Starting phenix.real_space_refine on Fri Aug 22 23:46:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wss_37823/08_2025/8wss_37823.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5624 2.51 5 N 1489 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1749 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1720 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 149 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 8797 At special positions: 0 Unit cell: (86.52, 122.776, 131.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1617 8.00 N 1489 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.08 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: 0.50 Conformation dependent library (CDL) restraints added in 449.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.911A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.623A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.108A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.959A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.672A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.944A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 225 removed outlier: 3.761A pdb=" N ASP H 224 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 225 " --> pdb=" O ALA H 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 221 through 225' Processing helix chain 'R' and resid 111 through 138 Processing helix chain 'R' and resid 145 through 173 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 181 through 216 removed outlier: 3.806A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 222 Processing helix chain 'R' and resid 224 through 250 removed outlier: 4.050A pdb=" N VAL R 228 " --> pdb=" O ARG R 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU R 231 " --> pdb=" O SER R 227 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 272 through 286 removed outlier: 4.262A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 303 Processing helix chain 'R' and resid 313 through 348 removed outlier: 3.675A pdb=" N CYS R 337 " --> pdb=" O VAL R 333 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 338 " --> pdb=" O PHE R 334 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 349 through 351 No H-bonds generated for 'chain 'R' and resid 349 through 351' Processing helix chain 'R' and resid 357 through 384 Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 392 removed outlier: 3.677A pdb=" N VAL R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.887A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.556A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.472A 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: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.798A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.482A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.580A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.659A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 147 through 149 removed outlier: 3.541A pdb=" N GLU H 247 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP H 177 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 161 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'R' and resid 253 through 254 433 hydrogen bonds defined for protein. 1203 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: 1.13 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2812 1.34 - 1.46: 2220 1.46 - 1.58: 3854 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 8983 Sorted by residual: bond pdb=" N ARG L 11 " pdb=" CA ARG L 11 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.37e-02 5.33e+03 7.13e+00 bond pdb=" N MET R 165 " pdb=" CA MET R 165 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.04e-02 9.25e+03 5.24e+00 bond pdb=" N ASN R 194 " pdb=" CA ASN R 194 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.97e+00 bond pdb=" N SER R 195 " pdb=" CA SER R 195 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.90e+00 bond pdb=" N GLN R 196 " pdb=" CA GLN R 196 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.56e+00 ... (remaining 8978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 11911 1.22 - 2.43: 212 2.43 - 3.65: 49 3.65 - 4.87: 12 4.87 - 6.08: 5 Bond angle restraints: 12189 Sorted by residual: angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" N LEU H 11 " ideal model delta sigma weight residual 114.23 116.73 -2.50 8.80e-01 1.29e+00 8.04e+00 angle pdb=" N THR R 272 " pdb=" CA THR R 272 " pdb=" C THR R 272 " ideal model delta sigma