Starting phenix.real_space_refine on Tue Mar 3 23:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_20901.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_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/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_20901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_20901.map" model { file = "/net/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_20901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uus_20901/03_2026/6uus_20901.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} 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: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3, 'TRP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 2.23, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 380.1 milliseconds 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: 0.28 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: 1.79 Time building geometry restraints manager: 1.01 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: 0.00 - 1.51: 12684 1.51 - 3.02: 191 3.02 - 4.53: 25 4.53 - 6.04: 5 6.04 - 7.56: 4 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 3.040 nonbonded pdb=" OD2 ASP A 229 " pdb=" OG SER N 112 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP R 70 " pdb=" OH TYR R 124 " model vdw 2.223 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.274 3.040 nonbonded pdb=" O THR R 102 " pdb=" OG1 THR R 122 " model vdw 2.294 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 9523 Z= 0.107 Angle : 0.502 7.555 12927 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 : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.27 % Allowed : 23.70 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 397 TYR 0.015 0.001 TYR N 60 PHE 0.009 0.001 PHE E 100 TRP 0.016 0.001 TRP R 229 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9514) covalent geometry : angle 0.50089 (12909) SS BOND : bond 0.00449 ( 9) SS BOND : angle 0.87028 ( 18) hydrogen bonds : bond 0.20809 ( 437) hydrogen bonds : angle 7.35230 ( 1248) *********************** 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 to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7782 (ttpt) cc_final: 0.7560 (tttm) REVERT: A 347 ARG cc_start: 0.7320 (ttp80) cc_final: 0.7031 (ttp-110) REVERT: A 390 GLN cc_start: 0.7441 (mt0) cc_final: 0.7211 (mt0) REVERT: B 46 ARG cc_start: 0.7485 (mpt180) cc_final: 0.7169 (mmt90) REVERT: B 66 ASP cc_start: 0.7106 (p0) cc_final: 0.6764 (p0) REVERT: B 219 ARG cc_start: 0.6877 (mmt90) cc_final: 0.6479 (mpt-90) REVERT: B 259 GLN cc_start: 0.6538 (tt0) cc_final: 0.6231 (tt0) REVERT: B 322 ASP cc_start: 0.6030 (m-30) cc_final: 0.5659 (m-30) REVERT: G 21 MET cc_start: 0.5795 (tpt) cc_final: 0.5548 (mmt) REVERT: G 47 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: N 95 TYR cc_start: 0.7406 (m-80) cc_final: 0.7142 (m-80) REVERT: N 105 ARG cc_start: 0.6112 (mtp180) cc_final: 0.5901 (mtm180) REVERT: N 108 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.5484 (t80) REVERT: R 139 LEU cc_start: 0.6452 (mm) cc_final: 0.6217 (mt) REVERT: R 147 ILE cc_start: 0.6784 (tt) cc_final: 0.6279 (mm) REVERT: R 276 LEU cc_start: 0.7726 (mt) cc_final: 0.6621 (tp) REVERT: R 321 LYS cc_start: 0.5920 (mmtm) cc_final: 0.5702 (mmtp) REVERT: R 332 MET cc_start: 0.5105 (tpt) cc_final: 0.4318 (ttm) REVERT: R 370 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5227 (t-90) REVERT: R 396 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4241 (mtp85) REVERT: E 64 VAL cc_start: 0.3525 (OUTLIER) cc_final: 0.3190 (t) outliers start: 32 outliers final: 9 residues processed: 171 average time/residue: 0.6055 time to fit residues: 110.3564 Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 370 HIS Chi-restraints excluded: chain R residue 396 ARG Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.208816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168236 restraints weight = 9738.991| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.56 r_work: 0.3709 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9523 Z= 0.135 Angle : 0.546 7.479 12927 Z= 0.296 Chirality : 0.042 0.144 1449 Planarity : 