Starting phenix.real_space_refine on Sat Dec 28 20:23:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.map" model { file = "/net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jso_36625/12_2024/8jso_36625.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 68 5.16 5 C 5764 2.51 5 N 1546 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9045 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2292 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 9045 At special positions: 0 Unit cell: (113.9, 130.05, 111.35, 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 68 16.00 O 1667 8.00 N 1546 7.00 C 5764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE R 401 " Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.046A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.649A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.113A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.883A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.616A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.557A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.664A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 51 removed outlier: 3.706A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.576A pdb=" N GLU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 123 removed outlier: 4.403A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS R 96 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 removed outlier: 3.860A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix removed outlier: 4.256A pdb=" N MET R 158 " --> pdb=" O PHE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 178 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 200 through 228 removed outlier: 4.116A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.058A pdb=" N VAL R 259 " --> pdb=" O ILE R 255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.963A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.614A pdb=" N ALA R 305 " --> pdb=" O PRO R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.926A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.871A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191 removed outlier: 7.332A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.385A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.153A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.594A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.963A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.589A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN S 82 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.510A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.580A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.961A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 4.022A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2899 1.34 - 1.46: 2070 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 9248 Sorted by residual: bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.22e+00 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.57e-02 4.06e+03 5.25e+00 bond pdb=" CA VAL R 150 " pdb=" CB VAL R 150 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.95e+00 bond pdb=" N SER B 331 " pdb=" CA SER B 331 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG MET Y 38 " pdb=" SD MET Y 38 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 12028 1.52 - 3.04: 400 3.04 - 4.56: 71 4.56 - 6.09: 15 6.09 - 7.61: 6 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.24 4.23 1.01e+00 9.80e-01 1.75e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 112.96 109.01 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA MET Y 38 " pdb=" CB MET Y 38 " pdb=" CG MET Y 38 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C LEU Y 37 " pdb=" N MET Y 38 " pdb=" CA MET Y 38 " ideal model delta sigma weight residual 121.14 115.75 5.39 1.75e+00 3.27e-01 9.48e+00 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 112.92 109.20 3.72 1.23e+00 6.61e-01 9.15e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4938 17.91 - 35.82: 440 35.82 - 53.72: 87 53.72 - 71.63: 12 71.63 - 89.54: 6 Dihedral angle restraints: 5483 sinusoidal: 2152 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual -86.00 -113.68 27.68 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ILE R 201 " pdb=" C ILE R 201 " pdb=" N