weight residual 113.18 109.75 3.43 1.33e+00 5.65e-01 6.63e+00 angle pdb=" O ASN R 194 " pdb=" C ASN R 194 " pdb=" N SER R 195 " ideal model delta sigma weight residual 122.12 124.64 -2.52 1.06e+00 8.90e-01 5.65e+00 angle pdb=" CA ASN R 194 " pdb=" C ASN R 194 " pdb=" O ASN R 194 " ideal model delta sigma weight residual 120.55 118.05 2.50 1.06e+00 8.90e-01 5.58e+00 angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" O GLY H 10 " ideal model delta sigma weight residual 122.33 120.55 1.78 8.10e-01 1.52e+00 4.80e+00 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 4952 13.91 - 27.82: 242 27.82 - 41.74: 87 41.74 - 55.65: 21 55.65 - 69.56: 2 Dihedral angle restraints: 5304 sinusoidal: 1992 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLN R 196 " pdb=" CB GLN R 196 " pdb=" CG GLN R 196 " pdb=" CD GLN R 196 " ideal model delta sinusoidal sigma weight residual -180.00 -122.57 -57.43 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU R 284 " pdb=" CA LEU R 284 " pdb=" CB LEU R 284 " pdb=" CG LEU R 284 " ideal model delta sinusoidal sigma weight residual -180.00 -125.25 -54.75 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA LYS G 46 " pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " pdb=" CD LYS G 46 " ideal model delta sinusoidal sigma weight residual -180.00 -125.41 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 835 0.024 - 0.049: 318 0.049 - 0.073: 135 0.073 - 0.097: 66 0.097 - 0.121: 51 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA MET R 112 " pdb=" N MET R 112 " pdb=" C MET R 112 " pdb=" CB MET R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 166 " pdb=" N PRO R 166 " pdb=" C PRO R 166 " pdb=" CB PRO R 166 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1402 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 112 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 113 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 14 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO G 55 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.015 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 94 2.65 - 3.21: 7892 3.21 - 3.77: 13415 3.77 - 4.34: 18204 4.34 - 4.90: 30790 Nonbonded interactions: 70395 Sorted by model distance: nonbonded pdb=" OD1 ASP A 229 " pdb=" CD1 LEU A 232 " model vdw 2.082 3.460 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG H 203 " pdb=" OD2 ASP H 224 " model vdw 2.254 3.120 ... (remaining 70390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8986 Z= 0.118 Angle : 0.703 58.956 12195 Z= 0.363 Chirality : 0.038 0.121 1405 Planarity : 0.003 0.049 1532 Dihedral : 9.953 69.560 3157 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 8.53 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1119 helix: 2.57 (0.27), residues: 376 sheet: 1.50 (0.32), residues: 273 loop : -0.85 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.010 0.001 TYR R 275 PHE 0.007 0.001 PHE R 161 TRP 0.006 0.001 TRP H 111 HIS 0.002 0.000 HIS R 179 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 8983) covalent geometry : angle 0.45624 (12189) SS BOND : bond 0.02631 ( 3) SS BOND : angle 24.10526 ( 6) hydrogen bonds : bond 0.17554 ( 433) hydrogen bonds : angle 5.48833 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7344 (mtm110) REVERT: A 29 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7314 (ttpt) REVERT: A 195 HIS cc_start: 0.7562 (m-70) cc_final: 0.7216 (t70) REVERT: A 252 SER cc_start: 0.8985 (t) cc_final: 0.8691 (m) REVERT: B 79 LEU cc_start: 0.8583 (mp) cc_final: 0.8357 (mt) REVERT: B 239 ASN cc_start: 0.8612 (m-40) cc_final: 0.8337 (m-40) REVERT: H 109 ASP cc_start: 0.8721 (p0) cc_final: 0.8507 (p0) REVERT: H 221 GLU cc_start: 0.7539 (pm20) cc_final: 0.7149 (pt0) REVERT: R 109 ASN cc_start: 0.4767 (p0) cc_final: 0.4100 (m-40) REVERT: R 127 ASN cc_start: 0.5928 (m-40) cc_final: 0.5722 (m-40) REVERT: R 198 THR cc_start: 0.8398 (t) cc_final: 0.8173 (m) REVERT: R 202 ILE cc_start: 0.8040 (mm) cc_final: 0.7795 (mt) REVERT: R 261 VAL cc_start: 0.7207 (m) cc_final: 0.6815 (p) REVERT: R 280 TYR cc_start: 0.6684 (t80) cc_final: 0.6442 (t80) outliers start: 4 outliers final: 1 residues processed: 247 average time/residue: 0.0980 time to fit residues: 32.4911 Evaluate side-chains 142 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN A 304 GLN B 183 HIS B 220 GLN B 230 ASN H 39 GLN H 143 GLN H 184 GLN R 171 GLN R 281 GLN R 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114859 restraints weight = 