0.004 0.047 1646 Dihedral : 6.299 70.094 1308 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.58 % Allowed : 22.98 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1160 helix: 0.40 (0.24), residues: 444 sheet: -1.14 (0.32), residues: 219 loop : -1.29 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 356 TYR 0.011 0.001 TYR N 80 PHE 0.018 0.002 PHE A 212 TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9514) covalent geometry : angle 0.54258 (12909) SS BOND : bond 0.00475 ( 9) SS BOND : angle 1.68745 ( 18) hydrogen bonds : bond 0.04210 ( 437) hydrogen bonds : angle 5.01690 ( 1248) *********************** 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 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7283 (tt0) cc_final: 0.7063 (tt0) REVERT: A 28 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7149 (mmpt) REVERT: B 46 ARG cc_start: 0.8340 (mpt180) cc_final: 0.8039 (mmt90) REVERT: B 59 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 66 ASP cc_start: 0.7439 (p0) cc_final: 0.7143 (p0) REVERT: B 76 ASP cc_start: 0.8210 (p0) cc_final: 0.7949 (p0) REVERT: B 219 ARG cc_start: 0.7393 (mmt90) cc_final: 0.7122 (mpt-90) REVERT: B 322 ASP cc_start: 0.6635 (m-30) cc_final: 0.6332 (m-30) REVERT: N 105 ARG cc_start: 0.6489 (mtp180) cc_final: 0.6042 (mtm180) REVERT: P 50 GLN cc_start: 0.2204 (OUTLIER) cc_final: 0.1362 (tm-30) REVERT: R 48 CYS cc_start: 0.3775 (OUTLIER) cc_final: 0.1904 (t) REVERT: R 74 CYS cc_start: 0.2180 (OUTLIER) cc_final: 0.1295 (p) REVERT: R 169 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.5029 (mt) REVERT: R 314 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7240 (ttp-170) REVERT: R 321 LYS cc_start: 0.6025 (mmtm) cc_final: 0.5768 (mmtp) REVERT: R 332 MET cc_start: 0.5592 (tpt) cc_final: 0.4593 (ttm) REVERT: R 375 PHE cc_start: 0.8049 (m-80) cc_final: 0.7804 (m-80) REVERT: E 64 VAL cc_start: 0.3599 (OUTLIER) cc_final: 0.3220 (t) outliers start: 35 outliers final: 8 residues processed: 156 average time/residue: 0.6370 time to fit residues: 105.7580 Evaluate side-chains 126 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 259 GLN B 268 ASN B 311 HIS ** B 340 ASN ** 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 140 ASN R 172 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.203272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160737 restraints weight = 9593.154| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.99 r_work: 0.3635 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9523 Z= 0.182 Angle : 0.613 7.196 12927 Z= 0.333 Chirality : 0.045 0.145 1449 Planarity : 0.005 0.049 1646 Dihedral : 5.393 57.643 1291 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.39 % Allowed : 22.57 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1160 helix: 0.84 (0.24), residues: 444 sheet: -0.83 (0.33), residues: 214 loop : -0.96 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 347 TYR 0.015 0.002 TYR R 49 PHE 0.016 0.002 PHE E 100 TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS R 149 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9514) covalent geometry : angle 0.60929 (12909) SS BOND : bond 0.00262 ( 9) SS BOND : angle 1.96804 ( 18) hydrogen bonds : bond 0.04612 ( 437) hydrogen bonds : angle 5.03221 ( 1248) *********************** 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 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7236 (mmpt) REVERT: B 5 ASP cc_start: 0.3531 (OUTLIER) cc_final: 0.2627 (p0) REVERT: B 43 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6502 (tp) REVERT: B 44 GLN cc_start: 0.7453 (mp10) cc_final: 0.7182 (mt0) REVERT: B 46 ARG cc_start: 0.8358 (mpt180) cc_final: 0.8062 (mmt90) REVERT: B 59 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7584 (t80) REVERT: B 322 ASP cc_start: 0.6865 (m-30) cc_final: 0.6636 (m-30) REVERT: N 61 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7290 (t) REVERT: R 48 CYS cc_start: 0.4120 (OUTLIER) cc_final: 0.2224 (t) REVERT: R 143 TYR cc_start: 0.6752 (m-10) cc_final: 0.6551 (m-10) REVERT: R 169 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5524 (mt) REVERT: R 314 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7326 (ttp-170) REVERT: R 321 LYS cc_start: 0.6168 (mmtm) cc_final: 0.5880 (mmtp) REVERT: R 332 MET cc_start: 0.5480 (tpt) cc_final: 0.4706 (ttm) REVERT: R 375 PHE cc_start: 0.8038 (m-80) cc_final: 0.7797 (m-80) REVERT: E 136 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7231 (tp) outliers start: 43 outliers final: 14 residues processed: 149 average time/residue: 0.5866 time to fit residues: 93.3285 Evaluate side-chains 133 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 126 GLN Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 113 optimal weight: 0.0070 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 94 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 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 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 53 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.206263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163504 restraints weight = 9767.474| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.24 r_work: 0.3674 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9523 Z= 0.116 Angle : 0.524 8.330 12927 Z= 0.282 Chirality : 0.042 0.143 1449 Planarity : 0.004 0.062 1646 Dihedral : 5.001 59.727 1291 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.98 % Allowed : 22.98 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1160 helix: 1.37 (0.25), residues: 443 sheet: -0.59 (0.33), residues: 209 loop : -0.78 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.008 0.001 TYR R 46 PHE 0.016 0.001 PHE E 100 TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9514) covalent geometry : angle 0.52191 (12909) SS BOND : bond 0.00176 ( 9) SS BOND : angle 1.28775 ( 18) hydrogen bonds : bond 0.03672 ( 437) hydrogen bonds : angle 4.65058 ( 1248) *********************** 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 156 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6479 (tm-30) REVERT: A 28 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7150 (mmpt) REVERT: B 46 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7995 (mmt90) REVERT: B 59 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7676 (t80) REVERT: B 76 ASP cc_start: 0.8286 (p0) cc_final: 0.8007 (p0) REVERT: B 322 ASP cc_start: 0.6828 (m-30) cc_final: 0.6606 (m-30) REVERT: G 21 MET cc_start: 0.5853 (tpt) cc_final: 0.5237 (mmt) REVERT: R 48 CYS cc_start: 0.4284 (OUTLIER) cc_final: 0.2165 (t) REVERT: R 49 TYR cc_start: 0.4538 (OUTLIER) cc_final: 0.3987 (t80) REVERT: R 169 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5497 (mt) REVERT: R 314 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7256 (ttp-170) REVERT: R 321 LYS cc_start: 0.6115 (mmtm) cc_final: 0.5872 (mmtp) REVERT: R 332 MET cc_start: 0.5331 (tpt) cc_final: 0.4669 (ttm) REVERT: R 363 GLU cc_start: 0.3212 (OUTLIER) cc_final: 0.2763 (pm20) REVERT: R 375 PHE cc_start: 0.7989 (m-80) cc_final: 0.7777 (m-80) REVERT: E 93 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.3455 (pp) REVERT: E 136 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7199 (tp) outliers start: 39 outliers final: 17 residues processed: 146 average time/residue: 0.6025 time to fit residues: 93.9515 Evaluate side-chains 138 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160889 restraints weight = 9707.450| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.09 r_work: 0.3641 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9523 Z= 0.142 Angle : 0.555 7.371 12927 Z= 0.301 Chirality : 0.043 0.141 1449 Planarity : 0.004 0.071 1646 Dihedral : 5.135 59.664 1291 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.70 % Allowed : 23.19 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1160 helix: 1.46 (0.25), residues: 443 sheet: -0.50 (0.33), residues: 211 loop : -0.68 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.011 0.001 TYR R 143 PHE 0.016 0.002 PHE E 100 TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9514) covalent geometry : angle 0.55206 (12909) SS BOND : bond 0.00169 ( 9) SS BOND : angle 1.61517 ( 18) hydrogen bonds : bond 0.03908 ( 437) hydrogen bonds : angle 4.66657 ( 1248) *********************** 