Starting phenix.real_space_refine on Thu Mar 14 08:11:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/03_2024/7wbj_32401.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/03_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_32401/03_2024/7wbj_32401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/03_2024/7wbj_32401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/03_2024/7wbj_32401.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbj_32401/03_2024/7wbj_32401.pdb" } 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 Residue "R GLU 223": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.07, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.8 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: 0.92 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: 2.63 Time building geometry restraints manager: 3.65 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: 100.09 - 106.88: 211 106.88 - 113.68: 5106 113.68 - 120.47: 3555 120.47 - 127.27: 3473 127.27 - 134.06: 100 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 ========== 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.390 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- 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 : 0.795 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: 118.9185 time to fit residues: 18444.4882 Evaluate side-chains 121 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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: 0.0970 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.0757 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= 0.222 Angle : 0.543 6.507 12445 Z= 0.281 Chirality : 0.042 0.147 1403 Planarity : 0.003 0.032 1584 Dihedral : 4.374 17.669 1241 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: -0.90 (0.25), residues: 1128 helix: 1.04 (0.27), residues: 403 sheet: -1.81 (0.35), residues: 196 loop : -1.39 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 219 HIS 0.003 0.001 HIS B 311 PHE 0.017 0.001 PHE R 151 TYR 0.019 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 145 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8180 (mt) REVERT: B 169 TRP cc_start: 0.8071 (m100) cc_final: 0.7582 (m100) REVERT: G 21 MET cc_start: 0.7656 (mpp) cc_final: 0.7454 (mpp) REVERT: G 38 MET cc_start: 0.7862 (pmm) cc_final: 0.7610 (pmm) REVERT: N 82 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7147 (tm-30) REVERT: N 94 TYR cc_start: 0.7740 (m-80) cc_final: 0.7114 (m-80) REVERT: N 117 TYR cc_start: 0.5988 (m-80) cc_final: 0.5731 (m-80) outliers start: 18 outliers final: 13 residues processed: 135 average time/residue: 0.1895 time to fit residues: 36.7267 Evaluate side-chains 126 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 271 CYS 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: 4.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.0060 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1174 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= 0.143 Angle : 0.479 6.112 12445 Z= 0.250 Chirality : 0.040 0.162 1403 Planarity : 0.003 0.030 1584 Dihedral : 4.022 17.373 1241 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.26 % Allowed : 11.92 % Favored : 85.82 % 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: 1.22 (0.27), residues: 415 sheet: -1.56 (0.35), residues: 191 loop : -1.27 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 219 HIS 0.003 0.000 HIS R 191 PHE 0.013 0.001 PHE B 241 TYR 0.017 0.001 TYR R 130 ARG 0.002 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 157 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.7905 (pmm) cc_final: 0.7657 (pmm) REVERT: N 82 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7904 (tm-30) REVERT: N 94 TYR cc_start: 0.7592 (m-80) cc_final: 0.6880 (m-80) REVERT: N 117 TYR cc_start: 0.6052 (m-80) cc_final: 0.5789 (m-80) outliers start: 22 outliers final: 13 residues processed: 148 average time/residue: 0.1909 time to fit residues: 40.4497 Evaluate side-chains 129 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 186 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN 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: 0.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9179 Z= 0.200 Angle : 0.501 7.554 12445 Z= 0.259 Chirality : 0.041 0.166 1403 Planarity : 0.003 0.030 1584 Dihedral : 4.061 16.477 1241 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.98 % Allowed : 14.29 % 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: -0.65 (0.26), residues: 1128 helix: 1.36 (0.28), residues: 405 sheet: -1.76 (0.34), residues: 197 loop : -1.31 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 169 HIS 0.002 0.001 HIS R 191 PHE 0.011 0.001 PHE B 241 TYR 0.017 0.001 TYR R 130 ARG 0.006 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 147 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 12 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7413 (mtp-110) REVERT: A 266 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8070 (mt) REVERT: B 169 TRP cc_start: 0.7768 (m100) cc_final: 0.7465 (m100) REVERT: G 38 MET cc_start: 0.7807 (pmm) cc_final: 0.7571 (pmm) REVERT: N 82 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8149 (tm-30) REVERT: N 94 TYR cc_start: 0.7669 (m-80) cc_final: 0.6986 (m-80) REVERT: N 117 TYR cc_start: 0.6155 (m-80) cc_final: 0.5846 (m-80) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.1884 time to fit residues: 36.6240 Evaluate side-chains 133 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 269 THR Chi-restraints excluded: chain R residue 300 ILE 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 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 285 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 21 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1429 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= 0.206 Angle : 0.500 6.697 12445 Z= 0.261 Chirality : 0.041 0.146 1403 Planarity : 0.003 0.053 1584 Dihedral : 4.056 17.190 1241 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.19 % Allowed : 15.01 % Favored : 81.81 % 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: 1.40 (0.28), residues: 405 sheet: -1.74 (0.34), residues: 195 loop : -1.25 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 PHE 0.011 0.001 PHE B 241 TYR 0.016 0.001 TYR R 130 ARG 0.004 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 151 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 12 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7417 (mtp-110) REVERT: B 169 TRP cc_start: 0.7870 (m100) cc_final: 0.7497 (m100) REVERT: G 38 MET cc_start: 0.7898 (pmm) cc_final: 0.7672 (pmm) REVERT: N 82 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8092 (tm-30) REVERT: N 94 TYR cc_start: 0.7701 (m-80) cc_final: 0.7067 (m-80) REVERT: N 117 TYR cc_start: 0.6144 (m-80) cc_final: 0.5869 (m-80) outliers start: 31 outliers final: 26 residues processed: 139 average time/residue: 0.2004 time to fit residues: 40.1301 Evaluate side-chains 137 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 114 CYS Chi-restraints excluded: chain B residue 157 ILE 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 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.0270 chunk 61 optimal weight: 5.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9179 Z= 0.178 Angle : 0.484 7.457 12445 Z= 0.251 Chirality : 0.040 0.140 1403 Planarity : 0.003 0.047 1584 Dihedral : 3.993 16.799 1241 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.19 % Allowed : 16.34 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.26), residues: 1128 helix: 1.47 (0.28), residues: 405 sheet: -1.69 (0.35), residues: 195 loop : -1.22 (0.27), residues: 528 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 0.015 0.001 PHE N 68 TYR 0.015 0.001 TYR R 130 ARG 0.004 0.000 ARG L 12 *********************** 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 154 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8378 (tp) cc_final: 0.8087 (mt) REVERT: L 12 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7429 (mtp-110) REVERT: A 266 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 169 TRP cc_start: 0.7907 (m100) cc_final: 0.7495 (m100) REVERT: G 38 MET cc_start: 0.7920 (pmm) cc_final: 0.7685 (pmm) REVERT: N 82 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8130 (tm-30) REVERT: N 94 TYR cc_start: 0.7657 (m-80) cc_final: 0.7016 (m-80) REVERT: N 117 TYR cc_start: 0.6101 (m-80) cc_final: 0.5874 (m-80) outliers start: 31 outliers final: 26 residues processed: 140 average time/residue: 0.1910 time to fit residues: 37.5961 Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 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 160 SER Chi-restraints excluded: chain B residue 161 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7188 moved from start: 0.1560 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= 0.251 Angle : 0.527 8.391 12445 Z= 0.273 Chirality : 0.041 0.144 1403 Planarity : 0.003 0.045 1584 Dihedral : 4.140 18.400 1241 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.80 % Allowed : 17.06 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1128 helix: 1.46 (0.28), residues: 403 sheet: -1.73 (0.35), residues: 195 loop : -1.17 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 340 PHE 0.012 0.001 PHE B 241 TYR 0.016 0.002 TYR R 130 ARG 0.008 0.000 ARG B 304 *********************** 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 158 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8028 (m100) cc_final: 0.7528 (m100) REVERT: G 38 MET cc_start: 0.7873 (pmm) cc_final: 0.7574 (pmm) REVERT: N 82 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8075 (tm-30) REVERT: N 94 TYR cc_start: 0.7818 (m-80) cc_final: 0.7274 (m-80) outliers start: 37 outliers final: 29 residues processed: 146 average time/residue: 0.1781 time to fit residues: 37.5541 Evaluate side-chains 145 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 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 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0470 chunk 20 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.1683 