Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:12:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2022/6uus_20901.pdb" } resolution = 2.4 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= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9308 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2734 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 749 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 5.74, per 1000 atoms: 0.62 Number of scatterers: 9308 At special positions: 0 Unit cell: (129.48, 98.77, 130.31, 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 65 16.00 O 1690 8.00 N 1624 7.00 C 5929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.04 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " 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: 3.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.592A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.520A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.565A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.622A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 4.161A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.646A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 133 through 166 Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 201 through 208 removed outlier: 4.049A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 241 removed outlier: 4.398A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.551A pdb=" N TYR R 256 " --> pdb=" O LEU R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 278 Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 320 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 removed outlier: 3.783A pdb=" N THR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 399 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.068A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 77 removed outlier: 4.065A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.234A pdb=" N THR E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 143 Proline residue: E 126 - end of helix removed outlier: 3.861A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.400A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.578A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.677A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.676A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.555A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.324A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.678A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.048A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 68 through 69 removed outlier: 3.875A pdb=" N THR R 68 " --> pdb=" O TRP R 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP R 75 " --> pdb=" O THR R 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 82 through 83 437 hydrogen bonds defined for protein. 1248 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: 2.45 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: 1.23 - 1.34: 3037 1.34 - 1.46: 2331 1.46 - 1.58: 4059 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 9514 Sorted by residual: bond pdb=" CA VAL R 342 " pdb=" CB VAL R 342 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.63e+00 bond pdb=" C ALA B 287 " pdb=" N GLY B 288 " ideal model delta sigma weight residual 1.332 1.325 0.007 6.60e-03 2.30e+04 1.04e+00 bond pdb=" C TRP E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 6.95e-01 bond pdb=" NE ARG R 67 " pdb=" CZ ARG R 67 " ideal model delta sigma weight residual 1.326 1.335 -0.009 1.10e-02 8.26e+03 6.48e-01 bond pdb=" CA ASP E 116 " pdb=" CB ASP E 116 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.94e-01 ... (remaining 9509 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 230 107.12 - 113.84: 5280 113.84 - 120.57: 3797 120.57 - 127.29: 3489 127.29 - 134.02: 113 Bond angle restraints: 12909 Sorted by residual: angle pdb=" C PRO E 115 " pdb=" N ASP E 116 " pdb=" CA ASP E 116 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ARG E 36 " pdb=" N LEU E 37 " pdb=" CA LEU E 37 " ideal model delta sigma weight residual 120.06 123.74 -3.68 1.19e+00 7.06e-01 9.59e+00 angle pdb=" CA LEU E 37 " pdb=" C LEU E 37 " pdb=" N PRO E 38 " ideal model delta sigma weight residual 121.08 118.09 2.99 1.08e+00 8.57e-01 7.68e+00 angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 110.38 114.08 -3.70 1.48e+00 4.57e-01 6.27e+00 angle pdb=" CA LEU E 37 " pdb=" C LEU E 37 " pdb=" O LEU E 37 " ideal model delta sigma weight residual 117.98 120.32 -2.34 9.70e-01 1.06e+00 5.84e+00 ... (remaining 12904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4882 17.97 - 35.94: 515 35.94 - 53.91: 181 53.91 - 71.87: 33 71.87 - 89.84: 10 Dihedral angle restraints: 5621 sinusoidal: 2158 harmonic: 3463 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 47.73 45.27 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA TYR R 49 " pdb=" C TYR R 49 " pdb=" N GLN R 50 " pdb=" CA GLN R 50 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -51.60 -34.40 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 5618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 852 0.027 - 0.053: 