed outlier: 3.672A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 219 removed outlier: 4.043A pdb=" N GLY R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 227 No H-bonds generated for 'chain 'R' and resid 224 through 227' Processing helix chain 'R' and resid 230 through 254 Proline residue: R 251 - end of helix removed outlier: 3.654A pdb=" N GLY R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 311 removed outlier: 3.605A pdb=" N TRP R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 356 removed outlier: 4.397A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 368 removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 397 removed outlier: 4.057A pdb=" N THR R 377 " --> pdb=" O LYS R 373 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 402 through 410 Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 37 removed outlier: 6.388A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.959A pdb=" N SER A 264 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE A 224 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 266 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 226 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE A 268 " --> pdb=" O VAL A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.135A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.153A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.605A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= I, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.830A pdb=" N ARG B 48 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'S' and resid 5 through 7 removed outlier: 4.318A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 115 through 117 removed outlier: 4.150A pdb=" N MET S 93 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE S 51 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR S 59 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'S' and resid 166 through 168 338 hydrogen bonds defined for protein. 978 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: 2.67 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1404 1.30 - 1.43: 2415 1.43 - 1.56: 5114 1.56 - 1.68: 3 1.68 - 1.81: 98 Bond restraints: 9034 Sorted by residual: bond pdb=" C23 7IC R 502 " pdb=" C24 7IC R 502 " ideal model delta sigma weight residual 1.597 1.386 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C25 7IC R 502 " pdb=" S26 7IC R 502 " ideal model delta sigma weight residual 1.555 1.726 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C22 7IC R 502 " pdb=" S26 7IC R 502 " ideal model delta sigma weight residual 1.555 1.725 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" C16 7IC R 502 " pdb=" C7 7IC R 502 " ideal model delta sigma weight residual 1.526 1.384 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N TRP R 356 " pdb=" CA TRP R 356 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.16e-02 7.43e+03 1.41e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 88.68 - 97.81: 2 97.81 - 106.95: 211 106.95 - 116.08: 5775 116.08 - 125.21: 6105 125.21 - 134.35: 153 Bond angle restraints: 12246 Sorted by residual: angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAO 9GF R 501 " ideal model delta sigma weight residual 109.06 88.68 20.38 3.00e+00 1.11e-01 4.61e+01 angle pdb=" N GLU A 14 " pdb=" CA GLU A 14 " pdb=" C GLU A 14 " ideal model delta sigma weight residual 113.50 105.96 7.54 1.23e+00 6.61e-01 3.75e+01 angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAT 9GF R 501 " ideal model delta sigma weight residual 109.00 127.31 -18.31 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C16 7IC R 502 " pdb=" C7 7IC R 502 " pdb=" C6 7IC R 502 " ideal model delta sigma weight residual 142.91 126.56 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C16 7IC R 502 " pdb=" C7 7IC R 502 " pdb=" N8 7IC R 502 " ideal model delta sigma weight residual 109.04 125.19 -16.15 3.00e+00 1.11e-01 2.90e+01 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4811 17.65 - 35.31: 423 35.31 - 52.96: 70 52.96 - 70.62: 11 70.62 - 88.27: 9 Dihedral angle restraints: 5324 sinusoidal: 2013 harmonic: 3311 Sorted by residual: dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" C ASN A 47 " pdb=" N ASN A 47 " pdb=" CA ASN A 47 " pdb=" CB ASN A 47 " ideal model delta harmonic sigma weight residual -122.60 -112.98 -9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" SG CYS R 257 " pdb=" CB CYS R 264 " pdb=" SG CYS R 264 " pdb=" CA CYS R 264 " ideal model delta sinusoidal sigma weight residual -73.00 -12.23 -60.77 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1218 0.062 - 0.125: 166 0.125 - 0.187: 20 0.187 - 0.249: 3 0.249 - 0.312: 2 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA ASN A 47 " pdb=" N ASN A 47 " pdb=" C ASN A 47 " pdb=" CB ASN A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA MET A 248 " pdb=" N MET A 248 " pdb=" C MET A 248 " pdb=" CB MET A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP S 74 " pdb=" N ASP S 74 " pdb=" C ASP S 74 " pdb=" CB ASP S 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1406 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 12 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" CD GLU B 12 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU B 12 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 12 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 356 " -0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP R 356 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP R 356 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 356 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 356 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 356 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 356 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 305 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLN A 305 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 305 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 306 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 780 2.74 - 3.28: 8968 3.28 - 3.82: 14284 3.82 - 4.36: 16411 4.36 - 4.90: 28179 Nonbonded interactions: 68622 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR S 95 " pdb=" O GLN S 171 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 2.440 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.263 2.520 nonbonded pdb=" OG SER A 6 " pdb=" OH TYR S 161 " model vdw 2.264 2.440 ... (remaining 68617 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 0.211 9034 Z= 0.332 Angle : 0.769 20.379 12246 Z= 0.408 Chirality : 0.046 0.312 1409 Planarity : 0.004 0.047 1532 Dihedral : 13.784 88.271 3181 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer Outliers : 0.53 % 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: -0.80 (0.25), residues: 1125 helix: 0.99 (0.28), residues: 358 sheet: -0.61 (0.34), residues: 236 loop : -1.56 (0.26), residues: 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.117 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 178 average time/residue: 0.1942 time to fit residues: 49.1669 Evaluate side-chains 139 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0816 time to fit residues: 1.7946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9034 Z= 0.196 Angle : 0.566 7.554 12246 Z= 0.298 Chirality : 0.042 0.186 1409 Planarity : 0.004 0.046 1532 Dihedral : 5.051 45.085 1239 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 1.49 % 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: -0.80 (0.25), residues: 1125 helix: 1.20 (0.27), residues: 358 sheet: -0.77 (0.33), residues: 254 loop : -1.68 (0.26), residues: 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.048 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 151 average time/residue: 0.1873 time to fit residues: 40.5519 Evaluate side-chains 143 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0809 time to fit residues: 3.