Starting phenix.real_space_refine on Sat Aug 23 00:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ia8_35298/08_2025/8ia8_35298.map" } resolution = 2.86 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= 0.019 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 5620 2.51 5 N 1506 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 8810 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2255 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8810 At special positions: 0 Unit cell: (91.8, 123.25, 125.8, 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 1616 8.00 N 1506 7.00 C 5620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " 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=2.04 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: 0.68 Conformation dependent library (CDL) restraints added in 428.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 35.9% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 51 removed outlier: 3.745A pdb=" N SER A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.540A pdb=" N SER A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.946A pdb=" N SER A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.547A pdb=" N ILE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.573A pdb=" N ALA A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.653A pdb=" N ILE A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.541A pdb=" N HIS A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.731A pdb=" N CYS A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.800A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.077A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.515A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.664A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.680A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.604A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.753A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.508A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.613A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.161A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ALA C 220 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.558A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.780A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.604A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.755A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.428A 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: 6.563A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.722A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.409A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.678A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.678A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1116 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: 1.50 Time building geometry restraints manager: 0.94 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: 2822 1.34 - 1.46: 2081 1.46 - 1.58: 3998 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8997 Sorted by residual: bond pdb=" C PRO A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.51e-02 4.39e+03 2.33e+00 bond pdb=" C VAL S 2 " pdb=" O VAL S 2 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.19e-02 7.06e+03 1.99e+00 bond pdb=" C ILE A 116 " pdb=" O ILE A 116 " ideal model delta sigma weight residual 1.239 1.224 0.015 1.13e-02 7.83e+03 1.82e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.71e+00 bond pdb=" C MET A 138 " pdb=" N ALA A 139 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.31e-02 5.83e+03 1.52e+00 ... (remaining 8992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11685 1.38 - 2.77: 415 2.77 - 4.15: 62 4.15 - 5.54: 23 5.54 - 6.92: 5 Bond angle restraints: 12190 Sorted by residual: angle pdb=" N GLY L 13 " pdb=" CA GLY L 13 " pdb=" C GLY L 13 " ideal model delta sigma weight residual 112.60 106.66 5.94 1.53e+00 4.27e-01 1.51e+01 angle pdb=" N SER A 117 " pdb=" CA SER A 117 " pdb=" C SER A 117 " ideal model delta sigma weight residual 113.88 109.22 4.66 1.23e+00 6.61e-01 1.43e+01 angle pdb=" CA GLY L 13 " pdb=" C GLY L 13 " pdb=" N LEU L 14 " ideal model delta sigma weight residual 114.78 118.92 -4.14 1.16e+00 7.43e-01 1.27e+01 angle pdb=" N CYS A 95 " pdb=" CA CYS A 95 " pdb=" C CYS A 95 " ideal model delta sigma weight residual 112.72 108.02 4.70 1.36e+00 5.41e-01 1.19e+01 angle pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N SER B 331 " ideal model delta sigma weight residual 114.74 118.43 -3.69 1.13e+00 7.83e-01 1.07e+01 ... (remaining 12185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 4692 14.14 - 28.29: 479 28.29 - 42.43: 121 42.43 - 56.57: 27 56.57 - 70.72: 8 Dihedral angle restraints: 5327 sinusoidal: 2054 harmonic: 3273 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 770 0.031 - 0.062: 409 0.062 - 0.093: 136 0.093 - 0.125: 67 0.125 - 0.156: 8 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1387 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 287 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 288 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 21 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 22 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO S 75 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.031 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 217 2.70 - 3.25: 8268 3.25 - 3.80: 12831 3.80 - 4.35: 17619 4.35 - 4.90: 30675 Nonbonded interactions: 69610 Sorted by model distance: nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 48 " model vdw 2.148 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.155 3.040 nonbonded pdb=" O LEU A 387 " pdb=" OG1 THR A 391 " model vdw 2.185 3.040 nonbonded pdb=" O VAL A 23 " pdb=" OG SER A 26 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG L 16 " pdb=" O TYR A 393 " model vdw 2.227 3.120 ... (remaining 69605 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: 2.170 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.005 0.040 9000 Z= 0.217 Angle : 0.632 6.920 12196 Z= 0.363 Chirality : 0.045 0.156 1390 Planarity : 0.004 0.078 1537 Dihedral : 12.725 70.718 3206 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.21 (0.24), residues: 1114 helix: -0.34 (0.27), residues: 375 sheet: -0.21 (0.32), residues: 280 loop : -1.48 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.014 0.001 TYR B 105 PHE 0.013 0.002 PHE A 164 TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8997) covalent geometry : angle 0.63156 (12190) SS BOND : bond 0.00573 ( 3) SS BOND : angle 1.48711 ( 6) hydrogen bonds : bond 0.25228 ( 388) hydrogen bonds : angle 8.27846 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.360 Fit side-chains REVERT: S 1 ASP cc_start: 0.7641 (t70) cc_final: 0.7426 (t70) outliers start: 4 outliers final: 0 residues processed: 144 average time/residue: 0.9036 time to fit residues: 135.8424 Evaluate side-chains 111 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085078 restraints weight = 11439.578| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.53 r_work: 0.2752 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9000 Z= 0.158 Angle : 0.604 6.984 12196 Z= 0.320 Chirality : 0.045 0.342 1390 Planarity : 0.005 0.063 1537 Dihedral : 4.595 24.025 1218 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.78 % Allowed : 9.10 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.50 (0.25), residues: 1114 helix: 0.55 (0.27), residues: 378 sheet: 0.17 (0.32), residues: 280 loop : -1.37 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.015 0.001 TYR S 190 PHE 0.014 0.001 PHE S 29 TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8997) covalent geometry : angle 0.60382 (12190) SS BOND : bond 0.00627 ( 3) SS BOND : angle 1.37985 ( 6) hydrogen bonds : bond 0.04847 ( 388) hydrogen bonds : angle 5.09607 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.367 Fit side-chains REVERT: A 151 PHE cc_start: 0.7881 (t80) cc_final: 0.7600 (t80) REVERT: A 365 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7651 (ptm160) REVERT: C 205 ARG cc_start: 0.8488 (mmp-170) cc_final: 0.8192 (mmt90) REVERT: C 330 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7850 (mtpt) REVERT: B 42 ARG cc_start: 0.8151 (tpt170) cc_final: 0.7805 (tmt170) REVERT: B 217 MET cc_start: 0.8346 (ptt) cc_final: 0.8096 (ptt) REVERT: G 42 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8066 (mm-30) REVERT: G 58 GLU cc_start: 0.8545 (pm20) cc_final: 0.7988 (pm20) REVERT: S 1 ASP cc_start: 0.7616 (t70) cc_final: 0.7272 (t0) outliers start: 17 outliers final: 6 residues processed: 130 average time/residue: 0.8665 time to fit residues: 117.9632 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.129603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085853 restraints weight = 11370.569| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.53 r_work: 0.2761 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9000 Z= 0.134 Angle : 0.561 8.773 12196 Z= 0.295 Chirality : 0.044 0.334 1390 Planarity : 0.004 0.064 1537 Dihedral : 4.333 22.452 1218 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.51 % Allowed : 10.56 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.17 (0.25), residues: 1114 helix: 0.98 (0.28), residues: 378 sheet: 0.29 (0.31), residues: 279 loop : -1.30 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE S 29 TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8997) covalent geometry : angle 0.55998 (12190) SS BOND : bond 0.00602 ( 3) SS BOND : angle 1.27214 ( 6) hydrogen bonds : bond 0.04181 ( 388) hydrogen bonds : angle 4.62809 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.373 Fit side-chains REVERT: A 84 LEU cc_start: 0.8430 (mt) cc_final: 0.7917 (tp) REVERT: A 155 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7041 (mp) REVERT: A 352 MET cc_start: 0.9022 (mtp) cc_final: 0.8647 (mtp) REVERT: A 365 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7749 (ptm160) REVERT: A 442 PHE cc_start: 0.7494 (t80) cc_final: 0.7289 (t80) REVERT: B 23 LYS cc_start: 0.8515 (tttp) cc_final: 0.8067 (tppt) REVERT: B 42 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7774 (tmt170) REVERT: B 198 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 217 MET cc_start: 0.8334 (ptt) cc_final: 0.8095 (ptt) REVERT: G 42 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8106 (mm-30) REVERT: G 58 GLU cc_start: 0.8549 (pm20) cc_final: 0.7979 (pm20) REVERT: S 1 ASP cc_start: 0.7478 (t70) cc_final: 0.7075 (t0) outliers start: 24 outliers final: 9 residues processed: 128 average time/residue: 0.8204 time to fit residues: 110.2952 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.131389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087602 restraints weight = 11492.063| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.56 r_work: 0.2778 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9000 Z= 0.110 Angle : 0.528 8.137 12196 Z= 0.278 Chirality : 0.043 0.242 1390 Planarity : 0.004 0.063 1537 Dihedral : 4.122 20.558 