360 0.053 - 0.080: 146 0.080 - 0.107: 63 0.107 - 0.133: 28 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1446 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 114 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 115 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO E 114 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 125 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO E 126 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 126 " -0.018 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1025 2.75 - 3.29: 9125 3.29 - 3.83: 15893 3.83 - 4.36: 18868 4.36 - 4.90: 32023 Nonbonded interactions: 76934 Sorted by model distance: nonbonded pdb=" O ASN R 187 " pdb=" OG1 THR R 191 " model vdw 2.214 2.440 nonbonded pdb=" OD2 ASP A 229 " pdb=" OG SER N 112 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP R 70 " pdb=" OH TYR R 124 " model vdw 2.223 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.274 2.440 nonbonded pdb=" O THR R 102 " pdb=" OG1 THR R 122 " model vdw 2.294 2.440 ... (remaining 76929 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5929 2.51 5 N 1624 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.910 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: 0.000 Extract box with map and model: 5.600 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 27.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.002 0.020 9514 Z= 0.129 Angle : 0.501 7.555 12909 Z= 0.297 Chirality : 0.039 0.133 1449 Planarity : 0.003 0.042 1646 Dihedral : 17.128 89.842 3350 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 3.27 % 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: -2.25 (0.22), residues: 1160 helix: -1.09 (0.23), residues: 433 sheet: -1.53 (0.30), residues: 222 loop : -1.71 (0.25), residues: 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 171 average time/residue: 1.0930 time to fit residues: 200.8767 Evaluate side-chains 128 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.5150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 239 ASN A 390 GLN B 259 GLN B 268 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 53 GLN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 9514 Z= 0.139 Angle : 0.487 7.458 12909 Z= 0.263 Chirality : 0.041 0.149 1449 Planarity : 0.004 0.045 1646 Dihedral : 3.914 21.061 1283 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 3.58 % 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: -0.78 (0.24), residues: 1160 helix: 0.61 (0.25), residues: 436 sheet: -1.05 (0.31), residues: 226 loop : -1.20 (0.28), residues: 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 152 average time/residue: 1.1346 time to fit residues: 185.3755 Evaluate side-chains 129 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0902 time to fit residues: 1.6659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 390 GLN B 268 ASN B 311 HIS N 1 GLN N 31 ASN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9514 Z= 0.196 Angle : 0.535 7.163 12909 Z= 0.290 Chirality : 0.042 0.139 1449 Planarity : 0.004 0.045 1646 Dihedral : 4.311 21.848 1283 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 3.37 % 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 (0.24), residues: 1160 helix: 1.15 (0.25), residues: 443 sheet: -0.66 (0.33), residues: 218 loop : -1.00 (0.27), residues: 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 141 average time/residue: 1.1616 time to fit residues: 176.2441 Evaluate side-chains 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0867 time to fit residues: 1.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 0.0270 chunk 105 optimal weight: 0.0870 chunk 112 optimal weight: 0.0060 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 overall best weight: 0.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS B 175 GLN B 176 GLN B 259 GLN B 268 ASN N 31 ASN N 123 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9514 Z= 0.127 Angle : 0.464 7.293 12909 Z= 0.249 Chirality : 0.040 0.139 1449 Planarity : 0.003 0.043 1646 Dihedral : 3.912 19.385 1283 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 3.37 % 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: 0.33 (0.25), residues: 1160 helix: 1.70 (0.25), residues: 437 sheet: -0.44 (0.33), residues: 222 loop : -0.76 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 145 average time/residue: 1.1407 time to fit residues: 178.1038 Evaluate side-chains 121 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1413 time to fit residues: 2.3623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.0030 chunk 28 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 390 GLN B 175 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 53 GLN N 123 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN R 250 GLN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9514 Z= 0.148 Angle : 0.484 7.147 12909 Z= 0.260 Chirality : 0.040 0.134 1449 Planarity : 0.004 0.042 1646 Dihedral : 3.977 20.241 1283 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 3.47 % 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 (0.25), residues: 1160 helix: 1.83 (0.25), residues: 438 sheet: -0.52 (0.32), residues: 