Starting phenix.real_space_refine on Tue Sep 24 23:12:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/09_2024/7wbj_32401.cif" } resolution = 3.42 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= -0.002 sd= 0.064 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 57 5.16 5 C 5704 2.51 5 N 1550 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8989 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2871 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1931 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2590 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 958 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 5.90, per 1000 atoms: 0.66 Number of scatterers: 8989 At special positions: 0 Unit cell: (87.822, 100.674, 167.076, 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 57 16.00 O 1678 8.00 N 1550 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 38 " - pdb=" SG CYS R 61 " distance=2.03 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 93 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 271 " distance=2.03 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=2.02 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: 2.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 31 through 38 removed outlier: 3.518A pdb=" N CYS R 38 " --> pdb=" O GLU R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 110 Processing helix chain 'R' and resid 115 through 151 removed outlier: 4.092A pdb=" N THR R 121 " --> pdb=" O GLU R 117 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR R 143 " --> pdb=" O MET R 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE R 146 " --> pdb=" O ALA R 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 156 through 182 removed outlier: 3.709A pdb=" N ASP R 180 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 219 Processing helix chain 'R' and resid 220 through 230 Processing helix chain 'R' and resid 239 through 261 removed outlier: 3.622A pdb=" N ALA R 243 " --> pdb=" O ARG R 239 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) Proline residue: R 252 - end of helix Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.578A pdb=" N VAL R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.092A pdb=" N SER R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 338 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 339 through 343 Processing helix chain 'R' and resid 354 through 362 Processing helix chain 'R' and resid 363 through 367 Processing helix chain 'R' and resid 368 through 376 removed outlier: 3.764A pdb=" N VAL R 373 " --> pdb=" O LEU R 369 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU R 374 " --> pdb=" O VAL R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 393 removed outlier: 4.502A pdb=" N GLU R 385 " --> pdb=" O GLU R 381 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG R 388 " --> pdb=" O CYS R 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.630A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.677A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.782A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.114A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.933A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.734A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.789A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.820A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 35 Processing helix chain 'G' and resid 36 through 44 removed outlier: 3.502A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 56 through 57 removed outlier: 4.037A pdb=" N ASP R 57 " --> pdb=" O THR R 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 91 through 93 removed outlier: 3.625A pdb=" N ASN R 92 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU R 100 " --> pdb=" O ASN R 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 214 removed outlier: 6.865A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.048A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.509A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.834A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 4.027A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.715A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.661A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.660A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1032 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: 2.53 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2663 1.33 - 1.46: 1655 1.46 - 1.58: 4787 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9179 Sorted by residual: bond pdb=" C ALA N 101 " pdb=" N PRO N 102 " ideal model delta sigma weight residual 1.329 1.385 -0.057 1.20e-02 6.94e+03 2.24e+01 bond pdb=" CA ALA N 101 " pdb=" C ALA N 101 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 1.526 1.507 0.019 9.20e-03 1.18e+04 4.34e+00 bond pdb=" C ILE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.84e+00 bond pdb=" CA CYS N 99 " pdb=" CB CYS N 99 " ideal model delta sigma weight residual 1.529 1.503 0.027 1.37e-02 5.33e+03 3.79e+00 ... (remaining 9174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12047 1.47 - 2.93: 316 2.93 - 4.40: 57 4.40 - 5.86: 15 5.86 - 7.33: 10 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.31 114.83 5.48 9.80e-01 1.04e+00 3.13e+01 angle pdb=" C VAL N 110 " pdb=" CA VAL N 110 " pdb=" CB VAL N 110 " ideal model delta sigma weight residual 111.29 117.65 -6.36 1.64e+00 3.72e-01 1.50e+01 angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 110.56 117.89 -7.33 1.94e+00 2.66e-01 1.43e+01 angle pdb=" N ILE R 31 " pdb=" CA ILE R 31 " pdb=" C ILE R 31 " ideal model delta sigma weight residual 113.42 109.12 4.30 1.17e+00 7.31e-01 1.35e+01 angle pdb=" N ALA N 101 " pdb=" CA ALA N 101 " pdb=" C ALA N 101 " ideal model delta sigma weight residual 109.44 115.67 -6.23 1.81e+00 3.05e-01 1.18e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4886 17.89 - 35.79: 467 35.79 - 53.68: 84 53.68 - 71.57: 17 71.57 - 89.47: 9 Dihedral angle restraints: 5463 sinusoidal: 2129 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 271 " pdb=" CB CYS R 271 " ideal model delta sinusoidal sigma weight residual 93.00 151.59 -58.59 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS R 52 " pdb=" SG CYS R 52 " pdb=" SG CYS R 93 " pdb=" CB CYS R 93 " ideal model delta sinusoidal sigma weight residual 93.00 130.23 -37.23 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" SG CYS R 52 " pdb=" CB CYS R 93 " pdb=" SG CYS R 93 " pdb=" CA CYS R 93 " ideal model delta sinusoidal sigma weight residual -73.00 -12.21 -60.79 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1192 0.062 - 0.125: 200 0.125 - 0.187: 8 0.187 - 0.250: 1 0.250 - 0.312: 2 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE R 59 " pdb=" N ILE R 59 " pdb=" C ILE R 59 " pdb=" CB ILE R 59 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA CYS B 204 " pdb=" N CYS B 204 " pdb=" C CYS B 204 " pdb=" CB CYS B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1400 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 101 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO N 102 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO N 102 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 102 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS N 99 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO N 100 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO N 100 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO N 100 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 279 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO R 280 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 280 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 280 " -0.017 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.72: 449 2.72 - 3.45: 13327 3.45 - 4.17: 20404 4.17 - 4.90: 37399 Nonbonded interactions: 71585 Sorted by model distance: nonbonded pdb=" C ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.264 3.270 nonbonded pdb=" CA ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.516 3.470 nonbonded pdb=" CB ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.562 3.440 nonbonded pdb=" O ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.659 3.040 nonbonded pdb=" CB ASN A 278 " pdb=" OD1 ASP N 106 " model vdw 1.844 3.440 ... (remaining 71580 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.970 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.004 0.057 9179 Z= 0.258 Angle : 0.609 7.326 12445 Z= 0.329 Chirality : 0.046 0.312 1403 Planarity : 0.004 0.042 1584 Dihedral : 14.592 89.466 3289 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.21 % Allowed : 0.51 % Favored : 99.28 % 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: -1.06 (0.25), residues: 1128 helix: 0.78 (0.27), residues: 406 sheet: -1.84 (0.34), residues: 202 loop : -1.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 281 HIS 0.003 0.001 HIS R 191 PHE 0.018 0.001 PHE B 278 TYR 0.014 0.001 TYR B 264 ARG 0.004 0.000 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 82 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7903 (tm-30) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.1923 time to fit residues: 42.5072 Evaluate side-chains 121 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.0030 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9179 Z= 0.216 Angle : 0.558 6.677 12445 Z= 0.291 Chirality : 0.042 0.149 1403 Planarity : 0.004 0.031 1584 Dihedral : 4.373 16.903 1241 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 9.46 % Favored : 88.69 % 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: -0.92 (0.25), residues: 1128 helix: 1.02 (0.27), residues: 402 sheet: -1.81 (0.34), residues: 198 loop : -1.38 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 219 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.001 PHE R 151 TYR 0.020 0.001 TYR R 130 ARG 0.003 0.000 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8150 (mt) REVERT: G 38 MET cc_start: 0.7888 (pmm) cc_final: 0.7014 (pmm) REVERT: N 82 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7021 (tm-30) REVERT: N 94 TYR cc_start: 0.7675 (m-80) cc_final: 0.7034 (m-80) REVERT: N 117 TYR cc_start: 0.5905 (m-80) cc_final: 0.5656 (m-80) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.1921 time to fit residues: 38.3280 Evaluate side-chains 125 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN G 59 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9179 Z= 0.154 Angle : 0.506 6.260 12445 Z= 0.265 Chirality : 0.041 0.169 1403 Planarity : 0.003 0.032 1584 Dihedral : 4.103 17.616 1241 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.06 % Allowed : 13.05 % Favored : 84.89 % 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: -0.73 (0.26), residues: 1128 helix: 1.15 (0.27), residues: 410 sheet: -1.76 (0.34), residues: 196 loop : -1.27 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 