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 165 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6531 (tm-30) REVERT: A 24 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6741 (ttpp) REVERT: A 28 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7187 (mmpt) REVERT: B 5 ASP cc_start: 0.3674 (OUTLIER) cc_final: 0.2679 (p0) REVERT: B 43 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6362 (tp) REVERT: B 46 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8014 (mmt90) REVERT: B 59 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 76 ASP cc_start: 0.8307 (p0) cc_final: 0.8078 (p0) REVERT: B 219 ARG cc_start: 0.7426 (mmt90) cc_final: 0.7109 (mpt-90) REVERT: B 322 ASP cc_start: 0.6908 (m-30) cc_final: 0.6693 (m-30) REVERT: G 21 MET cc_start: 0.5883 (tpt) cc_final: 0.5298 (mmt) REVERT: N 65 LYS cc_start: 0.7048 (ttmt) cc_final: 0.6598 (ttpt) REVERT: R 40 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.4964 (ttpt) REVERT: R 48 CYS cc_start: 0.4311 (OUTLIER) cc_final: 0.2206 (t) REVERT: R 49 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.4031 (t80) REVERT: R 169 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5708 (mt) REVERT: R 314 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7326 (ttp-170) REVERT: R 321 LYS cc_start: 0.6159 (mmtm) cc_final: 0.5913 (mmtp) REVERT: R 363 GLU cc_start: 0.3266 (OUTLIER) cc_final: 0.2926 (pm20) REVERT: E 93 ILE cc_start: 0.3856 (OUTLIER) cc_final: 0.3471 (pp) REVERT: E 136 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7201 (tp) outliers start: 46 outliers final: 13 residues processed: 156 average time/residue: 0.6139 time to fit residues: 102.2314 Evaluate side-chains 135 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 40 LYS Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163355 restraints weight = 9723.111| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.72 r_work: 0.3652 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9523 Z= 0.128 Angle : 0.535 6.852 12927 Z= 0.288 Chirality : 0.042 0.140 1449 Planarity : 0.004 0.068 1646 Dihedral : 5.044 58.905 1291 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.09 % Allowed : 24.31 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1160 helix: 1.57 (0.25), residues: 443 sheet: -0.34 (0.33), residues: 210 loop : -0.65 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.009 0.001 TYR N 95 PHE 0.016 0.002 PHE E 100 TRP 0.016 0.001 TRP A 234 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9514) covalent geometry : angle 0.53213 (12909) SS BOND : bond 0.00219 ( 9) SS BOND : angle 1.55984 ( 18) hydrogen bonds : bond 0.03690 ( 437) hydrogen bonds : angle 4.55223 ( 1248) *********************** 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 151 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6591 (tm-30) REVERT: A 24 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6755 (ttpp) REVERT: A 28 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7293 (mmpt) REVERT: B 5 ASP cc_start: 0.3857 (OUTLIER) cc_final: 0.2956 (p0) REVERT: B 43 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6231 (tp) REVERT: B 46 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8044 (mmt90) REVERT: B 59 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7729 (t80) REVERT: B 76 ASP cc_start: 0.8248 (p0) cc_final: 0.7888 (p0) REVERT: B 219 ARG cc_start: 0.7419 (mmt90) cc_final: 0.7122 (mpt-90) REVERT: B 322 ASP cc_start: 0.6938 (m-30) cc_final: 0.6727 (m-30) REVERT: N 43 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7598 (mttt) REVERT: N 65 LYS cc_start: 0.7130 (ttmt) cc_final: 0.6673 (ttpt) REVERT: R 48 CYS cc_start: 0.4234 (OUTLIER) cc_final: 0.2025 (t) REVERT: R 49 TYR cc_start: 0.4617 (OUTLIER) cc_final: 0.3868 (t80) REVERT: R 169 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5760 (mt) REVERT: R 314 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7364 (ttp-170) REVERT: R 321 LYS cc_start: 0.6185 (mmtm) cc_final: 0.5948 (mmtp) REVERT: R 333 LYS cc_start: 0.5221 (mmtt) cc_final: 0.4885 (mmmm) REVERT: R 363 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.2892 (pm20) REVERT: E 93 ILE cc_start: 0.3769 (OUTLIER) cc_final: 