Starting phenix.real_space_refine on Wed Apr 30 05:37:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uus_20901/04_2025/6uus_20901.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uus_20901/04_2025/6uus_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_20901/04_2025/6uus_20901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uus_20901/04_2025/6uus_20901.map" model { file = "/net/cci-nas-00/data/ceres_data/6uus_20901/04_2025/6uus_20901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uus_20901/04_2025/6uus_20901.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9308 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2734 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 749 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 5.52, per 1000 atoms: 0.59 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.592A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.520A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.565A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.622A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 4.161A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.646A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 133 through 166 Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 201 through 208 removed outlier: 4.049A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 241 removed outlier: 4.398A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.551A pdb=" N TYR R 256 " --> pdb=" O LEU R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 278 Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 320 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 removed outlier: 3.783A pdb=" N THR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 399 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.068A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 77 removed outlier: 4.065A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.234A pdb=" N THR E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 143 Proline residue: E 126 - end of helix removed outlier: 3.861A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.400A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.578A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.677A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.676A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.555A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.324A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.678A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.048A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 68 through 69 removed outlier: 3.875A pdb=" N THR R 68 " --> pdb=" O TRP R 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP R 75 " --> pdb=" O THR R 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 82 through 83 437 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.78 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: 1.440 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.060 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- 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 : 7.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.22), residues: 1160 helix: -1.09 (0.23), residues: 433 sheet: -1.53 (0.30), residues: 222 loop : -1.71 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 229 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE E 100 TYR 0.015 0.001 TYR N 60 ARG 0.008 0.001 ARG R 397 Details of bonding type rmsd hydrogen bonds : bond 0.20809 ( 437) hydrogen bonds : angle 7.35230 ( 1248) SS BOND : bond 0.00449 ( 9) SS BOND : angle 0.87028 ( 18) covalent geometry : bond 0.00195 ( 9514) covalent geometry : angle 0.50089 (12909) *********************** 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 : 1.003 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: 1.4101 time to fit residues: 256.8655 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 : 1.112 ------------------------------------------------------------------------------- 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 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 overall best weight: 1.8364 ------------------------------------------------------------------------------- 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 N 1 GLN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.202859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159622 restraints weight = 9548.592| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.93 r_work: 0.3633 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9523 Z= 0.221 Angle : 0.669 7.493 12927 Z= 0.365 Chirality : 0.046 0.147 1449 Planarity : 0.005 0.050 1646 Dihedral : 6.844 80.787 1308 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.09 % Allowed : 22.78 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1160 helix: 0.16 (0.24), residues: 439 sheet: -1.11 (0.31), residues: 223 loop : -1.30 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 211 HIS 0.008 0.002 HIS R 374 PHE 0.018 0.003 PHE E 100 TYR 0.012 0.002 TYR R 49 ARG 0.009 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 437) hydrogen bonds : angle 5.39414 ( 1248) SS BOND : bond 0.00883 ( 9) SS BOND : angle 2.40339 ( 18) covalent geometry : bond 0.00490 ( 9514) covalent geometry : angle 0.66348 (12909) *********************** 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: 40 poor density : 123 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7218 (mmpt) REVERT: B 5 ASP cc_start: 0.3361 (OUTLIER) cc_final: 0.2367 (p0) REVERT: B 46 ARG cc_start: 0.8347 (mpt180) cc_final: 0.8057 (mmt90) REVERT: B 59 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 66 ASP cc_start: 0.7420 (p0) cc_final: 0.7106 (p0) REVERT: B 219 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7083 (mpt-90) REVERT: B 322 ASP cc_start: 0.6749 (m-30) cc_final: 0.6459 (m-30) REVERT: G 47 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: P 50 GLN cc_start: 0.2269 (OUTLIER) cc_final: 0.1424 (tm-30) REVERT: R 48 CYS cc_start: 0.3723 (OUTLIER) cc_final: 0.1724 (t) REVERT: R 49 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.4111 (t80) REVERT: R 314 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7288 (ttp-170) REVERT: R 332 MET cc_start: 0.5629 (tpt) cc_final: 0.4657 (ttt) REVERT: R 375 PHE cc_start: 0.8027 (m-80) cc_final: 0.7740 (m-80) REVERT: E 136 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7173 (tp) outliers start: 40 outliers final: 14 residues processed: 156 average time/residue: 1.2014 time to fit residues: 200.9837 Evaluate side-chains 125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 5 ASP 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 G residue 47 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 23 VAL 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 49 TYR 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 E residue 64 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 176 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 3 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 R 140 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.203468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162036 restraints weight = 9644.980| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.71 r_work: 0.3623 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9523 Z= 0.163 Angle : 0.596 8.275 12927 Z= 0.321 Chirality : 0.044 0.142 1449 Planarity : 0.005 0.048 1646 Dihedral : 6.194 75.626 1298 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.80 % Allowed : 22.88 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1160 helix: 0.83 (0.25), residues: 443 sheet: -0.74 (0.32), residues: 221 loop : -1.03 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS R 374 PHE 0.017 0.002 PHE E 100 TYR 0.019 0.002 TYR N 60 ARG 0.008 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 437) hydrogen bonds : angle 5.01933 ( 1248) SS BOND : bond 0.00399 ( 9) SS BOND : angle 2.14790 ( 18) covalent geometry : bond 0.00361 ( 9514) covalent geometry : angle 0.59066 (12909) *********************** 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 162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7314 (mmpt) REVERT: A 34 LYS cc_start: 0.8252 (ttpp) cc_final: 0.8008 (tttp) REVERT: A 327 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: B 5 ASP cc_start: 0.3579 (OUTLIER) cc_final: 0.2643 (p0) REVERT: B 44 GLN cc_start: 0.7578 (mt0) cc_final: 0.7271 (mt0) REVERT: B 46 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8132 (mmt90) REVERT: B 59 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 66 ASP cc_start: 0.7369 (p0) cc_final: 0.7097 (p0) REVERT: B 322 ASP cc_start: 0.6935 (m-30) cc_final: 0.6678 (m-30) REVERT: G 47 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: P 50 GLN cc_start: 0.1297 (OUTLIER) cc_final: 0.0268 (tp-100) REVERT: R 48 CYS cc_start: 0.3958 (OUTLIER) cc_final: 0.1787 (t) REVERT: R 74 CYS cc_start: 0.2118 (OUTLIER) cc_final: 0.1162 (p) REVERT: R 169 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5662 (mt) REVERT: R 252 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7003 (mp) REVERT: R 314 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7429 (ttp-170) REVERT: R 332 MET cc_start: 0.5573 (tpt) cc_final: 0.4812 (ttm) REVERT: R 375 PHE