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 chunk 34 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9034 Z= 0.137 Angle : 0.519 7.706 12246 Z= 0.275 Chirality : 0.041 0.199 1409 Planarity : 0.003 0.042 1532 Dihedral : 4.815 46.610 1239 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.96 % 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: -0.54 (0.25), residues: 1125 helix: 1.44 (0.28), residues: 352 sheet: -0.55 (0.33), residues: 254 loop : -1.54 (0.27), residues: 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.139 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 153 average time/residue: 0.2066 time to fit residues: 44.8674 Evaluate side-chains 134 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0961 time to fit residues: 2.3850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.0060 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9034 Z= 0.222 Angle : 0.566 8.047 12246 Z= 0.301 Chirality : 0.042 0.191 1409 Planarity : 0.004 0.042 1532 Dihedral : 4.966 42.927 1239 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 2.45 % 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: -0.82 (0.25), residues: 1125 helix: 1.34 (0.27), residues: 352 sheet: -0.96 (0.34), residues: 242 loop : -1.66 (0.26), residues: 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.238 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 0.2100 time to fit residues: 46.1564 Evaluate side-chains 140 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0940 time to fit residues: 4.2415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9034 Z= 0.211 Angle : 0.571 8.047 12246 Z= 0.302 Chirality : 0.043 0.217 1409 Planarity : 0.004 0.041 1532 Dihedral : 4.999 43.007 1239 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.07 % 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: -0.86 (0.25), residues: 1125 helix: 1.34 (0.27), residues: 352 sheet: -0.98 (0.34), residues: 239 loop : -1.70 (0.26), residues: 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.080 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 143 average time/residue: 0.1932 time to fit residues: 39.5255 Evaluate side-chains 132 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0794 time to fit residues: 2.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9034 Z= 0.143 Angle : 0.528 8.676 12246 Z= 0.277 Chirality : 0.041 0.202 1409 Planarity : 0.003 0.038 1532 Dihedral : 4.762 45.523 1239 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.17 % 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: -0.66 (0.25), residues: 1125 helix: 1.47 (0.28), residues: 358 sheet: -0.78 (0.33), residues: 242 loop : -1.65 (0.27), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.922 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 146 average time/residue: 0.2014 time to fit residues: 41.7400 Evaluate side-chains 134 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0857 time to fit residues: 2.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9034 Z= 0.150 Angle : 0.531 8.919 12246 Z= 0.279 Chirality : 0.042 0.256 1409 Planarity : 0.003 0.038 1532 Dihedral : 4.714 43.244 1239 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.64 % 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: -0.63 (0.25), residues: 1125 helix: 1.51 (0.28), residues: 357 sheet: -0.81 (0.33), residues: 248 loop : -1.61 (0.27), residues: 520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.138 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.1973 time to fit residues: 41.4211 Evaluate side-chains 139 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1170 time to fit residues: 2.1153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9034 Z= 0.189 Angle : 0.572 9.337 12246 Z= 0.299 Chirality : 0.043 0.227 1409 Planarity : 0.003 0.039 1532 Dihedral : 4.834 39.455 1239 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.96 % 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: -0.84 (0.25), residues: 1125 helix: 1.33 (0.28), residues: 358 sheet: -1.00 (0.33), residues: 241 loop : -1.70 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.138 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 144 average time/residue: 0.1989 time to fit residues: 40.8153 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0834 time to fit residues: 2.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9034 Z= 0.151 Angle : 0.573 9.647 12246 Z= 0.295 Chirality : 0.043 0.251 1409 Planarity : 0.003 0.038 1532 Dihedral : 4.714 42.366 1239 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.43 % 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: -0.71 (0.25), residues: 1125 helix: 1.38 (0.28), residues: 357 sheet: -0.78 (0.33), residues: 242 loop : -1.65 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.075 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 145 average time/residue: 0.2134 time to fit residues: 43.4932 Evaluate side-chains 138 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 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: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9034 Z= 0.171 Angle : 0.583 9.656 12246 Z= 0.302 Chirality : 0.043 0.228 1409 Planarity : 0.004 0.065 1532 Dihedral : 4.727 39.996 1239 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.32 % 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: -0.75 (0.25), residues: 1125 helix: 1.29 (0.28), residues: 357 sheet: -0.75 (0.33), residues: 240 loop : -1.66 (0.26), residues: 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.169 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 140 average time/residue: 0.2134 time to fit residues: 42.5515 Evaluate side-chains 137 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1013 time to fit residues: 1.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.0020 chunk 5 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** 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 = 0.4568 r_free = 0.4568 target = 0.217721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.180291 restraints weight = 12412.790| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.04 r_work: 0.3949 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9034 Z= 0.146 Angle : 0.563 9.662 12246 Z= 0.292 Chirality : 0.042 0.219 1409 Planarity : 0.003 0.052 1532 Dihedral : 4.619 41.411 1239 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.32 % 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: -0.66 (0.25), residues: 1125 helix: 1.36 (0.28), residues: 357 sheet: -0.65 (0.34), residues: 236 loop : -1.62 (0.26), residues: 532 =============================================================================== Job complete usr+sys time: 2048.46 seconds wall clock time: 38 minutes 2.20 seconds (2282.20 seconds total)