0.3381 (pp) REVERT: E 136 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7247 (tp) outliers start: 40 outliers final: 15 residues processed: 144 average time/residue: 0.5659 time to fit residues: 86.8689 Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 0.0020 chunk 19 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.2002 ------------------------------------------------------------------------------- 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 220 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.209447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168185 restraints weight = 9712.898| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.82 r_work: 0.3735 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9523 Z= 0.097 Angle : 0.483 7.318 12927 Z= 0.259 Chirality : 0.041 0.143 1449 Planarity : 0.004 0.075 1646 Dihedral : 4.624 55.125 1290 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.96 % Allowed : 25.33 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1160 helix: 1.95 (0.26), residues: 437 sheet: -0.27 (0.32), residues: 218 loop : -0.44 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.011 0.001 TYR R 143 PHE 0.021 0.001 PHE R 182 TRP 0.015 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9514) covalent geometry : angle 0.48119 (12909) SS BOND : bond 0.00171 ( 9) SS BOND : angle 1.28985 ( 18) hydrogen bonds : bond 0.03053 ( 437) hydrogen bonds : angle 4.22521 ( 1248) *********************** 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 144 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6514 (tm-30) REVERT: A 24 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6674 (ttpp) REVERT: A 28 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7255 (mmpt) REVERT: A 35 GLN cc_start: 0.7430 (mm110) cc_final: 0.7131 (mm110) REVERT: B 5 ASP cc_start: 0.3810 (OUTLIER) cc_final: 0.2945 (p0) REVERT: B 46 ARG cc_start: 0.8285 (mpt180) cc_final: 0.7983 (mmt90) REVERT: B 59 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7553 (t80) REVERT: B 76 ASP cc_start: 0.8205 (p0) cc_final: 0.7877 (p0) REVERT: B 219 ARG cc_start: 0.7383 (mmt90) cc_final: 0.7110 (mpt-90) REVERT: B 322 ASP cc_start: 0.6821 (m-30) cc_final: 0.6597 (m-30) REVERT: N 65 LYS cc_start: 0.6964 (ttmt) cc_final: 0.6534 (ttpt) REVERT: R 169 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5524 (mt) REVERT: R 276 LEU cc_start: 0.7700 (mt) cc_final: 0.6535 (tp) REVERT: R 314 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7321 (tmm160) REVERT: R 333 LYS cc_start: 0.5116 (mmtt) cc_final: 0.4775 (mmmm) REVERT: R 363 GLU cc_start: 0.3280 (OUTLIER) cc_final: 0.2898 (pm20) REVERT: R 375 PHE cc_start: 0.8011 (m-80) cc_final: 0.7754 (m-80) REVERT: E 64 VAL cc_start: 0.3630 (OUTLIER) cc_final: 0.3378 (t) outliers start: 29 outliers final: 9 residues processed: 138 average time/residue: 0.6161 time to fit residues: 90.7953 Evaluate side-chains 119 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 220 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 ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.202532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159020 restraints weight = 9571.090| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.31 r_work: 0.3613 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9523 Z= 0.197 Angle : 0.631 10.234 12927 Z= 0.337 Chirality : 0.045 0.150 1449 Planarity : 0.005 0.044 1646 Dihedral : 5.297 58.878 1290 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.39 % Allowed : 24.00 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1160 helix: 1.52 (0.25), residues: 444 sheet: -0.38 (0.32), residues: 217 loop : -0.58 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 347 TYR 0.026 0.002 TYR N 60 PHE 0.025 0.002 PHE R 182 TRP 0.020 0.002 TRP A 234 HIS 0.008 0.002 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9514) covalent geometry : angle 0.62618 (12909) SS BOND : bond 0.00355 ( 9) SS BOND : angle 2.23596 ( 18) hydrogen bonds : bond 0.04319 ( 437) hydrogen bonds : angle 4.77554 ( 1248) *********************** 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 152 