11113.171| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.89 r_work: 0.3166 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8986 Z= 0.178 Angle : 0.590 7.882 12195 Z= 0.311 Chirality : 0.044 0.157 1405 Planarity : 0.004 0.045 1532 Dihedral : 4.051 35.653 1231 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.62 % Allowed : 12.47 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1119 helix: 2.46 (0.27), residues: 382 sheet: 1.46 (0.32), residues: 259 loop : -1.18 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.014 0.002 TYR R 275 PHE 0.024 0.002 PHE R 286 TRP 0.016 0.001 TRP B 339 HIS 0.007 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8983) covalent geometry : angle 0.58603 (12189) SS BOND : bond 0.01132 ( 3) SS BOND : angle 3.16474 ( 6) hydrogen bonds : bond 0.04242 ( 433) hydrogen bonds : angle 4.37417 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.255 Fit side-chains REVERT: A 24 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7374 (mtm110) REVERT: A 29 LYS cc_start: 0.7619 (ttmm) cc_final: 0.7206 (ttpt) REVERT: A 195 HIS cc_start: 0.8067 (m-70) cc_final: 0.7126 (t70) REVERT: A 247 MET cc_start: 0.8551 (mtp) cc_final: 0.8293 (mtt) REVERT: A 273 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 221 THR cc_start: 0.8917 (t) cc_final: 0.8600 (m) REVERT: B 268 ASN cc_start: 0.7988 (t0) cc_final: 0.7743 (t0) REVERT: B 274 THR cc_start: 0.9282 (m) cc_final: 0.9076 (p) REVERT: H 90 ASP cc_start: 0.8226 (m-30) cc_final: 0.7995 (m-30) REVERT: H 221 GLU cc_start: 0.7740 (pm20) cc_final: 0.7539 (pt0) REVERT: L 14 ARG cc_start: 0.5795 (ptt90) cc_final: 0.5475 (ptt180) REVERT: R 109 ASN cc_start: 0.4261 (p0) cc_final: 0.3876 (m-40) REVERT: R 112 MET cc_start: 0.5605 (pmm) cc_final: 0.5342 (pmm) REVERT: R 184 MET cc_start: 0.6124 (tpt) cc_final: 0.5866 (tpt) REVERT: R 202 ILE cc_start: 0.7993 (mm) cc_final: 0.7782 (mt) REVERT: R 261 VAL cc_start: 0.6856 (m) cc_final: 0.6598 (p) REVERT: R 280 TYR cc_start: 0.6796 (t80) cc_final: 0.6578 (t80) REVERT: R 303 ARG cc_start: 0.7377 (tpt170) cc_final: 0.7096 (mmm-85) outliers start: 34 outliers final: 17 residues processed: 175 average time/residue: 0.0827 time to fit residues: 19.9796 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 72 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115910 restraints weight = 11058.389| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8986 Z= 0.120 Angle : 0.520 6.219 12195 Z= 0.271 Chirality : 0.041 0.148 1405 Planarity : 0.003 0.044 1532 Dihedral : 3.770 15.964 1229 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 3.09 % Allowed : 13.43 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1119 helix: 2.48 (0.27), residues: 385 sheet: 1.33 (0.32), residues: 259 loop : -1.22 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.012 0.001 TYR H 191 PHE 0.011 0.001 PHE A 196 TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8983) covalent geometry : angle 0.51745 (12189) SS BOND : bond 0.00981 ( 3) SS BOND : angle 2.35207 ( 6) hydrogen bonds : bond 0.03564 ( 433) hydrogen bonds : angle 4.13177 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.207 Fit side-chains REVERT: A 24 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7415 (mtm110) REVERT: A 29 LYS cc_start: 0.7596 (ttmm) cc_final: 0.7249 (ttpt) REVERT: A 195 HIS cc_start: 0.8117 (m-70) cc_final: 0.7083 (t-170) REVERT: A 247 MET cc_start: 0.8576 (mtp) cc_final: 0.8303 (mtt) REVERT: A 273 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7589 (mm) REVERT: A 305 CYS cc_start: 0.8027 (t) cc_final: 0.7312 (m) REVERT: A 313 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7426 (tpt90) REVERT: B 129 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7805 (mmm-85) REVERT: B 136 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 146 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7805 (mp) REVERT: B 221 THR cc_start: 0.8868 (t) cc_final: 0.8570 (m) REVERT: B 243 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 268 ASN cc_start: 0.7959 (t0) cc_final: 0.7705 (t0) REVERT: H 90 ASP cc_start: 0.8292 (m-30) cc_final: 0.8041 (m-30) REVERT: H 193 MET cc_start: 0.8314 (ptm) cc_final: 0.7833 (ttp) REVERT: R 109 ASN cc_start: 0.4299 (p0) cc_final: 0.3870 (m-40) REVERT: R 112 MET cc_start: 0.5440 (pmm) cc_final: 0.5113 (pmm) REVERT: R 132 PHE cc_start: 0.7366 (t80) cc_final: 0.6748 (t80) REVERT: R 184 MET cc_start: 0.6126 (tpt) cc_final: 0.5916 (tpt) REVERT: R 202 ILE cc_start: 0.8003 (mm) cc_final: 0.7702 (mt) REVERT: R 280 TYR