Starting phenix.real_space_refine on Mon Jan 20 17:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7a_38096/01_2025/8x7a_38096_neut_trim.cif" } resolution = 2.56 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= -0.001 sd= 0.029 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 5028 2.51 5 N 1399 2.21 5 O 1466 1.98 5 H 7679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3761 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 4782 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 851 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1849 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4357 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y9J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.31, per 1000 atoms: 0.47 Number of scatterers: 15628 At special positions: 0 Unit cell: (81.03, 106.58, 128.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1466 8.00 N 1399 7.00 C 5028 6.00 H 7679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 42.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.678A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.256A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.804A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.890A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.502A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.704A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 19 through 41 removed outlier: 3.608A pdb=" N GLY R 27 " --> pdb=" O MET R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 66 removed outlier: 3.605A pdb=" N THR R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 78 removed outlier: 3.659A pdb=" N VAL R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 123 removed outlier: 4.768A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 129 Processing helix chain 'R' and resid 131 through 151 Proline residue: R 141 - end of helix Processing helix chain 'R' and resid 152 through 157 Processing helix chain 'R' and resid 183 through 221 Processing helix chain 'R' and resid 233 through 264 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 271 through 283 Processing helix chain 'R' and resid 283 through 292 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 307 Processing helix chain 'R' and resid 307 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.562A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.426A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.511A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.838A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.270A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 161 through 163 411 hydrogen bonds defined for protein. 1164 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: 5.93 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.25: 8967 1.25 - 1.68: 6741 1.68 - 2.11: 78 2.11 - 2.54: 0 2.54 - 2.97: 1 Bond restraints: 15787 Sorted by residual: bond pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 1.332 2.972 -1.639 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 1.393 1.670 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C19 Y9J R 401 " pdb=" C20 Y9J R 401 " ideal model delta sigma weight residual 1.389 1.209 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C18 Y9J R 401 " pdb=" C19 Y9J R 401 " ideal model delta sigma weight residual 1.394 1.215 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" CA MET R 244 " pdb=" C MET R 244 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.50e+01 ... (remaining 15782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.53: 28349 12.53 - 25.06: 6 25.06 - 37.60: 1 37.60 - 50.13: 0 50.13 - 62.66: 2 Bond angle restraints: 28358 Sorted by residual: angle pdb=" O ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 122.27 59.61 62.66 1.16e+00 7.43e-01 2.92e+03 angle pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 118.79 150.01 -31.22 1.22e+00 6.72e-01 6.55e+02 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" H ASP B 205 " ideal model delta sigma weight residual 124.38 66.43 57.95 3.00e+00 1.11e-01 3.73e+02 angle pdb=" C14 Y9J R 401 " pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 121.72 143.69 -21.97 3.00e+00 1.11e-01 5.36e+01 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 121.54 135.26 -13.72 1.91e+00 2.74e-01 5.16e+01 ... (remaining 28353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 7234 21.03 - 42.07: 193 42.07 - 63.10: 73 63.10 - 84.14: 10 84.14 - 105.17: 1 Dihedral angle restraints: 7511 sinusoidal: 3974 