169 HIS 0.004 0.001 HIS R 191 PHE 0.013 0.001 PHE B 241 TYR 0.017 0.001 TYR R 130 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8065 (mt) REVERT: B 169 TRP cc_start: 0.7734 (m100) cc_final: 0.7457 (m100) REVERT: B 303 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: G 38 MET cc_start: 0.7885 (pmm) cc_final: 0.7462 (pmm) REVERT: N 82 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8130 (tm-30) REVERT: N 94 TYR cc_start: 0.7616 (m-80) cc_final: 0.6931 (m-80) REVERT: N 117 TYR cc_start: 0.5999 (m-80) cc_final: 0.5753 (m-80) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 0.1890 time to fit residues: 38.7738 Evaluate side-chains 130 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9179 Z= 0.231 Angle : 0.527 7.351 12445 Z= 0.276 Chirality : 0.042 0.172 1403 Planarity : 0.003 0.031 1584 Dihedral : 4.130 16.719 1241 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.91 % Allowed : 13.36 % Favored : 82.73 % 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: -0.74 (0.26), residues: 1128 helix: 1.16 (0.27), residues: 409 sheet: -1.80 (0.34), residues: 198 loop : -1.27 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 PHE 0.012 0.001 PHE B 241 TYR 0.017 0.001 TYR R 130 ARG 0.007 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 12 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7414 (mtp-110) REVERT: A 266 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 169 TRP cc_start: 0.7852 (m100) cc_final: 0.7525 (m100) REVERT: B 234 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 303 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: B 339 TRP cc_start: 0.7542 (OUTLIER) cc_final: 0.7069 (m-90) REVERT: G 38 MET cc_start: 0.7977 (pmm) cc_final: 0.7524 (pmm) REVERT: N 82 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8185 (tm-30) REVERT: N 94 TYR cc_start: 0.7723 (m-80) cc_final: 0.7227 (m-80) REVERT: N 117 TYR cc_start: 0.6103 (m-80) cc_final: 0.5842 (m-80) outliers start: 38 outliers final: 21 residues processed: 143 average time/residue: 0.1946 time to fit residues: 39.8835 Evaluate side-chains 138 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9179 Z= 0.163 Angle : 0.497 7.319 12445 Z= 0.260 Chirality : 0.041 0.162 1403 Planarity : 0.003 0.031 1584 Dihedral : 3.962 16.665 1241 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.47 % Allowed : 16.44 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.26), residues: 1128 helix: 1.35 (0.28), residues: 404 sheet: -1.72 (0.34), residues: 194 loop : -1.26 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 191 PHE 0.012 0.001 PHE N 68 TYR 0.015 0.001 TYR R 130 ARG 0.005 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 12 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7354 (mtp-110) REVERT: A 221 MET cc_start: 0.7904 (ttm) cc_final: 0.7683 (tpp) REVERT: A 266 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 169 TRP cc_start: 0.7827 (m100) cc_final: 0.7520 (m100) REVERT: B 234 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: B 339 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.7161 (m-90) REVERT: G 38 MET cc_start: 0.8026 (pmm) cc_final: 0.7595 (pmm) REVERT: N 94 TYR cc_start: 0.7673 (m-80) cc_final: 0.7061 (m-80) REVERT: N 117 TYR cc_start: 0.5912 (m-80) cc_final: 0.5706 (m-80) outliers start: 24 outliers final: 15 residues processed: 142 average time/residue: 0.1970 time to fit residues: 40.0770 Evaluate side-chains 130 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9179 Z= 0.224 Angle : 0.521 7.277 12445 Z= 0.272 Chirality : 0.041 0.145 1403 Planarity : 0.003 0.032 1584 Dihedral : 4.031 18.227 1241 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.29 % Allowed : 17.06 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1128 helix: 1.35 (0.27), residues: 405 sheet: -1.76 (0.34), residues: 196 loop : -1.23 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 340 PHE 0.016 0.001 PHE N 68 TYR 0.016 0.001 TYR R 130 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: R 356 GLN cc_start: 0.7241 (pp30) cc_final: 0.6307 (pm20) REVERT: L 12 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7382 (mtp-110) REVERT: B 169 TRP cc_start: 0.7949 (m100) cc_final: 0.7576 (m100) REVERT: B 234 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: B 339 TRP cc_start: 0.7477 (OUTLIER) cc_final: 0.7094 (m-90) REVERT: G 38 MET cc_start: 0.7825 (pmm) cc_final: 0.7442 (pmm) REVERT: N 82 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8087 (tm-30) REVERT: N 94 TYR cc_start: 0.7723 (m-80) cc_final: 0.7147 (m-80) REVERT: N 117 TYR cc_start: 0.6063 (m-80) cc_final: 0.5862 (m-80) outliers start: 32 outliers final: 26 residues processed: 142 average time/residue: 0.2008 time to fit residues: 40.4930 Evaluate side-chains 143 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9179 Z= 0.167 Angle : 0.500 8.975 12445 Z= 0.260 Chirality : 0.041 0.140 1403 Planarity : 0.004 0.055 1584 Dihedral : 3.949 19.448 1241 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.39 % Allowed : 17.88 % Favored : 78.73 % 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: -0.50 (0.26), residues: 1128 helix: 1.42 (0.27), residues: 415 sheet: -1.67 (0.35), residues: 187 loop : -1.23 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 PHE 0.016 0.001 PHE N 68 TYR 0.015 0.001 TYR R 130 ARG 0.004 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8393 (tp) cc_final: 0.8088 (mt) REVERT: R 356 GLN cc_start: 