cc_start: 0.8054 (m-80) cc_final: 0.7832 (m-80) REVERT: E 136 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7282 (tp) outliers start: 47 outliers final: 19 residues processed: 154 average time/residue: 1.1935 time to fit residues: 197.1388 Evaluate side-chains 142 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER 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 46 ARG 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 B residue 316 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 47 GLU 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 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 126 GLN 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 252 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 102 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 176 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 53 GLN P 50 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.205217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162570 restraints weight = 9602.810| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.88 r_work: 0.3656 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2604 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= 0.123 Angle : 0.533 7.032 12927 Z= 0.287 Chirality : 0.042 0.144 1449 Planarity : 0.004 0.047 1646 Dihedral : 5.899 69.912 1298 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.98 % Allowed : 23.39 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1160 helix: 1.26 (0.25), residues: 443 sheet: -0.64 (0.33), residues: 211 loop : -0.80 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS R 374 PHE 0.016 0.001 PHE E 100 TYR 0.017 0.001 TYR N 60 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 437) hydrogen bonds : angle 4.72410 ( 1248) SS BOND : bond 0.00186 ( 9) SS BOND : angle 1.62914 ( 18) covalent geometry : bond 0.00268 ( 9514) covalent geometry : angle 0.52985 (12909) *********************** 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 160 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6669 (tm-30) REVERT: A 28 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7316 (mmpt) REVERT: A 35 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7246 (mm110) REVERT: B 5 ASP cc_start: 0.3762 (OUTLIER) cc_final: 0.2830 (p0) REVERT: B 44 GLN cc_start: 0.7603 (mt0) cc_final: 0.7368 (mt0) REVERT: B 46 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8080 (mmt90) REVERT: B 59 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 66 ASP cc_start: 0.7264 (p0) cc_final: 0.7044 (p0) REVERT: B 322 ASP cc_start: 0.6897 (m-30) cc_final: 0.6643 (m-30) REVERT: P 50 GLN cc_start: 0.1788 (OUTLIER) cc_final: 0.0650 (tp-100) REVERT: R 40 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5673 (ttpt) REVERT: R 48 CYS cc_start: 0.4078 (OUTLIER) cc_final: 0.1499 (t) REVERT: R 49 TYR cc_start: 0.4579 (OUTLIER) cc_final: 0.4176 (t80) REVERT: R 74 CYS cc_start: 0.2167 (OUTLIER) cc_final: 0.0780 (p) REVERT: R 169 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5592 (mt) REVERT: R 314 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7362 (ttp-170) REVERT: R 332 MET cc_start: 0.5503 (tpt) cc_final: 0.4828 (ttm) REVERT: R 375 PHE cc_start: 0.8031 (m-80) cc_final: 0.7817 (m-80) outliers start: 39 outliers final: 13 residues processed: 150 average time/residue: 1.2000 time to fit residues: 192.9521 Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 349 SER 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 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 15 LEU 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 P residue 50 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 E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.0370 chunk 108 optimal weight: 6.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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** P 50 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165352 restraints weight = 9605.805| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.68 r_work: 0.3681 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9523 Z= 0.110 Angle : 0.501 6.834 12927 Z= 0.271 Chirality : 0.041 0.141 1449 Planarity : 0.004 0.045 1646 Dihedral : 4.956 58.297 1291 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.78 % Allowed : 24.31 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1160 helix: 1.52 (0.25), residues: 443 sheet: -0.60 (0.32), residues: 215 loop : -0.64 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS R 374 PHE 0.016 0.001 PHE E 100 TYR 0.025 0.001 TYR N 60 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 437) hydrogen bonds : angle 4.52070 ( 1248) SS BOND : bond 0.00109 ( 9) SS BOND : angle 1.39867 ( 18) covalent geometry : bond 0.00235 ( 9514) covalent geometry : angle 0.49904 (12909) *********************** 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 153 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6590 (tm-30) REVERT: A 28 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7217 (mmpt) REVERT: B 25 CYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5367 (t) REVERT: B 44 GLN cc_start: 0.7568 (mt0) cc_final: 0.7343 (mt0) REVERT: B 46 ARG cc_start: 0.8305 (mpt180) cc_final: 0.7972 (mmt90) REVERT: B 59 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 322 ASP cc_start: 0.6608 (m-30) cc_final: 0.6405 (m-30) REVERT: G 21 MET cc_start: 0.5870 (tpt) cc_final: 0.5273 (mmt) REVERT: R 48 CYS cc_start: 0.4155 (OUTLIER) cc_final: 0.2065 (t) REVERT: R 49 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.4304 (t80) REVERT: R 169 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5506 (mt) REVERT: R 363 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.2844 (pm20) REVERT: E 142 LYS cc_start: 0.5654 (ttpp) cc_final: 0.4971 (tttt) outliers start: 37 outliers final: 15 residues processed: 144 average time/residue: 1.1794 time to fit residues: 182.1347 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 : 1.107 ------------------------------------------------------------------------------- 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 25 CYS Chi-restraints excluded: chain B residue 29 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 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 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 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 0.0060 chunk 86 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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** N 53 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166316 restraints weight = 9628.100| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.47 r_work: 0.3668 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9523 Z= 0.130 Angle : 0.538 7.586 12927 Z= 0.289 Chirality : 0.042 0.139 1449 Planarity : 0.004 0.045 1646 Dihedral : 5.033 58.908 1291 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.70 % Allowed : 23.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1160 helix: 1.58 (0.25), residues: 443 sheet: -0.46 (0.32), residues: 211 loop : -0.60 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS R 374 PHE 0.023 0.002 PHE R 182 TYR 0.026 0.001 TYR N 60 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 437) hydrogen bonds : angle 4.55465 ( 1248) SS BOND : bond 0.00152 ( 9) SS BOND : angle 1.55109 ( 18) covalent geometry : bond 0.00283 ( 9514) covalent geometry : angle 0.53511 (12909) *********************** 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 161 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6620 (tm-30) REVERT: A 24 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6715 (ttpp) REVERT: A 28 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7270 (mmpt) REVERT: A 35 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7243 (mm-40) REVERT: A 216 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6768 (mmpt) REVERT: B 5 ASP cc_start: 0.3784 (OUTLIER) cc_final: 0.2918 (p0) REVERT: B 25 CYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5394 (t) REVERT: B 44 GLN cc_start: 0.7565 (mt0) cc_final: 0.7310 (mt0) REVERT: B 46 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7989 (mmt90) REVERT: B 59 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7740 (t80) REVERT: B 219 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7075 (mpt-90) REVERT: N 65 LYS cc_start: 0.7068 (ttmt) cc_final: 0.6570 (ttpt) REVERT: R 48 CYS cc_start: 0.4164 (OUTLIER) cc_final: 0.1947 (t) REVERT: R 49 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.4287 (t80) REVERT: R 169 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5625 (mt) REVERT: R 333 LYS cc_start: 0.5233 (mmtt) cc_final: 0.4973 (mmmm) REVERT: R 363 GLU cc_start: 0.3330 (OUTLIER) cc_final: 0.2935 (pm20) REVERT: R 369 MET cc_start: 0.6631 (ttp) cc_final: 0.6369 (ttp) outliers start: 46 outliers final: 16 residues processed: 150 average time/residue: 1.3513 time to fit residues: 217.0346 Evaluate side-chains 140 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 35 GLN 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 25 CYS Chi-restraints excluded: chain B residue 29 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 81 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 15 LEU 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 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 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 202 GLN R 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.206712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166337 restraints weight = 9685.812| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.53 r_work: 0.3694 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9523 Z= 0.110 Angle : 0.505 8.307 12927 Z= 0.270 Chirality : 0.041 0.140 1449 Planarity : 0.004 0.044 1646 Dihedral : 4.829 57.183 1291 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.58 % Allowed : 24.