235 loop : -0.60 (0.29), residues: 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 129 average time/residue: 1.1283 time to fit residues: 156.7667 Evaluate side-chains 123 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.1533 time to fit residues: 2.4380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 53 GLN N 123 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9514 Z= 0.144 Angle : 0.476 7.032 12909 Z= 0.256 Chirality : 0.041 0.137 1449 Planarity : 0.004 0.042 1646 Dihedral : 3.957 20.468 1283 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.96 % 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: 0.60 (0.25), residues: 1160 helix: 1.92 (0.25), residues: 438 sheet: -0.42 (0.31), residues: 233 loop : -0.54 (0.29), residues: 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 134 average time/residue: 1.1159 time to fit residues: 161.0934 Evaluate side-chains 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1071 time to fit residues: 1.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 111 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 31 ASN N 53 GLN R 39 ASN R 114 HIS ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 9514 Z= 0.152 Angle : 0.498 10.584 12909 Z= 0.265 Chirality : 0.041 0.133 1449 Planarity : 0.004 0.041 1646 Dihedral : 3.997 21.029 1283 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 3.27 % 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: 0.68 (0.25), residues: 1160 helix: 1.97 (0.25), residues: 438 sheet: -0.41 (0.32), residues: 224 loop : -0.46 (0.28), residues: 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 139 average time/residue: 1.1508 time to fit residues: 172.1496 Evaluate side-chains 128 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1081 time to fit residues: 1.8742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 0.0050 chunk 107 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 53 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9514 Z= 0.180 Angle : 0.527 11.205 12909 Z= 0.279 Chirality : 0.042 0.136 1449 Planarity : 0.004 0.041 1646 Dihedral : 4.195 23.088 1283 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.55 % 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: 0.59 (0.25), residues: 1160 helix: 1.84 (0.25), residues: 444 sheet: -0.40 (0.31), residues: 233 loop : -0.50 (0.28), residues: 483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 132 average time/residue: 1.2189 time to fit residues: 172.9615 Evaluate side-chains 120 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1503 time to fit residues: 1.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 0.0060 chunk 67 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 53 GLN R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9514 Z= 0.167 Angle : 0.519 11.235 12909 Z= 0.273 Chirality : 0.041 0.146 1449 Planarity : 0.004 0.041 1646 Dihedral : 4.162 23.754 1283 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.25 % 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: 0.64 (0.25), residues: 1160 helix: 1.89 (0.25), residues: 444 sheet: -0.35 (0.32), residues: 215 loop : -0.50 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 1.1376 time to fit residues: 150.9840 Evaluate side-chains 117 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.0170 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9514 Z= 0.302 Angle : 0.651 11.281 12909 Z= 0.346 Chirality : 0.046 0.148 1449 Planarity : 0.005 0.042 1646 Dihedral : 4.763 31.429 1283 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1160 helix: 1.47 (0.25), residues: 440 sheet: -0.49 (0.32), residues: 222 loop : -0.63 (0.27), residues: 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 127 average time/residue: 1.1442 time to fit residues: 156.6303 Evaluate side-chains 122 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1262 time to fit residues: 1.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 66 optimal weight: 0.0870 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS B 175 GLN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 39 ASN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168167 restraints weight = 9610.981| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.45 r_work: 0.3905 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3854 rms_B_bonded: 1.66 restraints_weight: 0.1250 r_work: 0.3818 rms_B_bonded: 2.13 restraints_weight: 0.0625 r_work: 0.3768 rms_B_bonded: 2.90 restraints_weight: 0.0312 r_work: 0.3694 rms_B_bonded: 4.23 restraints_weight: 0.0156 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9514 Z= 0.150 Angle : 0.519 11.139 12909 Z= 0.272 Chirality : 0.041 0.147 1449 Planarity : 0.004 0.041 1646 Dihedral : 4.259 28.161 1283 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.25 % 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: 0.57 (0.25), residues: 1160 helix: 1.83 (0.25), residues: 444 sheet: -0.35 (0.32), residues: 216 loop : -0.56 (0.28), residues: 500 =============================================================================== Job complete usr+sys time: 3253.81 seconds wall clock time: 58 minutes 36.37 seconds (3516.37 seconds total)