PRO R 202 " pdb=" CA PRO R 202 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -180.00 -135.81 -44.19 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1084 0.047 - 0.094: 250 0.094 - 0.140: 60 0.140 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB ILE R 201 " pdb=" CA ILE R 201 " pdb=" CG1 ILE R 201 " pdb=" CG2 ILE R 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR A 292 " pdb=" CA THR A 292 " pdb=" OG1 THR A 292 " pdb=" CG2 THR A 292 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1394 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 201 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO R 202 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 281 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO R 282 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 282 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 282 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO S 151 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.023 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1323 2.76 - 3.29: 8742 3.29 - 3.83: 14254 3.83 - 4.36: 16207 4.36 - 4.90: 28857 Nonbonded interactions: 69383 Sorted by model distance: nonbonded pdb=" NE2 GLN A 52 " pdb=" OD1 ASP A 335 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.227 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.278 3.040 ... (remaining 69378 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: 1.180 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.003 0.050 9248 Z= 0.213 Angle : 0.668 7.608 12520 Z= 0.374 Chirality : 0.042 0.234 1397 Planarity : 0.004 0.079 1584 Dihedral : 13.944 89.539 3326 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1129 helix: 1.54 (0.27), residues: 393 sheet: -0.72 (0.33), residues: 243 loop : -1.94 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 148 HIS 0.005 0.001 HIS B 266 PHE 0.024 0.001 PHE A 307 TYR 0.009 0.001 TYR S 173 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.931 Fit side-chains REVERT: A 307 PHE cc_start: 0.8004 (t80) cc_final: 0.7803 (t80) REVERT: B 17 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9056 (tm-30) REVERT: B 295 ASN cc_start: 0.8143 (m-40) cc_final: 0.7904 (m-40) REVERT: B 308 LEU cc_start: 0.8041 (mp) cc_final: 0.7781 (mp) REVERT: R 31 VAL cc_start: 0.8535 (p) cc_final: 0.8286 (p) REVERT: R 222 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6744 (tmm160) REVERT: S 11 LEU cc_start: 0.6560 (pt) cc_final: 0.5728 (tt) REVERT: S 95 TYR cc_start: 0.6714 (m-10) cc_final: 0.6118 (m-10) REVERT: S 227 TYR cc_start: 0.6983 (m-80) cc_final: 0.6499 (m-80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2112 time to fit residues: 52.1138 Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 110 ASN B 293 ASN R 59 ASN S 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9248 Z= 0.231 Angle : 0.603 10.368 12520 Z= 0.312 Chirality : 0.043 0.182 1397 Planarity : 0.004 0.055 1584 Dihedral : 4.696 53.922 1252 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.52 % Allowed : 8.32 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1129 helix: 1.93 (0.27), residues: 388 sheet: -0.70 (0.32), residues: 260 loop : -1.89 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 165 TYR 0.016 0.001 TYR R 172 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.059 Fit side-chains REVERT: B 197 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7471 (mmp80) REVERT: B 295 ASN cc_start: 0.8228 (m-40) cc_final: 0.7827 (m-40) REVERT: S 95 TYR cc_start: 0.6784 (m-10) cc_final: 0.6306 (m-10) REVERT: S 173 TYR cc_start: 0.7885 (m-80) cc_final: 0.7645 (m-80) REVERT: S 174 LEU cc_start: 0.6843 (tp) cc_final: 0.6309 (mp) REVERT: S 228 TYR cc_start: 0.6574 (m-80) cc_final: 0.6346 (m-80) REVERT: Y 44 HIS cc_start: 0.8303 (m90) cc_final: 0.7652 (m-70) outliers start: 15 outliers final: 9 residues processed: 172 average time/residue: 0.2075 time to fit residues: 50.0232 Evaluate side-chains 154 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9248 Z= 0.343 Angle : 0.655 10.924 12520 Z= 0.337 Chirality : 0.045 0.159 1397 Planarity : 0.005 0.055 1584 Dihedral : 4.847 51.325 1252 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.93 % Allowed : 12.17 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1129 helix: 1.67 (0.27), residues: 395 sheet: -0.83 (0.31), residues: 267 loop : -1.95 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.007 0.001 HIS B 91 PHE 0.026 0.002 PHE R 165 TYR 0.021 0.002 TYR R 172 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.047 Fit side-chains REVERT: A 38 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8770 (tt) REVERT: B 10 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: B 256 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8558 (tpt170) REVERT: B 295 ASN cc_start: 0.8291 (m-40) cc_final: 0.7835 (m-40) REVERT: S 95 TYR cc_start: 0.6901 (m-10) cc_final: 0.6385 (m-10) REVERT: S 174 LEU cc_start: 0.6824 (tp) cc_final: 0.6320 (mp) REVERT: S 228 TYR cc_start: 0.6508 (m-80) cc_final: 0.6303 (m-80) REVERT: Y 44 HIS cc_start: 0.8331 (m90) cc_final: 0.7735 (m-70) outliers start: 19 outliers final: 13 residues processed: 170 average time/residue: 0.2273 time to fit residues: 53.1671 Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9248 Z= 0.153 Angle : 0.572 11.011 12520 Z= 0.290 Chirality : 0.042 0.165 1397 Planarity : 0.004 0.045 1584 Dihedral : 4.612 49.244 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.93 % Allowed : 14.00 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1129 helix: 2.00 (0.27), residues: 389 sheet: -0.77 (0.31), residues: 272 loop : -1.79 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.001 PHE R 91 TYR 0.016 0.001 TYR S 103 ARG 0.005 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.030 Fit side-chains REVERT: A 38 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 10 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: B 253 PHE cc_start: 0.8359 (m-10) cc_final: 0.8130 (m-10) REVERT: B 254 ASP cc_start: 0.8449 (t0) cc_final: 0.7393 (p0) REVERT: B 256 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8332 (tpt170) REVERT: B 295 ASN cc_start: 0.8307 (m-40) cc_final: 0.7942 (m-40) REVERT: B 308 LEU cc_start: 0.7924 (mp) cc_final: 0.7537 (mp) REVERT: R 81 MET cc_start: 0.8185 (ttp) cc_final: 0.7835 (ttm) REVERT: R 222 ARG cc_start: 0.7399 (ttp80) cc_final: 0.6848 (tmm160) REVERT: S 95 TYR cc_start: 0.6601 (m-10) cc_final: 0.6246 (m-10) REVERT: S 174 LEU cc_start: 0.6854 (tp) cc_final: 0.6449 (mp) REVERT: S 230 MET cc_start: 0.3263 (mmm) cc_final: 0.3034 (mmm) REVERT: Y 28 ILE cc_start: 0.8616 (pt) cc_final: 0.8276 (pt) REVERT: Y 38 MET cc_start: 0.8234 (pmm) cc_final: 0.7928 (pmm) REVERT: Y 44 HIS cc_start: 0.8226 (m90) cc_final: 0.7355 (m170) outliers start: 19 outliers final: 9 residues processed: 175 average time/residue: 0.2086 time to fit residues: 51.2358 Evaluate side-chains 165 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN R 63 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9248 Z= 0.322 Angle : 0.655 10.494 12520 Z= 0.333 Chirality : 0.044 0.152 1397 Planarity : 0.005 0.049 1584 Dihedral : 4.807 49.283 1252 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.14 % Allowed : 14.91 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1129 helix: 1.63 (0.27), residues: 399 sheet: -0.85 (0.31), residues: 273 loop : -1.86 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.020 0.002 PHE R 91 TYR 0.020 0.002 TYR R 27 ARG 0.005 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.034 Fit side-chains REVERT: A 38 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8749 (tt) REVERT: B 10 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: B 214 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: B 295 ASN cc_start: 0.8288 (m-40) cc_final: 0.7877 (m-40) REVERT: R 81 MET cc_start: 0.8200 (ttp) cc_final: 0.7837 (ttm) REVERT: R 105 MET cc_start: 0.8132 (ttt) cc_final: 0.7780 (ttt) REVERT: S 51 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5946 (mp) REVERT: S 95 TYR cc_start: 0.6708 (m-10) cc_final: 0.6271 (m-10) REVERT: S 174 LEU cc_start: 0.6897 (tp) cc_final: 0.6527 (mp) REVERT: Y 38 MET cc_start: 0.8086 (pmm) cc_final: 0.7827 (pmm) REVERT: Y 44 HIS cc_start: 0.8315 (m90) cc_final: 0.7472 (m170) outliers start: 31 outliers final: 16 residues processed: 166 average time/residue: 0.2043 time to fit residues: 47.2004 Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9248 Z= 0.190 Angle : 0.607 10.770 12520 Z= 0.304 Chirality : 0.042 0.168 1397 Planarity : 0.004 0.051 1584 Dihedral : 4.653 49.297 1252 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.33 % Allowed : 16.13 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1129 helix: 1.88 (0.27), residues: 395 sheet: -0.80 (0.31), residues: 278 loop : -1.79 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE R 91 TYR 0.020 0.001 TYR R 172 ARG 0.006 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.958 Fit side-chains REVERT: A 38 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 198 MET cc_start: 0.7374 (mmp) cc_final: 0.7082 (mmm) REVERT: B 10 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: B 197 ARG cc_start: 0.7956 (mmp80) cc_final: 0.7552 (mmp80) REVERT: B 254 ASP cc_start: 0.8570 (t0) cc_final: 0.7546 (p0) REVERT: B 256 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8432 (tpt170) REVERT: B 295 ASN cc_start: 0.8247 (m-40) cc_final: 0.7817 (m-40) REVERT: R 81 MET cc_start: 0.8231 (ttp) cc_final: 0.7867 (ttm) REVERT: R 222 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6904 (tmm160) REVERT: S 95 TYR cc_start: 0.6699 (m-10) cc_final: 0.6298 (m-10) REVERT: S 174 LEU cc_start: 0.6909 (tp) cc_final: 0.6555 (mp) REVERT: Y 44 HIS cc_start: 0.8270 (m90) cc_final: 0.7440 (m170) outliers start: 23 outliers final: 17 residues processed: 169 average time/residue: 0.2072 time to fit residues: 48.9305 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.0050 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9248 Z= 0.155 Angle : 0.599 10.645 12520 Z= 0.296 Chirality : 0.042 0.182 1397 Planarity : 0.004 0.052 1584 Dihedral : 4.492 50.827 1252 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.74 % Allowed : 16.23 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1129 helix: 2.01 (0.27), residues: 396 sheet: -0.71 (0.31), residues: 278 loop : -1.72 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.016 0.001 PHE R 91 TYR 0.016 0.001 TYR R 172 ARG 0.005 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7378 (ttp-110) REVERT: A 38 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 198 MET cc_start: 0.7317 (mmp) cc_final: 0.7031 (mmm) REVERT: B 10 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: B 175 GLN cc_start: 0.7806 (pm20) cc_final: 0.7357 (pm20) REVERT: B 295 ASN cc_start: 0.8235 (m-40) cc_final: 0.7803 (m-40) REVERT: R 81 MET cc_start: 0.8205 (ttp) cc_final: 0.7856 (ttm) REVERT: S 95 TYR cc_start: 0.6747 (m-10) cc_final: 0.6322 (m-10) REVERT: Y 44 HIS cc_start: 0.8164 (m90) cc_final: 0.7325 (m170) outliers start: 27 outliers final: 18 residues processed: 175 average time/residue: 0.2230 time to fit residues: 55.1083 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9248 Z= 0.392 Angle : 0.729 11.126 12520 Z= 0.369 Chirality : 0.046 0.170 1397 Planarity : 0.005 0.055 1584 Dihedral : 4.927 50.445 1252 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.94 % Allowed : 17.34 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1129 helix: 1.55 (0.26), residues: 400 sheet: -0.86 (0.31), residues: 275 loop : -1.82 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 36 HIS 0.007 0.001 HIS B 91 PHE 0.022 0.002 PHE R 91 TYR 0.023 0.002 TYR S 103 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.939 Fit side-chains REVERT: A 38 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 10 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: B 175 GLN cc_start: 0.8022 (pm20) cc_final: 0.7549 (pm20) REVERT: B 259 GLN cc_start: 0.8464 (tp40) cc_final: 0.8154 (tp40) REVERT: B 295 ASN cc_start: 0.8332 (m-40) cc_final: 0.7921 (m-40) REVERT: R 86 GLU cc_start: 0.7244 (tp30) cc_final: 0.7029 (tp30) REVERT: R 105 MET cc_start: 0.8150 (ttt) cc_final: 0.7777 (ttt) REVERT: R 222 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6909 (tmm160) REVERT: S 51 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.5971 (mp) REVERT: S 95 TYR cc_start: 0.6617 (m-10) cc_final: 0.6050 (m-10) REVERT: S 174 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6365 (mp) REVERT: S 219 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6494 (tt) REVERT: Y 44 HIS cc_start: 0.8311 (m90) cc_final: 0.7501 (m170) outliers start: 29 outliers final: 20 residues processed: 171 average time/residue: 0.2159 time to fit residues: 51.8826 Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9248 Z= 0.221 Angle : 0.663 10.971 12520 Z= 0.331 Chirality : 0.043 0.207 1397 Planarity : 0.004 0.054 1584 Dihedral : 