harmonic: 3537 Sorted by residual: dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual -180.00 -74.83 -105.17 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" C MET R 244 " pdb=" N MET R 244 " pdb=" CA MET R 244 " pdb=" CB MET R 244 " ideal model delta harmonic sigma weight residual -122.60 -110.06 -12.54 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ALA R 265 " pdb=" N ALA R 265 " pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta harmonic sigma weight residual -122.60 -134.35 11.75 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 7508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1158 0.074 - 0.149: 86 0.149 - 0.223: 5 0.223 - 0.298: 1 0.298 - 0.372: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CA ALA R 265 " pdb=" N ALA R 265 " pdb=" C ALA R 265 " pdb=" CB ALA R 265 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA VAL R 25 " pdb=" N VAL R 25 " pdb=" C VAL R 25 " pdb=" CB VAL R 25 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C13 Y9J R 401 " pdb=" C12 Y9J R 401 " pdb=" C14 Y9J R 401 " pdb=" C9 Y9J R 401 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1248 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 203 " 0.036 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" N ASP B 205 " -0.362 2.00e-02 2.50e+03 pdb=" CA ASP B 205 " 0.141 2.00e-02 2.50e+03 pdb=" H ASP B 205 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 203 " 0.182 2.00e-02 2.50e+03 1.90e-01 3.60e+02 pdb=" C ALA B 203 " -0.318 2.00e-02 2.50e+03 pdb=" O ALA B 203 " 0.062 2.00e-02 2.50e+03 pdb=" N ASP B 205 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 84 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU R 84 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU R 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 85 " 0.024 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 846 2.21 - 2.80: 32540 2.80 - 3.40: 42878 3.40 - 4.00: 55049 4.00 - 4.60: 86034 Nonbonded interactions: 217347 Sorted by model distance: nonbonded pdb=" O SER B 189 " pdb=" HG SER B 201 " model vdw 1.607 2.450 nonbonded pdb=" H THR B 221 " pdb=" OE2 GLU G 22 " model vdw 1.609 2.450 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.625 2.450 nonbonded pdb="HD21 ASN R 203 " pdb=" OG1 THR R 245 " model vdw 1.633 2.450 nonbonded pdb=" O LYS N 33 " pdb=" H CYS N 99 " model vdw 1.645 2.450 ... (remaining 217342 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.260 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.230 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.019 1.639 8108 Z= 1.554 Angle : 0.993 62.660 11001 Z= 0.688 Chirality : 0.040 0.372 1251 Planarity : 0.006 0.190 1419 Dihedral : 8.424 105.175 2894 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Cbeta Deviations : 0.21 % 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: -0.63 (0.25), residues: 1028 helix: 0.95 (0.25), residues: 394 sheet: -0.65 (0.32), residues: 210 loop : -1.59 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 271 HIS 0.002 0.000 HIS B 142 PHE 0.005 0.001 PHE R 24 TYR 0.023 0.001 TYR R 75 ARG 0.002 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 2.4470 time to fit residues: 814.6810 Evaluate side-chains 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 5 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** 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 = 0.3981 r_free = 0.3981 target = 0.122971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093111 restraints weight = 47718.560| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.49 r_work: 0.3351 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8108 Z= 0.302 Angle : 0.615 6.404 11001 Z= 0.324 Chirality : 0.040 0.146 1251 Planarity : 0.005 0.063 1419 Dihedral : 5.243 74.091 1171 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 3.09 % Allowed : 20.17 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1030 helix: 2.03 (0.26), residues: 399 sheet: -0.66 (0.30), residues: 248 loop : -0.75 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS A 41 PHE 0.011 0.001 PHE N 68 TYR 0.023 0.002 TYR A 37 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8604 (m-30) cc_final: 0.8390 (m-30) REVERT: B 226 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: G 38 MET cc_start: 0.7733 (mtp) cc_final: 0.7275 (mtp) REVERT: G 42 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8516 (mm-30) REVERT: N 46 GLU cc_start: 0.7388 (pt0) cc_final: 0.6926 (mm-30) REVERT: R 41 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7801 (mpt180) REVERT: R 107 MET cc_start: 0.8411 (tpp) cc_final: 0.8012 (tpt) REVERT: R 138 LEU cc_start: 0.8572 (mm) cc_final: 0.8095 (tt) outliers start: 25 outliers final: 12 residues processed: 190 average time/residue: 2.0316 time to fit residues: 415.6668 Evaluate side-chains 161 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 88 ASN B 340 ASN N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 HIS R 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093780 restraints weight = 47428.458| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.53 r_work: 0.3355 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8108 Z= 0.187 Angle : 0.535 6.693 11001 Z= 0.274 Chirality : 0.038 0.135 1251 Planarity : 0.004 0.056 1419 Dihedral : 4.990 74.143 1171 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.09 % Allowed : 22.40 % Favored : 74.50 % 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: 0.91 (0.26), residues: 1030 helix: 2.46 (0.26), residues: 397 sheet: -0.47 (0.31), residues: 247 loop : -0.58 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 220 PHE 0.016 0.001 PHE R 102 TYR 0.015 0.001 TYR A 37 ARG 0.009 0.000 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8526 (m-30) cc_final: 0.8317 (m-30) REVERT: B 42 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6935 (tmm-80) REVERT: B 264 TYR cc_start: 0.6366 (m-80) cc_final: 0.5772 (m-80) REVERT: G 32 LYS cc_start: 0.8662 (tppp) cc_final: 0.8073 (tmmt) REVERT: N 46 GLU cc_start: 0.7394 (pt0) cc_final: 0.6940 (mm-30) REVERT: N 120 GLN cc_start: 0.8892 (tp40) cc_final: 0.8635 (mm-40) REVERT: R 86 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.3839 (mtm180) REVERT: R 107 MET cc_start: 0.8381 (tpp) cc_final: 0.7995 (tpt) REVERT: R 138 LEU cc_start: 0.8559 (mm) cc_final: 0.8091 (tt) outliers start: 25 outliers final: 11 residues processed: 173 average time/residue: 1.9892 time to fit residues: 371.7267 Evaluate side-chains 161 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 234 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087809 restraints weight = 48028.846| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.55 r_work: 0.3275 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8108 Z= 0.272 Angle : 0.561 7.055 11001 Z= 0.291 Chirality : 0.039 0.141 1251 Planarity : 0.004 0.047 1419 Dihedral : 5.101 74.244 1171 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.21 % Allowed : 20.79 % Favored : 75.00 % 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: 0.93 (0.26), residues: 1030 helix: 2.52 (0.26), residues: 403 sheet: -0.62 (0.31), residues: 252 loop : -0.55 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.001 PHE R 102 TYR 0.017 0.001 TYR A 37 ARG 0.006 0.001 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8741 (mt0) cc_final: 0.8265 (tp40) REVERT: A 230 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 368 ASP cc_start: 0.8728 (m-30) cc_final: 0.8451 (m-30) REVERT: B 279 SER cc_start: 0.9281 (m) cc_final: 0.8949 (t) REVERT: N 46 GLU cc_start: 0.7542 (pt0) cc_final: 0.7130 (mm-30) REVERT: N 81 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7139 (tm) REVERT: N 120 GLN cc_start: 0.8939 (tp40) cc_final: 0.8726 (mm-40) REVERT: R 86 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.3921 (mtm180) REVERT: R 107 MET cc_start: 0.8445 (tpp) cc_final: 0.8109 (tpt) REVERT: R 138 LEU cc_start: 0.8627 (mm) cc_final: 0.8148 (tt) outliers start: 34 outliers final: 10 residues processed: 167 average time/residue: 2.1239 time to fit residues: 381.1001 Evaluate side-chains 144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 163 GLN ** R 237 HIS ** 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 = 0.3912 r_free = 0.3912 target = 0.118859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088635 restraints weight = 47771.314| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.54 r_work: 0.3282 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8108 Z= 0.176 Angle : 0.529 7.139 11001 Z= 0.269 Chirality : 0.038 0.134 1251 Planarity : 0.003 0.044 1419 Dihedral : 4.830 73.135 1171 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.85 % Allowed : 21.91 % Favored : 75.25 % 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: 1.17 (0.27), residues: 1030 helix: 2.79 (0.26), residues: 397 sheet: -0.57 (0.31), residues: 250 loop : -0.40 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.013 0.001 TYR A 37 ARG 0.005 0.000 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8729 (mt0) cc_final: 0.8264 (tp40) REVERT: A 230 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 368 ASP cc_start: 0.8658 (m-30) cc_final: 0.8447 (m-30) REVERT: B 264 TYR cc_start: 0.6697 (m-80) cc_final: 0.6046 (m-80) REVERT: N 46 GLU cc_start: 0.7461 (pt0) cc_final: 0.7077 (mm-30) REVERT: N 120 GLN cc_start: 0.8945 (tp40) cc_final: 0.8725 (mm-40) REVERT: R 86 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.3886 (mtm180) REVERT: R 93 ASP cc_start: 0.8506 (m-30) cc_final: 0.8276 (m-30) REVERT: R 107 MET cc_start: 0.8416 (tpp) cc_final: 0.8022 (tpt) REVERT: R 138 LEU cc_start: 0.8612 (mm) cc_final: 0.8154 (tt) outliers start: 23 outliers final: 12 residues processed: 162 average time/residue: 2.1659 time to fit residues: 378.3438 Evaluate side-chains 151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3874 r_free = 0.3874 target = 0.116116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085546 restraints weight = 48444.493| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.53 r_work: 0.3243 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8108 Z= 0.293 Angle : 0.574 7.170 11001 Z= 0.299 Chirality : 0.039 0.153 1251 Planarity : 0.004 0.043 1419 Dihedral : 5.078 72.172 1171 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.48 % Allowed : 23.51 % Favored : 74.01 % 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: 1.14 (0.27), residues: 1030 helix: 2.70 (0.26), residues: 398 sheet: -0.63 (0.32), residues: 252 loop : -0.30 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.006 0.001 HIS R 237 PHE 0.014 0.002 PHE R 102 TYR 0.015 0.002 TYR R 188 ARG 0.009 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8776 (mt0) cc_final: 0.8323 (tp40) REVERT: A 368 ASP cc_start: 0.8806 (m-30) cc_final: 0.8417 (m-30) REVERT: B 279 SER cc_start: 0.9271 (m) cc_final: 0.8942 (t) REVERT: N 46 GLU cc_start: 0.7543 (pt0) cc_final: 0.7242 (mm-30) REVERT: R 86 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.3893 (mtm180) REVERT: R 93 ASP cc_start: 0.8532 (m-30) cc_final: 0.8300 (m-30) REVERT: R 138 LEU cc_start: 0.8580 (mm) cc_final: 0.8101 (tt) outliers start: 20 outliers final: 11 residues processed: 154 average time/residue: 2.2961 time to fit residues: 378.4285 Evaluate side-chains 143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 234 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087426 restraints weight = 48061.795| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.53 r_work: 0.3265 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8108 Z= 0.163 Angle : 0.538 7.325 11001 Z= 0.274 Chirality : 0.038 0.164 1251 Planarity : 0.004 0.049 1419 Dihedral : 4.787 70.696 1171 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.98 % Allowed : 24.13 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1030 helix: 2.99 (0.26), residues: 398 sheet: -0.59 (0.32), residues: 246 loop : -0.29 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS R 237 PHE 0.017 0.001 PHE R 102 TYR 0.011 0.001 TYR A 37 ARG 0.008 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8753 (mt0) cc_final: 0.8293 (tp40) REVERT: A 368 ASP cc_start: 0.8665 (m-30) cc_final: 0.8406 (m-30) REVERT: N 46 GLU cc_start: 0.7480 (pt0) cc_final: 0.7153 (mm-30) REVERT: R 86 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.3848 (mtm180) REVERT: R 107 MET cc_start: 0.8488 (tpp) cc_final: 0.8131 (tpt) REVERT: R 138 LEU cc_start: 0.8584 (mm) cc_final: 0.8141 (tt) REVERT: R 290 TRP cc_start: 0.8084 (m-10) cc_final: 0.7842 (m100) outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 2.0830 time to fit residues: 345.7724 Evaluate side-chains 142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 4 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.116120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085771 restraints weight = 48224.311| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.51 r_work: 0.3244 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8108 Z= 0.228 Angle : 0.561 7.753 11001 Z= 0.288 Chirality : 0.038 0.138 1251 Planarity : 0.004 0.043 1419 Dihedral : 4.839 70.379 1171 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.61 % Allowed : 24.88 % Favored : 73.51 % 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: 1.41 (0.27), residues: 1030 helix: 3.04 (0.26), residues: 397 sheet: -0.60 (0.32), residues: 251 loop : -0.20 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.013 0.001 TYR A 37 ARG 0.009 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8561 (tpp80) REVERT: A 31 GLN cc_start: 0.8782 (mt0) cc_final: 0.8331 (tp40) REVERT: A 368 ASP cc_start: 0.8752 (m-30) cc_final: 0.8350 (m-30) REVERT: A 379 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8800 (ttm110) REVERT: N 46 GLU cc_start: 0.7520 (pt0) cc_final: 0.7213 (mm-30) REVERT: R 86 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.3676 (ttm170) REVERT: R 107 MET cc_start: 0.8489 (tpp) cc_final: 0.8122 (tpt) REVERT: R 138 LEU cc_start: 0.8584 (mm) cc_final: 0.8124 (tt) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 2.3843 time to fit residues: 363.5637 Evaluate side-chains 137 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.117000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086887 restraints weight = 48074.505| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.48 r_work: 0.3270 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8108 Z= 0.174 Angle : 0.555 8.083 11001 Z= 0.281 Chirality : 0.038 0.135 1251 Planarity : 0.004 0.044 1419 Dihedral : 4.715 69.492 1171 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.61 % Allowed : 25.00 % Favored : 73.39 % 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: 1.47 (0.27), residues: 1030 helix: 3.11 (0.26), residues: 398 sheet: -0.60 (0.32), residues: 244 loop : -0.18 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.017 0.001 PHE R 102 TYR 0.011 0.001 TYR A 37 ARG 0.010 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8564 (tpp80) REVERT: A 31 GLN cc_start: 0.8768 (mt0) cc_final: 0.8317 (tp40) REVERT: A 368 ASP cc_start: 0.8679 (m-30) cc_final: 0.8397 (m-30) REVERT: B 190 LEU cc_start: 0.8888 (tt) cc_final: 0.8553 (pp) REVERT: N 46 GLU cc_start: 0.7485 (pt0) cc_final: 0.7138 (mm-30) REVERT: R 86 ARG cc_start: 0.5606 (OUTLIER) cc_final: 0.3623 (ttm170) REVERT: R 107 MET cc_start: 0.8445 (tpp) cc_final: 0.8119 (tpt) REVERT: R 138 LEU cc_start: 0.8570 (mm) cc_final: 0.8127 (tt) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 2.2589 time to fit residues: 346.4428 Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3885 r_free = 0.3885 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086662 restraints weight = 48549.747| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.50 r_work: 0.3266 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8108 Z= 0.189 Angle : 0.563 8.182 11001 Z= 0.286 Chirality : 0.038 0.147 1251 Planarity : 0.004 0.043 1419 Dihedral : 4.703 68.555 1171 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.36 % Allowed : 25.00 % Favored : 73.64 % 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: 1.47 (0.27), residues: 1030 helix: 3.09 (0.26), residues: 398 sheet: -0.56 (0.32), residues: 244 loop : -0.20 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 290 HIS 0.008 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.011 0.001 TYR A 37 ARG 0.005 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8567 (tpp80) REVERT: A 31 GLN cc_start: 0.8778 (mt0) cc_final: 0.8334 (tp40) REVERT: A 368 ASP cc_start: 0.8711 (m-30) cc_final: 0.8434 (m-30) REVERT: A 379 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8776 (ttm110) REVERT: B 190 LEU cc_start: 0.8908 (tt) cc_final: 0.8578 (pp) REVERT: G 21 MET cc_start: 0.9038 (ttp) cc_final: 0.8795 (ttp) REVERT: N 46 GLU cc_start: 0.7494 (pt0) cc_final: 0.7176 (mm-30) REVERT: R 86 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.3600 (ttm170) REVERT: R 107 MET cc_start: 0.8455 (tpp) cc_final: 0.8038 (tpt) REVERT: R 138 LEU cc_start: 0.8556 (mm) cc_final: 0.8108 (tt) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 2.4740 time to fit residues: 362.8287 Evaluate side-chains 134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.114597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084086 restraints weight = 48822.526| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.50 r_work: 0.3214 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8108 Z= 0.307 Angle : 0.600 8.213 11001 Z= 0.313 Chirality : 0.039 0.137 1251 Planarity : 0.004 0.042 1419 Dihedral : 5.089 69.680 1171 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.49 % Allowed : 25.12 % Favored : 73.39 % 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: 1.18 (0.27), residues: 1030 helix: 2.75 (0.26), residues: 403 sheet: -0.62 (0.33), residues: 244 loop : -0.37 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 290 HIS 0.012 0.001 HIS R 237 PHE 0.015 0.002 PHE R 102 TYR 0.015 0.002 TYR R 188 ARG 0.009 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12743.40 seconds wall clock time: 229 minutes 2.04 seconds (13742.04 seconds total)