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1160 helix: 1.73 (0.25), residues: 443 sheet: -0.37 (0.32), residues: 216 loop : -0.52 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE E 100 TYR 0.027 0.001 TYR N 60 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 437) hydrogen bonds : angle 4.38265 ( 1248) SS BOND : bond 0.00168 ( 9) SS BOND : angle 1.41757 ( 18) covalent geometry : bond 0.00238 ( 9514) covalent geometry : angle 0.50266 (12909) *********************** 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 150 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6546 (tm-30) REVERT: A 24 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6696 (ttpp) REVERT: A 28 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7241 (mmpt) REVERT: A 35 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7203 (mm110) REVERT: B 5 ASP cc_start: 0.3832 (OUTLIER) cc_final: 0.3003 (p0) REVERT: B 46 ARG cc_start: 0.8284 (mpt180) cc_final: 0.7955 (mmt90) REVERT: B 59 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7732 (t80) REVERT: B 219 ARG cc_start: 0.7345 (mmt90) cc_final: 0.7040 (mpt-90) REVERT: N 65 LYS cc_start: 0.7019 (ttmt) cc_final: 0.6544 (ttpt) REVERT: R 48 CYS cc_start: 0.4210 (OUTLIER) cc_final: 0.2049 (t) REVERT: R 49 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.4112 (t80) REVERT: R 182 PHE cc_start: 0.7156 (t80) cc_final: 0.5974 (m-80) REVERT: R 276 LEU cc_start: 0.7788 (mt) cc_final: 0.6587 (tp) REVERT: R 314 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7229 (tmm160) REVERT: R 333 LYS cc_start: 0.5112 (mmtt) cc_final: 0.4806 (mmmm) REVERT: R 363 GLU cc_start: 0.3328 (OUTLIER) cc_final: 0.2875 (pm20) REVERT: R 369 MET cc_start: 0.6551 (ttp) cc_final: 0.6276 (ttp) REVERT: R 375 PHE cc_start: 0.8014 (m-80) cc_final: 0.7769 (m-80) REVERT: E 64 VAL cc_start: 0.3608 (OUTLIER) cc_final: 0.3321 (t) outliers start: 35 outliers final: 16 residues processed: 141 average time/residue: 1.2703 time to fit residues: 192.2973 Evaluate side-chains 132 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 35 GLN 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 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 15 LEU 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 122 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 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9064 > 50: distance: 11 - 14: 21.095 distance: 14 - 15: 20.031 distance: 15 - 18: 14.727 distance: 16 - 17: 41.257 distance: 16 - 19: 29.124 distance: 19 - 20: 16.473 distance: 20 - 21: 24.083 distance: 20 - 23: 43.513 distance: 21 - 22: 4.776 distance: 21 - 24: 50.678 distance: 24 - 25: 21.696 distance: 25 - 26: 37.281 distance: 25 - 28: 36.204 distance: 26 - 29: 33.686 distance: 29 - 30: 35.102 distance: 30 - 31: 42.889 distance: 30 - 33: 15.115 distance: 31 - 32: 41.199 distance: 31 - 34: 27.204 distance: 34 - 35: 22.710 distance: 35 - 36: 8.276 distance: 35 - 38: 39.891 distance: 36 - 37: 34.944 distance: 36 - 48: 9.104 distance: 38 - 39: 10.397 distance: 39 - 40: 31.803 distance: 39 - 41: 18.360 distance: 40 - 42: 34.895 distance: 41 - 43: 34.836 distance: 41 - 44: 13.262 distance: 42 - 43: 20.049 distance: 43 - 45: 21.718 distance: 44 - 46: 15.638 distance: 45 - 47: 8.265 distance: 46 - 47: 18.698 distance: 48 - 49: 30.810 distance: 49 - 50: 28.769 distance: 49 - 52: 23.307 distance: 50 - 51: 23.230 distance: 50 - 54: 32.568 distance: 52 - 53: 48.376 distance: 53 - 103: 32.636 distance: 54 - 55: 35.105 distance: 55 - 56: 13.216 distance: 55 - 58: 9.125 distance: 56 - 57: 20.071 distance: 56 - 62: 29.321 distance: 58 - 59: 31.314 distance: 59 - 60: 21.231 distance: 59 - 61: 9.134 distance: 62 - 63: 32.161 distance: 63 - 64: 37.300 distance: 63 - 66: 21.131 distance: 64 - 65: 40.401 distance: 64 - 67: 23.595 distance: 67 - 68: 24.259 distance: 68 - 69: 35.296 distance: 68 - 71: 25.734 distance: 69 - 70: 36.903 distance: 69 - 72: 37.460 distance: 72 - 73: 36.789 distance: 73 - 74: 24.742 distance: 73 - 76: 14.437 distance: 74 - 75: 35.536 distance: 74 - 77: 23.939