cc_start: 0.6724 (t80) cc_final: 0.6509 (t80) outliers start: 29 outliers final: 17 residues processed: 159 average time/residue: 0.0996 time to fit residues: 21.3970 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112186 restraints weight = 11229.783| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.98 r_work: 0.3121 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8986 Z= 0.147 Angle : 0.536 7.189 12195 Z= 0.280 Chirality : 0.042 0.163 1405 Planarity : 0.004 0.045 1532 Dihedral : 3.917 16.976 1229 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 13.86 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1119 helix: 2.48 (0.27), residues: 385 sheet: 1.05 (0.31), residues: 266 loop : -1.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.013 0.001 TYR R 275 PHE 0.011 0.001 PHE A 196 TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8983) covalent geometry : angle 0.53388 (12189) SS BOND : bond 0.01035 ( 3) SS BOND : angle 2.24731 ( 6) hydrogen bonds : bond 0.03738 ( 433) hydrogen bonds : angle 4.17546 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7514 (mtm110) REVERT: A 29 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7355 (ttpt) REVERT: A 195 HIS cc_start: 0.8116 (m-70) cc_final: 0.7135 (t-170) REVERT: A 273 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7609 (mm) REVERT: A 305 CYS cc_start: 0.8129 (t) cc_final: 0.7418 (m) REVERT: A 313 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7438 (tpt90) REVERT: B 46 ARG cc_start: 0.8190 (mpt180) cc_final: 0.7850 (mtm-85) REVERT: B 136 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 146 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 221 THR cc_start: 0.8867 (t) cc_final: 0.8575 (m) REVERT: B 243 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (t) REVERT: G 42 GLU cc_start: 0.8126 (tt0) cc_final: 0.7922 (tt0) REVERT: H 23 SER cc_start: 0.8299 (m) cc_final: 0.8058 (t) REVERT: H 193 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7982 (ttp) REVERT: H 221 GLU cc_start: 0.7879 (pm20) cc_final: 0.7672 (pm20) REVERT: R 112 MET cc_start: 0.5375 (pmm) cc_final: 0.5174 (pmm) REVERT: R 132 PHE cc_start: 0.7453 (t80) cc_final: 0.6669 (t80) REVERT: R 185 CYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5597 (t) REVERT: R 202 ILE cc_start: 0.8052 (mm) cc_final: 0.7772 (mt) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.1062 time to fit residues: 23.0385 Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.0040 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106689 restraints weight = 11181.563| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.00 r_work: 0.3033 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8986 Z= 0.168 Angle : 0.553 7.905 12195 Z= 0.291 Chirality : 0.043 0.213 1405 Planarity : 0.004 0.044 1532 Dihedral : 4.089 18.258 1229 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.52 % Allowed : 14.39 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1119 helix: 2.38 (0.27), residues: 384 sheet: 0.97 (0.32), residues: 265 loop : -1.36 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.012 0.001 TYR H 191 PHE 0.011 0.002 PHE H 27 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8983) covalent geometry : angle 0.55067 (12189) SS BOND : bond 0.01152 ( 3) SS BOND : angle 2.23531 ( 6) hydrogen bonds : bond 0.04002 ( 433) hydrogen bonds : angle 4.24522 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7774 (ttm110) REVERT: A 29 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7371 (ttpt) REVERT: A 195 HIS cc_start: 0.8207 (m-70) cc_final: 0.7201 (t-170) REVERT: A 273 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7547 (mm) REVERT: A 305 CYS cc_start: 0.8101 (t) cc_final: 0.7413 (m) REVERT: B 46 ARG cc_start: 0.8263 (mpt180) cc_final: 0.7933 (mtm-85) REVERT: B 136 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 146 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8192 (mp) REVERT: B 221 THR cc_start: 0.8872 (t) cc_final: 0.8584 (m) REVERT: B 243 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8477 (t) REVERT: H 23 SER cc_start: 0.8408 (m) cc_final: 0.8140 (t) REVERT: H 38 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.8187 (ttm170) REVERT: H 193 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: H 221 GLU cc_start: 0.7896 (pm20) cc_final: 0.7540 (pm20) REVERT: R 165 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7271 (ttt) REVERT: R 185 CYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5642 (t) REVERT: R 187 LEU