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6705 (ttpp) REVERT: A 28 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7221 (mmpt) REVERT: A 327 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: B 5 ASP cc_start: 0.3866 (OUTLIER) cc_final: 0.2985 (p0) REVERT: B 43 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6344 (tp) REVERT: B 46 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (mmt90) REVERT: B 59 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7667 (t80) REVERT: B 197 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6354 (mtm-85) REVERT: B 219 ARG cc_start: 0.7385 (mmt90) cc_final: 0.7082 (mpt-90) REVERT: N 61 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7338 (t) REVERT: N 65 LYS cc_start: 0.7093 (ttmt) cc_final: 0.6634 (ttpt) REVERT: R 169 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5875 (mt) REVERT: R 314 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7345 (ttp-170) REVERT: R 333 LYS cc_start: 0.5304 (mmtt) cc_final: 0.4973 (mmmm) REVERT: R 363 GLU cc_start: 0.3147 (OUTLIER) cc_final: 0.2920 (pm20) REVERT: R 375 PHE cc_start: 0.7993 (m-80) cc_final: 0.7757 (m-80) REVERT: E 133 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6509 (tpt) REVERT: E 136 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7215 (tp) outliers start: 43 outliers final: 13 residues processed: 143 average time/residue: 0.6385 time to fit residues: 97.3442 Evaluate side-chains 132 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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 ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.204822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164075 restraints weight = 9607.433| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.59 r_work: 0.3655 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9523 Z= 0.131 Angle : 0.552 9.888 12927 Z= 0.294 Chirality : 0.042 0.149 1449 Planarity : 0.004 0.044 1646 Dihedral : 5.059 59.048 1290 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.86 % Allowed : 25.74 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1160 helix: 1.70 (0.25), residues: 444 sheet: -0.41 (0.32), residues: 215 loop : -0.59 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.030 0.001 TYR N 60 PHE 0.021 0.002 PHE R 182 TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9514) covalent geometry : angle 0.54742 (12909) SS BOND : bond 0.00271 ( 9) SS BOND : angle 1.91032 ( 18) hydrogen bonds : bond 0.03662 ( 437) hydrogen bonds : angle 4.56751 ( 1248) *********************** 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 138 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6650 (tm-30) REVERT: A 24 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6746 (ttpp) REVERT: A 28 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7305 (mmpt) REVERT: A 216 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6788 (mmpt) REVERT: B 5 ASP cc_start: 0.4053 (OUTLIER) cc_final: 0.3096 (p0) REVERT: B 46 ARG cc_start: 0.8341 (mpt180) cc_final: 0.8031 (mmt90) REVERT: B 59 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 76 ASP cc_start: 0.8217 (p0) cc_final: 0.7932 (p0) REVERT: B 134 ARG cc_start: 0.7368 (pmm-80) cc_final: 0.6911 (ptp-170) REVERT: B 219 ARG cc_start: 0.7406 (mmt90) cc_final: 0.7132 (mpt-90) REVERT: N 65 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6676 (ttpt) REVERT: R 49 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.4293 (m-10) REVERT: R 169 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5816 (mt) REVERT: R 276 LEU cc_start: 0.7765 (mt) cc_final: 0.6592 (tp) REVERT: R 314 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7337 (ttp-170) REVERT: R 321 LYS cc_start: 0.6170 (mmtm) cc_final: 0.5903 (mmtp) REVERT: R 332 MET cc_start: 0.6414 (tmm) cc_final: 0.4901 (ptt) REVERT: R 333 LYS cc_start: 0.5251 (mmtt) cc_final: 0.5019 (mmmm) REVERT: R 363 GLU cc_start: 0.3255 (OUTLIER) cc_final: 0.2966 (pm20) REVERT: R 375 PHE cc_start: 0.8056 (m-80) cc_final: 0.7782 (m-80) REVERT: E 64 VAL cc_start: 0.3662 (OUTLIER) cc_final: 0.3399 (t) REVERT: E 136 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7218 (tp) outliers start: 28 outliers