0.7233 (pp30) cc_final: 0.6296 (pm20) REVERT: L 12 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7318 (mtp-110) REVERT: A 266 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 169 TRP cc_start: 0.7895 (m100) cc_final: 0.7569 (m100) REVERT: B 234 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: B 339 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.7201 (m-90) REVERT: G 38 MET cc_start: 0.7924 (pmm) cc_final: 0.7521 (pmm) REVERT: N 82 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8095 (tm-30) REVERT: N 94 TYR cc_start: 0.7693 (m-80) cc_final: 0.7056 (m-80) REVERT: N 117 TYR cc_start: 0.5985 (m-80) cc_final: 0.5779 (m-80) outliers start: 33 outliers final: 21 residues processed: 144 average time/residue: 0.1828 time to fit residues: 37.8642 Evaluate side-chains 138 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9179 Z= 0.163 Angle : 0.506 8.374 12445 Z= 0.261 Chirality : 0.041 0.140 1403 Planarity : 0.003 0.050 1584 Dihedral : 3.938 20.066 1241 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.19 % Allowed : 18.71 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.26), residues: 1128 helix: 1.47 (0.27), residues: 413 sheet: -1.55 (0.35), residues: 185 loop : -1.23 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 281 HIS 0.003 0.001 HIS R 191 PHE 0.011 0.001 PHE N 27 TYR 0.014 0.001 TYR R 130 ARG 0.003 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8384 (tp) cc_final: 0.8085 (mt) REVERT: R 356 GLN cc_start: 0.7164 (pp30) cc_final: 0.6300 (pm20) REVERT: A 266 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 68 ARG cc_start: 0.5855 (mtp-110) cc_final: 0.5625 (mtp-110) REVERT: B 169 TRP cc_start: 0.7885 (m100) cc_final: 0.7556 (m100) REVERT: B 234 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: G 38 MET cc_start: 0.7865 (pmm) cc_final: 0.7567 (pmm) REVERT: N 82 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8107 (tm-30) REVERT: N 94 TYR cc_start: 0.7679 (m-80) cc_final: 0.7070 (m-80) outliers start: 31 outliers final: 24 residues processed: 145 average time/residue: 0.1836 time to fit residues: 38.3736 Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 105 optimal weight: 0.0770 chunk 64 optimal weight: 0.3980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9179 Z= 0.143 Angle : 0.501 8.421 12445 Z= 0.258 Chirality : 0.040 0.150 1403 Planarity : 0.003 0.050 1584 Dihedral : 3.886 20.340 1241 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.88 % Allowed : 19.42 % Favored : 77.70 % 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: -0.31 (0.26), residues: 1128 helix: 1.57 (0.27), residues: 415 sheet: -1.40 (0.35), residues: 196 loop : -1.19 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 339 HIS 0.003 0.001 HIS R 191 PHE 0.011 0.001 PHE N 27 TYR 0.013 0.001 TYR R 130 ARG 0.008 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8368 (tp) cc_final: 0.8083 (mt) REVERT: L 12 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7322 (mtp-110) REVERT: A 266 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 169 TRP cc_start: 0.7843 (m100) cc_final: 0.7488 (m100) REVERT: G 38 MET cc_start: 0.7798 (pmm) cc_final: 0.7392 (pmm) REVERT: N 82 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8138 (tm-30) REVERT: N 94 TYR cc_start: 0.7726 (m-80) cc_final: 0.7123 (m-80) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.1984 time to fit residues: 39.7566 Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9179 Z= 0.218 Angle : 0.547 9.407 12445 Z= 0.280 Chirality : 0.042 0.149 1403 Planarity : 0.003 0.048 1584 Dihedral : 3.990 20.048 1241 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.67 % Allowed : 20.45 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1128 helix: 1.53 (0.27), residues: 415 sheet: -1.62 (0.34), residues: 204 loop : -1.14 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 219 HIS 0.004 0.001 HIS R 340 PHE 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR R 130 ARG 0.007 0.000 ARG L 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8390 (tp) cc_final: 0.8097 (mt) REVERT: L 12 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7305 (mtp-110) REVERT: B 169 TRP cc_start: 0.7902 (m100) cc_final: 0.7520 (m100) REVERT: G 38 MET cc_start: 0.7849 (pmm) cc_final: 0.7599 (pmm) REVERT: N 82 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8069 (tm-30) REVERT: N 94 TYR cc_start: 0.7778 (m-80) cc_final: 0.7211 (m-80) outliers start: 26 outliers final: 24 residues processed: 132 average time/residue: 0.1937 time to fit residues: 36.5840 Evaluate side-chains 137 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0030 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137551 restraints weight = 12586.941| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.05 r_work: 0.3571 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9179 Z= 0.177 Angle : 0.523 9.085 12445 Z= 0.268 Chirality : 0.041 0.149 1403 Planarity : 0.003 0.048 1584 Dihedral : 3.952 20.936 1241 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.67 % Allowed : 20.55 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1128 helix: 1.50 (0.27), residues: 418 sheet: -1.56 (0.34), residues: 204 loop : -1.08 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS R 191 PHE 0.011 0.001 PHE N 27 TYR 0.015 0.001 TYR R 130 ARG 0.007 0.000 ARG L 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.29 seconds wall clock time: 38 minutes 33.97 seconds (2313.97 seconds total)