Starting phenix.real_space_refine on Thu Feb 13 12:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_32401.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_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/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_32401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_32401.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_32401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbj_32401/02_2025/7wbj_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-5592/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: 5.51, per 1000 atoms: 0.61 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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: 0.94 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: 2.59 Time building geometry restraints manager: 2.74 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: 1.250 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.140 Find NCS groups from input model: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.023 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: 0.2046 time to fit residues: 45.0569 Evaluate side-chains 121 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.189189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151282 restraints weight = 12809.599| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.06 r_work: 0.3659 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7399 (t0) REVERT: A 266 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 391 TYR cc_start: 0.7461 (m-80) cc_final: 0.7247 (m-80) REVERT: B 169 TRP cc_start: 0.8448 (m100) cc_final: 0.8245 (m100) REVERT: G 38 MET cc_start: 0.8075 (pmm) cc_final: 0.7173 (pmm) REVERT: N 82 GLN cc_start: 0.8087 (tm-30) cc_final: 0.6939 (tm-30) REVERT: N 94 TYR cc_start: 0.7939 (m-80) cc_final: 0.7253 (m-80) REVERT: N 117 TYR cc_start: 0.6029 (m-80) cc_final: 0.5755 (m-80) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.1916 time to fit residues: 38.1751 Evaluate side-chains 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 8 ASP 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 21 optimal weight: 0.2980 chunk 106 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136441 restraints weight = 12749.427| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.04 r_work: 0.3561 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9179 Z= 0.182 Angle : 0.517 6.294 12445 Z= 0.270 Chirality : 0.041 0.163 1403 Planarity : 0.003 0.032 1584 Dihedral : 4.168 17.532 1241 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.77 % Allowed : 12.44 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1128 helix: 1.09 (0.27), residues: 408 sheet: -1.78 (0.34), residues: 194 loop : -1.27 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS R 191 PHE 0.013 0.001 PHE B 241 TYR 0.018 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 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7771 (t0) cc_final: 0.7484 (t0) REVERT: A 221 MET cc_start: 0.8633 (ttm) cc_final: 0.8257 (tpp) REVERT: A 266 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 391 TYR cc_start: 0.7379 (m-80) cc_final: 0.7143 (m-80) REVERT: B 169 TRP cc_start: 0.8564 (m100) cc_final: 0.8274 (m100) REVERT: B 258 ASP cc_start: 0.6775 (t0) cc_final: 0.6570 (t70) REVERT: B 303 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: G 38 MET cc_start: 0.8047 (pmm) cc_final: 0.7544 (pmm) REVERT: N 82 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7968 (tm-30) REVERT: N 94 TYR cc_start: 0.8080 (m-80) cc_final: 0.7258 (m-80) REVERT: N 117 TYR cc_start: 0.6106 (m-80) cc_final: 0.5797 (m-80) outliers start: 27 outliers final: 15 residues processed: 142 average time/residue: 0.2013 time to fit residues: 40.7959 Evaluate side-chains 129 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.183307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144498 restraints weight = 12995.456| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.26 r_work: 0.3563 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9179 Z= 0.454 Angle : 0.667 7.762 12445 Z= 0.348 Chirality : 0.046 0.179 1403 Planarity : 0.004 0.036 1584 Dihedral : 4.765 19.253 1241 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.73 % Allowed : 14.90 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1128 helix: 0.74 (0.26), residues: 407 sheet: -2.20 (0.33), residues: 211 loop : -1.34 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 219 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.002 PHE B 151 TYR 0.024 0.002 TYR N 60 ARG 0.007 0.001 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 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7744 (t70) cc_final: 0.7385 (t0) REVERT: L 12 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8188 (mtp-110) REVERT: B 58 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 234 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 292 PHE cc_start: 0.7964 (m-10) cc_final: 0.7659 (m-80) REVERT: B 303 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: G 38 MET cc_start: 0.8172 (pmm) cc_final: 0.7722 (pmm) REVERT: N 82 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8300 (tm-30) REVERT: N 117 TYR cc_start: 0.6290 (m-80) cc_final: 0.6026 (m-80) outliers start: 46 outliers final: 29 residues processed: 149 average time/residue: 0.2017 time to fit residues: 42.6665 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 254 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 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL 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 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL 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 58 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 103 optimal weight: 0.1980 chunk 98 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 308 GLN N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.187487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138742 restraints weight = 12635.112| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.38 r_work: 0.3536 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9179 Z= 0.164 Angle : 0.511 7.000 12445 Z= 0.270 Chirality : 0.041 0.168 1403 Planarity : 0.003 0.030 1584 Dihedral : 4.214 17.171 1241 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.36 % Allowed : 18.19 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1128 helix: 1.21 (0.27), residues: 406 sheet: -1.85 (0.34), residues: 195 loop : -1.27 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 281 HIS 0.004 0.001 HIS R 191 PHE 0.010 0.001 PHE B 241 TYR 0.016 0.001 TYR R 375 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 153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 342 MET cc_start: 0.7975 (tpp) cc_final: 0.7725 (tpp) REVERT: L 8 ASP cc_start: 0.7771 (t70) cc_final: 0.7478 (t0) REVERT: L 12 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8165 (mtp-110) REVERT: A 311 TYR cc_start: 0.7966 (m-80) cc_final: 0.7717 (m-80) REVERT: A 391 TYR cc_start: 0.7325 (m-80) cc_final: 0.6981 (m-80) REVERT: B 339 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7491 (m-90) REVERT: G 38 MET cc_start: 0.8119 (pmm) cc_final: 0.7639 (pmm) REVERT: N 13 GLN cc_start: 0.5294 (mm-40) cc_final: 0.5089 (mm-40) REVERT: N 82 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8031 (tm-30) REVERT: N 94 TYR cc_start: 0.8199 (m-80) cc_final: 0.7615 (m-80) REVERT: N 117 TYR cc_start: 0.6143 (m-80) cc_final: 0.5815 (m-80) outliers start: 23 outliers final: 16 residues processed: 147 average time/residue: 0.1953 time to fit residues: 41.3145 Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 222 VAL 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 96 ARG 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 90 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.185552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137260 restraints weight = 12704.631| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.50 r_work: 0.3485 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1711 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= 0.241 Angle : 0.527 7.558 12445 Z= 0.277 Chirality : 0.042 0.151 1403 Planarity : 0.004 0.050 1584 Dihedral : 4.279 20.752 1241 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.98 % Allowed : 18.71 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1128 helix: 1.21 (0.27), residues: 406 sheet: -1.84 (0.34), residues: 195 loop : -1.20 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 PHE 0.018 0.001 PHE N 68 TYR 0.016 0.001 TYR R 130 ARG 0.005 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 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 356 GLN cc_start: 0.6374 (pm20) cc_final: 0.6129 (pm20) REVERT: L 8 ASP cc_start: 0.7877 (t70) cc_final: 0.7555 (t0) REVERT: L 12 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8124 (mtp-110) REVERT: A 391 TYR cc_start: 0.7336 (m-80) cc_final: 0.6997 (m-80) REVERT: B 258 ASP cc_start: 0.6883 (t0) cc_final: 0.6667 (t70) REVERT: B 339 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7399 (m-90) REVERT: G 38 MET cc_start: 0.8151 (pmm) cc_final: 0.7680 (pmm) REVERT: N 82 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8029 (tm-30) REVERT: N 94 TYR cc_start: 0.8287 (m-80) cc_final: 0.7714 (m-80) REVERT: N 117 TYR cc_start: 0.6322 (m-80) cc_final: 0.5981 (m-80) outliers start: 29 outliers final: 23 residues processed: 140 average time/residue: 0.2005 time to fit residues: 40.2290 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 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 186 ASP 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 64 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.186180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137952 restraints weight = 12762.076| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.53 r_work: 0.3507 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9179 Z= 0.213 Angle : 0.520 7.888 12445 Z= 0.271 Chirality : 0.041 0.149 1403 Planarity : 0.003 0.041 1584 Dihedral : 4.210 21.768 1241 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.29 % Allowed : 19.01 % 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: -0.60 (0.26), residues: 1128 helix: 1.28 (0.27), residues: 411 sheet: -1.87 (0.34), residues: 196 loop : -1.14 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 PHE 0.018 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 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7795 (t70) cc_final: 0.7477 (t0) REVERT: L 12 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8131 (mtp-110) REVERT: A 311 TYR cc_start: 0.7920 (m-80) cc_final: 0.7693 (m-80) REVERT: A 391 TYR cc_start: 0.7399 (m-80) cc_final: 0.7058 (m-80) REVERT: B 258 ASP cc_start: 0.6841 (t0) cc_final: 0.6616 (t70) REVERT: G 38 MET cc_start: 0.8187 (pmm) cc_final: 0.7686 (pmm) REVERT: N 82 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8015 (tm-30) REVERT: N 94 TYR cc_start: 0.8259 (m-80) cc_final: 0.7644 (m-80) REVERT: N 117 TYR cc_start: 0.6326 (m-80) cc_final: 0.5994 (m-80) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.2031 time to fit residues: 42.3262 Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 74 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 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 64 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.186137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134069 restraints weight = 12909.893| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.09 r_work: 0.3524 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9179 Z= 0.212 Angle : 0.520 7.841 12445 Z= 0.271 Chirality : 0.041 0.152 1403 Planarity : 0.003 0.046 1584 Dihedral : 4.173 18.990 1241 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.08 % Allowed : 20.45 % Favored : 76.46 % 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: -0.58 (0.26), residues: 1128 helix: 1.34 (0.27), residues: 410 sheet: -1.85 (0.34), residues: 196 loop : -1.17 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 PHE 0.014 0.001 PHE B 241 TYR 0.015 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 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8197 (tp) cc_final: 0.7957 (mt) REVERT: L 8 ASP cc_start: 0.7762 (t70) cc_final: 0.7459 (t0) REVERT: A 221 MET cc_start: 0.8674 (ttm) cc_final: 0.8372 (ttm) REVERT: A 391 TYR cc_start: 0.7413 (m-80) cc_final: 0.7095 (m-80) REVERT: G 38 MET cc_start: 0.8264 (pmm) cc_final: 0.7745 (pmm) REVERT: N 82 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 94 TYR cc_start: 0.8227 (m-80) cc_final: 0.7654 (m-80) REVERT: N 117 TYR cc_start: 0.6329 (m-80) cc_final: 0.5947 (m-80) outliers start: 30 outliers final: 25 residues processed: 139 average time/residue: 0.1986 time to fit residues: 39.3414 Evaluate side-chains 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 384 CYS 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 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 245 SER 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 G residue 54 VAL Chi-restraints excluded: chain N residue 64 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.184957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132842 restraints weight = 12895.592| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.08 r_work: 0.3514 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9179 Z= 0.263 Angle : 0.554 8.031 12445 Z= 0.289 Chirality : 0.042 0.168 1403 Planarity : 0.004 0.044 1584 Dihedral : 4.279 19.582 1241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.08 % Allowed : 20.66 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1128 helix: 1.28 (0.27), residues: 409 sheet: -1.94 (0.34), residues: 201 loop : -1.15 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 PHE 0.015 0.001 PHE B 241 TYR 0.016 0.002 TYR R 130 ARG 0.007 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 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7912 (t70) cc_final: 0.7608 (t0) REVERT: L 12 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8131 (mtp-110) REVERT: A 221 MET cc_start: 0.8675 (ttm) cc_final: 0.8403 (ttm) REVERT: A 391 TYR cc_start: 0.7441 (m-80) cc_final: 0.7176 (m-80) REVERT: B 339 TRP cc_start: 0.7859 (OUTLIER) cc_final: 0.7406 (m-90) REVERT: G 38 MET cc_start: 0.8227 (pmm) cc_final: 0.7854 (pmm) REVERT: N 82 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8207 (tm-30) REVERT: N 94 TYR cc_start: 0.8306 (m-80) cc_final: 0.7747 (m-80) REVERT: N 117 TYR cc_start: 0.6340 (m-80) cc_final: 0.6033 (m-80) outliers start: 30 outliers final: 25 residues processed: 137 average time/residue: 0.2061 time to fit residues: 39.8331 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 384 CYS 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 74 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 245 SER 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 64 VAL Chi-restraints excluded: chain N residue 69 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.185699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136494 restraints weight = 12819.421| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.33 r_work: 0.3503 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9179 Z= 0.233 Angle : 0.559 11.693 12445 Z= 0.292 Chirality : 0.042 0.152 1403 Planarity : 0.004 0.046 1584 Dihedral : 4.275 19.706 1241 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.08 % Allowed : 20.97 % Favored : 75.95 % 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: 1.31 (0.27), residues: 410 sheet: -1.92 (0.34), residues: 201 loop : -1.11 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 PHE 0.016 0.001 PHE B 241 TYR 0.016 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 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8208 (tp) cc_final: 0.7970 (mt) REVERT: L 8 ASP cc_start: 0.7955 (t70) cc_final: 0.7643 (t0) REVERT: L 12 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8132 (mtp-110) REVERT: A 221 MET cc_start: 0.8694 (ttm) cc_final: 0.8430 (ttm) REVERT: A 311 TYR cc_start: 0.7970 (m-80) cc_final: 0.7731 (m-80) REVERT: A 391 TYR cc_start: 0.7342 (m-80) cc_final: 0.7051 (m-80) REVERT: B 339 TRP cc_start: 0.7857 (OUTLIER) cc_final: 0.7449 (m-90) REVERT: G 38 MET cc_start: 0.8212 (pmm) cc_final: 0.7845 (pmm) REVERT: N 82 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8189 (tm-30) REVERT: N 94 TYR cc_start: 0.8312 (m-80) cc_final: 0.7736 (m-80) REVERT: N 117 TYR cc_start: 0.6338 (m-80) cc_final: 0.6018 (m-80) outliers start: 30 outliers final: 27 residues processed: 133 average time/residue: 0.1991 time to fit residues: 37.7676 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 384 CYS 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 74 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 245 SER 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 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR 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 7 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 105 optimal weight: 0.0040 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.189433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148860 restraints weight = 12742.880| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.37 r_work: 0.3563 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9179 Z= 0.148 Angle : 0.516 9.654 12445 Z= 0.269 Chirality : 0.040 0.148 1403 Planarity : 0.003 0.051 1584 Dihedral : 4.002 19.120 1241 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.47 % Allowed : 21.99 % Favored : 75.54 % 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: -0.45 (0.26), residues: 1128 helix: 1.36 (0.27), residues: 417 sheet: -1.71 (0.35), residues: 196 loop : -1.07 (0.28), residues: 515 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 0.014 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: 4598.92 seconds wall clock time: 82 minutes 34.28 seconds (4954.28 seconds total)