cc_start: 0.7027 (tt) cc_final: 0.6469 (mt) REVERT: R 202 ILE cc_start: 0.8057 (mm) cc_final: 0.7838 (mt) outliers start: 33 outliers final: 23 residues processed: 145 average time/residue: 0.1001 time to fit residues: 19.3399 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110013 restraints weight = 11261.616| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3076 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8986 Z= 0.117 Angle : 0.506 6.385 12195 Z= 0.267 Chirality : 0.041 0.166 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.879 17.907 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.94 % Allowed : 14.71 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1119 helix: 2.45 (0.27), residues: 386 sheet: 1.03 (0.32), residues: 259 loop : -1.33 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.013 0.001 TYR H 191 PHE 0.010 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8983) covalent geometry : angle 0.50492 (12189) SS BOND : bond 0.00809 ( 3) SS BOND : angle 1.85888 ( 6) hydrogen bonds : bond 0.03490 ( 433) hydrogen bonds : angle 4.06449 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7603 (mtm110) REVERT: A 29 LYS cc_start: 0.7652 (ttmm) cc_final: 0.7299 (ttpt) REVERT: A 195 HIS cc_start: 0.8175 (m-70) cc_final: 0.7183 (t-170) REVERT: A 247 MET cc_start: 0.8622 (mtp) cc_final: 0.8307 (mtt) REVERT: A 252 SER cc_start: 0.8903 (t) cc_final: 0.8575 (m) REVERT: A 273 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7592 (mm) REVERT: A 305 CYS cc_start: 0.8073 (t) cc_final: 0.7401 (m) REVERT: B 46 ARG cc_start: 0.8275 (mpt180) cc_final: 0.7937 (mtm-85) REVERT: B 136 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 146 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 221 THR cc_start: 0.8819 (t) cc_final: 0.8547 (m) REVERT: B 243 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8435 (t) REVERT: H 7 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8507 (t) REVERT: H 23 SER cc_start: 0.8364 (m) cc_final: 0.8108 (t) REVERT: H 38 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8071 (ttm170) REVERT: H 193 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: H 221 GLU cc_start: 0.7859 (pm20) cc_final: 0.7479 (pm20) REVERT: R 185 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5623 (t) REVERT: R 187 LEU cc_start: 0.7037 (tt) cc_final: 0.6489 (mt) REVERT: R 202 ILE cc_start: 0.8031 (mm) cc_final: 0.7762 (mt) outliers start: 37 outliers final: 22 residues processed: 152 average time/residue: 0.1160 time to fit residues: 23.3661 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109079 restraints weight = 11242.534| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.98 r_work: 0.3074 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8986 Z= 0.120 Angle : 0.508 6.457 12195 Z= 0.268 Chirality : 0.041 0.179 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.829 17.754 1229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 4.05 % Allowed : 14.39 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1119 helix: 2.49 (0.27), residues: 385 sheet: 0.97 (0.32), residues: 259 loop : -1.28 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 325 TYR 0.013 0.001 TYR H 191 PHE 0.010 0.001 PHE H 27 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8983) covalent geometry : angle 0.50685 (12189) SS BOND : bond 0.00849 ( 3) SS BOND : angle 1.88797 ( 6) hydrogen bonds : bond 0.03474 ( 433) hydrogen bonds : angle 4.02815 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.263 Fit side-chains REVERT: A 24 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7601 (mtm110) REVERT: A 29 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7294 (ttpt) REVERT: A 195 HIS cc_start: 0.8169 (m-70) cc_final: 0.7165 (t-170) REVERT: A 273 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 305 CYS cc_start: 0.8071 (t) cc_final: 0.7386 (m) REVERT: A 313 ARG cc_start: 0.7772 (tpt90) cc_final: 0.7518 (tpt90) REVERT: B 46 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7896 (mtm-85) REVERT: B 136 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8733 (p) REVERT: B 146 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 221 THR cc_start: 0.8823 (t) cc_final: 0.8543 (m) REVERT: B 243 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8419 (t) REVERT: H 23 SER cc_start: 0.8365 (m) cc_final: 0.8106 (t) REVERT: H 38 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.8064 (ttm170) REVERT: H 167 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8969 (tt) REVERT: H 193 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: H 221 GLU cc_start: 0.7825 (pm20) cc_final: 0.7379 (pm20) REVERT: R 127 ASN cc_start: 0.6627 (m-40) cc_final: 0.6358 (m110) REVERT: R 185 CYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5688 (t) REVERT: R 187 LEU cc_start: 0.6918 (tt) cc_final: 0.6391 (mt) REVERT: R 202 ILE cc_start: 0.8025 (mm) cc_final: 0.7755 (mt) outliers start: 38 outliers final: 25 residues processed: 149 average time/residue: 0.1022 time to fit residues: 20.4405 Evaluate side-chains 158 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109570 restraints weight = 11193.370| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.92 r_work: 0.3081 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8986 Z= 0.119 Angle : 0.510 6.445 12195 Z= 0.269 Chirality : 0.042 0.279 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.838 17.861 1229 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.73 % Allowed : 14.82 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1119 helix: 2.48 (0.27), residues: 385 sheet: 0.93 (0.32), residues: 259 loop : -1.28 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 325 TYR 0.012 0.001 TYR H 191 PHE 0.009 0.001 PHE H 27 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8983) covalent geometry : angle 0.50628 (12189) SS BOND : bond 0.00775 ( 3) SS BOND : angle 2.91822 ( 6) hydrogen bonds : bond 0.03449 ( 433) hydrogen bonds : angle 3.99194 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.287 Fit side-chains REVERT: A 24 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7613 (mtm110) REVERT: A 29 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7296 (ttpt) REVERT: A 195 HIS cc_start: 0.8156 (m-70) cc_final: 0.7194 (t-170) REVERT: A 198 MET cc_start: 0.8740 (ttm) cc_final: 0.8438 (mtm) REVERT: A 273 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7612 (mm) REVERT: A 305 CYS cc_start: 0.8151 (t) cc_final: 0.7399 (m) REVERT: B 46 ARG cc_start: 0.8263 (mpt180) cc_final: 0.7935 (mtm-85) REVERT: B 136 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8747 (p) REVERT: B 146 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 221 THR cc_start: 0.8821 (t) cc_final: 0.8540 (m) REVERT: B 243 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8413 (t) REVERT: H 23 SER cc_start: 0.8370 (m) cc_final: 0.8132 (t) REVERT: H 38 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.8058 (ttm170) REVERT: H 193 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8064 (ttp) REVERT: H 221 GLU cc_start: 0.7804 (pm20) cc_final: 0.7381 (pm20) REVERT: R 165 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7162 (tmm) REVERT: R 185 CYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5640 (t) REVERT: R 187 LEU cc_start: 0.6948 (tt) cc_final: 0.6394 (mt) REVERT: R 202 ILE cc_start: 0.8033 (mm) cc_final: 0.7766 (mt) outliers start: 35 outliers final: 23 residues processed: 150 average time/residue: 0.1073 time to fit residues: 21.3169 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 0.1980 chunk 59 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109511 restraints weight = 11258.465| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.01 r_work: 0.3078 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8986 Z= 0.112 Angle : 0.511 6.341 12195 Z= 0.269 Chirality : 0.041 0.224 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.797 17.841 1229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.52 % Allowed : 15.25 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1119 helix: 2.50 (0.27), residues: 385 sheet: 0.91 (0.32), residues: 259 loop : -1.25 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 325 TYR 0.013 0.001 TYR H 191 PHE 0.011 0.001 PHE R 223 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8983) covalent geometry : angle 0.50812 (12189) SS BOND : bond 0.00802 ( 3) SS BOND : angle 2.57744 ( 6) hydrogen bonds : bond 0.03348 ( 433) hydrogen bonds : angle 3.97816 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.242 Fit side-chains REVERT: A 24 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7607 (mtm110) REVERT: A 29 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7230 (ttpt) REVERT: A 195 HIS cc_start: 0.8193 (m-70) cc_final: 0.7179 (t-170) REVERT: A 198 MET cc_start: 0.8771 (ttm) cc_final: 0.8470 (mtm) REVERT: A 247 MET cc_start: 0.8588 (mtm) cc_final: 0.8272 (mtt) REVERT: A 273 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7592 (mm) REVERT: A 305 CYS cc_start: 0.8146 (t) cc_final: 0.7387 (m) REVERT: B 136 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 146 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7993 (mp) REVERT: B 221 THR cc_start: 0.8815 (t) cc_final: 0.8529 (m) REVERT: B 243 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (t) REVERT: H 23 SER cc_start: 0.8376 (m) cc_final: 0.8134 (t) REVERT: H 38 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.8056 (ttm170) REVERT: H 193 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8068 (ttp) REVERT: H 221 GLU cc_start: 0.7825 (pm20) cc_final: 0.7426 (pm20) REVERT: R 185 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5573 (t) REVERT: R 187 LEU cc_start: 0.6952 (tt) cc_final: 0.6406 (mt) REVERT: R 198 THR cc_start: 0.8345 (t) cc_final: 0.7888 (t) REVERT: R 202 ILE cc_start: 0.8018 (mm) cc_final: 0.7758 (mt) outliers start: 33 outliers final: 23 residues processed: 145 average time/residue: 0.1005 time to fit residues: 19.2248 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103536 restraints weight = 11273.403| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.87 r_work: 0.3065 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8986 Z= 0.144 Angle : 0.545 6.813 12195 Z= 0.287 Chirality : 0.042 0.223 1405 Planarity : 0.004 0.046 1532 Dihedral : 3.962 17.978 1229 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 3.41 % Allowed : 15.14 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1119 helix: 2.42 (0.27), residues: 385 sheet: 0.88 (0.32), residues: 259 loop : -1.28 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 325 TYR 0.011 0.001 TYR H 191 PHE 0.011 0.001 PHE R 223 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8983) covalent geometry : angle 0.54136 (12189) SS BOND : bond 0.01087 ( 3) SS BOND : angle 2.82014 ( 6) hydrogen bonds : bond 0.03685 ( 433) hydrogen bonds : angle 4.10526 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.659 Fit side-chains REVERT: A 21 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7922 (ttp-110) REVERT: A 24 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7560 (mtm110) REVERT: A 29 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7242 (ttpt) REVERT: A 195 HIS cc_start: 0.8146 (m-70) cc_final: 0.7131 (t-170) REVERT: A 198 MET cc_start: 0.8778 (ttm) cc_final: 0.8469 (mtm) REVERT: A 247 MET cc_start: 0.8552 (mtm) cc_final: 0.8223 (mtt) REVERT: A 273 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 305 CYS cc_start: 0.8107 (t) cc_final: 0.7347 (m) REVERT: B 46 ARG cc_start: 0.8242 (mpt180) cc_final: 0.7923 (mtm-85) REVERT: B 136 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 146 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 221 THR cc_start: 0.8842 (t) cc_final: 0.8556 (m) REVERT: B 243 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (t) REVERT: H 23 SER cc_start: 0.8332 (m) cc_final: 0.8077 (t) REVERT: H 38 ARG cc_start: 0.8481 (ttp-170) cc_final: 0.8118 (ttm170) REVERT: H 193 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8075 (ttp) REVERT: R 127 ASN cc_start: 0.7015 (m-40) cc_final: 0.6512 (m110) REVERT: R 185 CYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5657 (t) REVERT: R 187 LEU cc_start: 0.6949 (tt) cc_final: 0.6393 (mt) REVERT: R 198 THR cc_start: 0.8339 (t) cc_final: 0.7912 (t) REVERT: R 202 ILE cc_start: 0.8020 (mm) cc_final: 0.7761 (mt) outliers start: 32 outliers final: 25 residues processed: 144 average time/residue: 0.1067 time to fit residues: 20.4199 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108074 restraints weight = 11078.622| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.95 r_work: 0.3054 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8986 Z= 0.133 Angle : 0.535 6.534 12195 Z= 0.282 Chirality : 0.042 0.205 1405 Planarity : 0.004 0.046 1532 Dihedral : 3.937 17.758 1229 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.09 % Allowed : 15.46 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1119 helix: 2.42 (0.27), residues: 385 sheet: 0.83 (0.32), residues: 260 loop : -1.28 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 325 TYR 0.012 0.001 TYR H 191 PHE 0.012 0.001 PHE R 223 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8983) covalent geometry : angle 0.53175 (12189) SS BOND : bond 0.00953 ( 3) SS BOND : angle 2.63502 ( 6) hydrogen bonds : bond 0.03553 ( 433) hydrogen bonds : angle 4.06064 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.38 seconds wall clock time: 44 minutes 29.26 seconds (2669.26 seconds total)