final: 13 residues processed: 133 average time/residue: 0.6153 time to fit residues: 87.0489 Evaluate side-chains 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.205398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159720 restraints weight = 9667.062| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.16 r_work: 0.3638 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9523 Z= 0.125 Angle : 0.541 9.224 12927 Z= 0.289 Chirality : 0.042 0.145 1449 Planarity : 0.004 0.045 1646 Dihedral : 4.970 58.370 1290 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.55 % Allowed : 26.66 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1160 helix: 1.77 (0.25), residues: 444 sheet: -0.40 (0.32), residues: 215 loop : -0.55 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.029 0.001 TYR N 60 PHE 0.017 0.002 PHE R 92 TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9514) covalent geometry : angle 0.53714 (12909) SS BOND : bond 0.00234 ( 9) SS BOND : angle 1.81516 ( 18) hydrogen bonds : bond 0.03586 ( 437) hydrogen bonds : angle 4.51581 ( 1248) ********************** 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 131 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6453 (ttpp) REVERT: A 28 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7124 (mmpt) REVERT: A 216 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6770 (mmpt) REVERT: B 5 ASP cc_start: 0.3995 (OUTLIER) cc_final: 0.3028 (p0) REVERT: B 46 ARG cc_start: 0.8369 (mpt180) cc_final: 0.8038 (mmt90) REVERT: B 59 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7823 (t80) REVERT: B 76 ASP cc_start: 0.8293 (p0) cc_final: 0.7887 (p0) REVERT: B 134 ARG cc_start: 0.7314 (pmm-80) cc_final: 0.6806 (ptp-170) REVERT: B 219 ARG cc_start: 0.7418 (mmt90) cc_final: 0.7088 (mpt-90) REVERT: N 61 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7275 (t) REVERT: N 65 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6546 (ttpt) REVERT: R 49 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.4315 (m-80) REVERT: R 169 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5728 (mt) REVERT: R 276 LEU cc_start: 0.7759 (mt) cc_final: 0.6549 (tp) REVERT: R 314 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7379 (tmm160) REVERT: R 321 LYS cc_start: 0.6063 (mmtm) cc_final: 0.5795 (mmtp) REVERT: R 332 MET cc_start: 0.6397 (tmm) cc_final: 0.4835 (ptt) REVERT: R 333 LYS cc_start: 0.5138 (mmtt) cc_final: 0.4852 (mmmm) REVERT: R 363 GLU cc_start: 0.3168 (OUTLIER) cc_final: 0.2885 (pm20) REVERT: R 375 PHE cc_start: 0.8025 (m-80) cc_final: 0.7750 (m-80) REVERT: E 64 VAL cc_start: 0.3788 (OUTLIER) cc_final: 0.3558 (t) REVERT: E 136 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7139 (tp) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.6601 time to fit residues: 88.5179 Evaluate side-chains 127 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 363 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.0040 chunk 27 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 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 R 39 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.205760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163384 restraints weight = 9606.717| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.78 r_work: 0.3668 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9523 Z= 0.121 Angle : 0.531 8.575 12927 Z= 0.284 Chirality : 0.042 0.144 1449 Planarity : 0.004 0.043 1646 Dihedral : 4.899 57.911 1290 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.47 % Allowed : 25.43 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1160 helix: 1.87 (0.25), residues: 444 sheet: -0.34 (0.32), residues: 214 loop : -0.53 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.029 0.001 TYR N 60 PHE 0.016 0.001 PHE E 100 TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9514) covalent geometry : angle 0.52739 (12909) SS BOND : bond 0.00236 ( 9) SS BOND : angle 1.70379 ( 18) hydrogen bonds : bond 0.03494 ( 437) hydrogen bonds : angle 4.45026 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4906.28 seconds wall clock time: 83 minutes 55.57 seconds (5035.57 seconds total)