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= 0.164 Angle : 0.487 8.304 12445 Z= 0.252 Chirality : 0.040 0.140 1403 Planarity : 0.003 0.047 1584 Dihedral : 4.032 20.707 1241 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.29 % Allowed : 18.40 % 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: -0.46 (0.26), residues: 1128 helix: 1.51 (0.28), residues: 406 sheet: -1.71 (0.35), residues: 199 loop : -1.16 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 PHE 0.023 0.001 PHE N 68 TYR 0.015 0.001 TYR R 130 ARG 0.007 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 157 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8379 (tp) cc_final: 0.8088 (mt) REVERT: L 12 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7379 (mtp-110) REVERT: A 266 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8152 (mt) REVERT: B 169 TRP cc_start: 0.7948 (m100) cc_final: 0.7528 (m100) REVERT: G 38 MET cc_start: 0.7887 (pmm) cc_final: 0.7582 (pmm) REVERT: N 94 TYR cc_start: 0.7714 (m-80) cc_final: 0.7113 (m-80) outliers start: 32 outliers final: 27 residues processed: 144 average time/residue: 0.1826 time to fit residues: 37.9726 Evaluate side-chains 145 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 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 186 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.7181 moved from start: 0.1676 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= 0.239 Angle : 0.529 7.568 12445 Z= 0.274 Chirality : 0.041 0.147 1403 Planarity : 0.003 0.046 1584 Dihedral : 4.167 23.021 1241 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.29 % Allowed : 19.32 % Favored : 77.39 % 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: -0.48 (0.26), residues: 1128 helix: 1.52 (0.28), residues: 403 sheet: -1.71 (0.35), residues: 194 loop : -1.20 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 340 PHE 0.012 0.001 PHE B 241 TYR 0.016 0.001 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 153 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8394 (tp) cc_final: 0.8101 (mt) REVERT: L 12 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7388 (mtp-110) REVERT: A 317 ARG cc_start: 0.6847 (ptp90) cc_final: 0.6622 (ptp90) REVERT: B 169 TRP cc_start: 0.8014 (m100) cc_final: 0.7523 (m100) REVERT: G 38 MET cc_start: 0.7972 (pmm) cc_final: 0.7632 (pmm) REVERT: N 94 TYR cc_start: 0.7865 (m-80) cc_final: 0.7257 (m-80) outliers start: 32 outliers final: 29 residues processed: 141 average time/residue: 0.1835 time to fit residues: 37.7443 Evaluate side-chains 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE 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 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN 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 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 69 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9179 Z= 0.139 Angle : 0.491 8.100 12445 Z= 0.253 Chirality : 0.040 0.150 1403 Planarity : 0.003 0.051 1584 Dihedral : 3.957 23.273 1241 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 20.14 % Favored : 77.49 % 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: 1.61 (0.28), residues: 406 sheet: -1.61 (0.34), residues: 209 loop : -1.16 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 PHE 0.016 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 148 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8363 (tp) cc_final: 0.8095 (mt) REVERT: L 12 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7347 (mtp-110) REVERT: A 266 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8076 (mt) REVERT: B 169 TRP cc_start: 0.7929 (m100) cc_final: 0.7493 (m100) REVERT: G 38 MET cc_start: 0.7891 (pmm) cc_final: 0.7592 (pmm) REVERT: N 94 TYR cc_start: 0.7699 (m-80) cc_final: 0.7119 (m-80) outliers start: 23 outliers final: 20 residues processed: 140 average time/residue: 0.1822 time to fit residues: 36.6755 Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 19 VAL 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 186 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 82 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 = 0.4285 r_free = 0.4285 target = 0.188361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137295 restraints weight = 12553.154| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.00 r_work: 0.3566 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9179 Z= 0.168 Angle : 0.496 7.793 12445 Z= 0.256 Chirality : 0.040 0.151 1403 Planarity : 0.003 0.051 1584 Dihedral : 3.973 24.164 1241 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.57 % Allowed : 20.35 % Favored : 77.08 % 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: -0.35 (0.26), residues: 1128 helix: 1.63 (0.28), residues: 406 sheet: -1.58 (0.35), residues: 205 loop : -1.16 (0.28), residues: 517 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 0.017 0.001 PHE R 151 TYR 0.014 0.001 TYR R 130 ARG 0.006 0.000 ARG L 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.39 seconds wall clock time: 344 minutes 51.75 seconds (20691.75 seconds total)