4.744 49.339 1252 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.54 % Allowed : 16.94 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1129 helix: 1.77 (0.27), residues: 396 sheet: -0.72 (0.31), residues: 271 loop : -1.81 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.001 PHE R 91 TYR 0.022 0.001 TYR S 103 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.939 Fit side-chains REVERT: A 38 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 10 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: B 17 GLN cc_start: 0.8970 (pp30) cc_final: 0.8508 (pp30) REVERT: B 175 GLN cc_start: 0.7939 (pm20) cc_final: 0.7446 (pm20) REVERT: B 254 ASP cc_start: 0.8242 (t70) cc_final: 0.7696 (p0) REVERT: B 256 ARG cc_start: 0.7817 (tpt90) cc_final: 0.7353 (tpt170) REVERT: B 259 GLN cc_start: 0.8436 (tp40) cc_final: 0.8021 (tp40) REVERT: B 295 ASN cc_start: 0.8327 (m-40) cc_final: 0.7935 (m-40) REVERT: R 105 MET cc_start: 0.7935 (ttt) cc_final: 0.7579 (ttt) REVERT: R 222 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6881 (tmm160) REVERT: S 51 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.5930 (mp) REVERT: S 95 TYR cc_start: 0.6608 (m-10) cc_final: 0.6055 (m-10) REVERT: S 174 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6378 (mp) REVERT: Y 28 ILE cc_start: 0.8480 (pt) cc_final: 0.8125 (pt) REVERT: Y 44 HIS cc_start: 0.8276 (m90) cc_final: 0.7413 (m170) outliers start: 25 outliers final: 19 residues processed: 174 average time/residue: 0.2000 time to fit residues: 49.0210 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9248 Z= 0.172 Angle : 0.648 11.243 12520 Z= 0.322 Chirality : 0.043 0.207 1397 Planarity : 0.004 0.054 1584 Dihedral : 4.592 50.918 1252 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.54 % Allowed : 17.04 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1129 helix: 1.98 (0.27), residues: 395 sheet: -0.66 (0.31), residues: 276 loop : -1.69 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 63 PHE 0.014 0.001 PHE R 91 TYR 0.021 0.001 TYR S 103 ARG 0.005 0.000 ARG R 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7246 (t0) cc_final: 0.6791 (t0) REVERT: A 38 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8552 (tt) REVERT: B 10 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: B 17 GLN cc_start: 0.9012 (pp30) cc_final: 0.8565 (pp30) REVERT: B 254 ASP cc_start: 0.8217 (t70) cc_final: 0.7699 (p0) REVERT: B 256 ARG cc_start: 0.7804 (tpt90) cc_final: 0.7349 (tpt170) REVERT: B 259 GLN cc_start: 0.8391 (tp40) cc_final: 0.7959 (tp40) REVERT: B 295 ASN cc_start: 0.8309 (m-40) cc_final: 0.7907 (m-40) REVERT: R 81 MET cc_start: 0.8113 (ttp) cc_final: 0.7761 (ttm) REVERT: R 105 MET cc_start: 0.7847 (ttt) cc_final: 0.7474 (ttt) REVERT: R 311 PHE cc_start: 0.7643 (t80) cc_final: 0.7396 (t80) REVERT: S 51 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.5968 (mp) REVERT: S 95 TYR cc_start: 0.6569 (m-10) cc_final: 0.6051 (m-10) REVERT: S 174 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6319 (mp) REVERT: S 219 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6499 (tt) REVERT: S 227 TYR cc_start: 0.6501 (m-80) cc_final: 0.6239 (m-80) REVERT: Y 28 ILE cc_start: 0.8440 (pt) cc_final: 0.8079 (pt) REVERT: Y 44 HIS cc_start: 0.8062 (m90) cc_final: 0.7168 (m170) outliers start: 25 outliers final: 15 residues processed: 174 average time/residue: 0.2154 time to fit residues: 52.1875 Evaluate side-chains 174 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.205264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139051 restraints weight = 11690.469| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.22 r_work: 0.3446 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9248 Z= 0.176 Angle : 0.652 10.161 12520 Z= 0.321 Chirality : 0.042 0.178 1397 Planarity : 0.004 0.054 1584 Dihedral : 4.565 51.583 1252 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.23 % Allowed : 17.44 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1129 helix: 1.94 (0.27), residues: 400 sheet: -0.70 (0.31), residues: 278 loop : -1.59 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.015 0.001 PHE R 91 TYR 0.021 0.001 TYR S 103 ARG 0.005 0.000 ARG R 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.52 seconds wall clock time: 41 minutes 41.80 seconds (2501.80 seconds total)