1218 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.20 % Allowed : 12.03 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.08 (0.25), residues: 1114 helix: 1.26 (0.29), residues: 377 sheet: 0.29 (0.31), residues: 281 loop : -1.11 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.010 0.001 PHE S 110 TRP 0.012 0.001 TRP B 297 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8997) covalent geometry : angle 0.52737 (12190) SS BOND : bond 0.00534 ( 3) SS BOND : angle 1.12488 ( 6) hydrogen bonds : bond 0.03586 ( 388) hydrogen bonds : angle 4.34618 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.379 Fit side-chains REVERT: A 84 LEU cc_start: 0.8432 (mt) cc_final: 0.7941 (tp) REVERT: A 98 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6643 (tt) REVERT: A 155 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7059 (mp) REVERT: A 352 MET cc_start: 0.8938 (mtp) cc_final: 0.8605 (mtp) REVERT: A 365 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7849 (ptm160) REVERT: A 442 PHE cc_start: 0.7521 (t80) cc_final: 0.7296 (t80) REVERT: C 275 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 23 LYS cc_start: 0.8442 (tttp) cc_final: 0.7988 (tppt) REVERT: B 42 ARG cc_start: 0.8226 (tpt170) cc_final: 0.7785 (tmt170) REVERT: B 198 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 217 MET cc_start: 0.8321 (ptt) cc_final: 0.8116 (ptt) REVERT: G 42 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8089 (mm-30) REVERT: G 58 GLU cc_start: 0.8565 (pm20) cc_final: 0.7997 (pm20) REVERT: S 1 ASP cc_start: 0.7156 (t70) cc_final: 0.6935 (t70) outliers start: 21 outliers final: 6 residues processed: 130 average time/residue: 0.8061 time to fit residues: 110.0905 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 98 optimal weight: 0.0030 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 259 GLN S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.086284 restraints weight = 11491.063| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.57 r_work: 0.2765 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9000 Z= 0.119 Angle : 0.530 8.252 12196 Z= 0.279 Chirality : 0.043 0.204 1390 Planarity : 0.004 0.042 1537 Dihedral : 4.067 20.662 1218 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 13.08 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.21 (0.26), residues: 1114 helix: 1.37 (0.28), residues: 380 sheet: 0.34 (0.31), residues: 281 loop : -1.03 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.012 0.001 TYR S 190 PHE 0.010 0.001 PHE A 107 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8997) covalent geometry : angle 0.52995 (12190) SS BOND : bond 0.00557 ( 3) SS BOND : angle 1.17424 ( 6) hydrogen bonds : bond 0.03611 ( 388) hydrogen bonds : angle 4.23281 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.401 Fit side-chains REVERT: A 84 LEU cc_start: 0.8468 (mt) cc_final: 0.7967 (tp) REVERT: A 155 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7024 (mp) REVERT: A 352 MET cc_start: 0.8928 (mtp) cc_final: 0.8531 (mtp) REVERT: A 365 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7873 (ptm160) REVERT: A 442 PHE cc_start: 0.7524 (t80) cc_final: 0.7303 (t80) REVERT: C 242 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7852 (ttm-80) REVERT: C 245 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7949 (mp0) REVERT: B 19 ARG cc_start: 0.8314 (tmm160) cc_final: 0.8107 (tmm160) REVERT: B 23 LYS cc_start: 0.8404 (tttp) cc_final: 0.7976 (tppt) REVERT: B 46 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7143 (mmp80) REVERT: B 198 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 217 MET cc_start: 0.8308 (ptt) cc_final: 0.8105 (ptt) REVERT: G 42 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8078 (mm-30) REVERT: G 58 GLU cc_start: 0.8524 (pm20) cc_final: 0.7936 (pm20) outliers start: 22 outliers final: 11 residues processed: 125 average time/residue: 0.8323 time to fit residues: 109.0727 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086996 restraints weight = 11561.575| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.58 r_work: 0.2796 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9000 Z= 0.111 Angle : 0.518 8.525 12196 Z= 0.271 Chirality : 0.042 0.143 1390 Planarity : 0.004 0.044 1537 Dihedral : 4.006 20.061 1218 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.41 % Allowed : 13.81 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.26), residues: 1114 helix: 1.49 (0.28), residues: 381 sheet: 0.34 (0.31), residues: 281 loop : -0.96 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.012 0.001 TYR S 190 PHE 0.010 0.001 PHE S 110 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8997) covalent geometry : angle 0.51768 (12190) SS BOND : bond 0.00477 ( 3) SS BOND : angle 1.23715 ( 6) hydrogen bonds : bond 0.03451 ( 388) hydrogen bonds : angle 4.17039 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.355 Fit side-chains REVERT: A 84 LEU cc_start: 0.8488 (mt) cc_final: 0.7992 (tp) REVERT: A 98 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 155 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7172 (mp) REVERT: A 352 MET cc_start: 0.8911 (mtp) cc_final: 0.8618 (mtp) REVERT: A 442 PHE cc_start: 0.7522 (t80) cc_final: 0.7321 (t80) REVERT: C 242 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7911 (ttm-80) REVERT: C 245 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7914 (mp0) REVERT: B 19 ARG cc_start: 0.8308 (tmm160) cc_final: 0.8085 (tmm160) REVERT: B 23 LYS cc_start: 0.8367 (tttp) cc_final: 0.7949 (tppt) REVERT: B 46 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7142 (mmp80) REVERT: B 198 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8379 (pp) REVERT: G 42 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8058 (mm-30) REVERT: G 58 GLU cc_start: 0.8526 (pm20) cc_final: 0.7903 (pm20) outliers start: 23 outliers final: 9 residues processed: 126 average time/residue: 0.8285 time to fit residues: 109.4803 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.086356 restraints weight = 11575.805| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.58 r_work: 0.2778 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9000 Z= 0.125 Angle : 0.542 8.806 12196 Z= 0.283 Chirality : 0.042 0.141 1390 Planarity : 0.004 0.046 1537 Dihedral : 4.030 20.584 1218 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.99 % Allowed : 14.85 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.34 (0.25), residues: 1114 helix: 1.51 (0.28), residues: 381 sheet: 0.43 (0.31), residues: 273 loop : -0.99 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.012 0.001 TYR S 190 PHE 0.009 0.001 PHE B 151 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8997) covalent geometry : angle 0.54129 (12190) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.24126 ( 6) hydrogen bonds : bond 0.03588 ( 388) hydrogen bonds : angle 4.16268 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.364 Fit side-chains REVERT: A 84 LEU cc_start: 0.8553 (mt) cc_final: 0.8040 (tp) REVERT: A 98 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6642 (tt) REVERT: A 155 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 352 MET cc_start: 0.8914 (mtp) cc_final: 0.8624 (mtp) REVERT: C 242 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.8006 (ttm-80) REVERT: C 245 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7917 (mp0) REVERT: C 275 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 23 LYS cc_start: 0.8351 (tttp) cc_final: 0.7936 (tppt) REVERT: B 198 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 215 GLU cc_start: 0.8523 (mp0) cc_final: 0.7719 (mp0) REVERT: B 254 ASP cc_start: 0.8213 (t70) cc_final: 0.7882 (t70) REVERT: G 42 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8074 (mm-30) REVERT: G 58 GLU cc_start: 0.8534 (pm20) cc_final: 0.7903 (pm20) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.7633 time to fit residues: 100.9750 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.130782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086819 restraints weight = 11408.627| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.54 r_work: 0.2779 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9000 Z= 0.129 Angle : 0.537 9.032 12196 Z= 0.280 Chirality : 0.042 0.137 1390 Planarity : 0.004 0.049 1537 Dihedral : 4.043 20.966 1218 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 15.48 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.38 (0.25), residues: 1114 helix: 1.56 (0.28), residues: 381 sheet: 0.43 (0.31), residues: 273 loop : -0.97 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.012 0.001 TYR S 190 PHE 0.009 0.001 PHE C 189 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8997) covalent geometry : angle 0.53624 (12190) SS BOND : bond 0.00578 ( 3) SS BOND : angle 1.21941 ( 6) hydrogen bonds : bond 0.03601 ( 388) hydrogen bonds : angle 4.16488 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.370 Fit side-chains REVERT: A 84 LEU cc_start: 0.8555 (mt) cc_final: 0.8037 (tp) REVERT: A 98 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6640 (tt) REVERT: A 155 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7233 (mp) REVERT: A 352 MET cc_start: 0.8932 (mtp) cc_final: 0.8637 (mtp) REVERT: C 242 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7966 (ttm-80) REVERT: C 245 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7913 (mp0) REVERT: B 19 ARG cc_start: 0.8317 (tmm160) cc_final: 0.8086 (tmm160) REVERT: B 23 LYS cc_start: 0.8355 (tttp) cc_final: 0.7934 (tppt) REVERT: B 198 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 215 GLU cc_start: 0.8532 (mp0) cc_final: 0.7728 (mp0) REVERT: B 234 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: B 254 ASP cc_start: 0.8266 (t70) cc_final: 0.7945 (t70) REVERT: G 42 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8058 (mm-30) REVERT: G 58 GLU cc_start: 0.8555 (pm20) cc_final: 0.7921 (pm20) REVERT: S 7 SER cc_start: 0.8951 (t) cc_final: 0.8499 (p) REVERT: S 76 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7718 (pmtt) outliers start: 22 outliers final: 12 residues processed: 129 average time/residue: 0.7900 time to fit residues: 107.1033 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086575 restraints weight = 11498.920| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.57 r_work: 0.2795 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9000 Z= 0.117 Angle : 0.538 9.122 12196 Z= 0.280 Chirality : 0.042 0.136 1390 Planarity : 0.004 0.063 1537 Dihedral : 4.008 20.164 1218 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 15.69 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.45 (0.25), residues: 1114 helix: 1.64 (0.28), residues: 382 sheet: 0.47 (0.32), residues: 271 loop : -0.94 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 365 TYR 0.012 0.001 TYR S 190 PHE 0.011 0.001 PHE A 164 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8997) covalent geometry : angle 0.53791 (12190) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.14080 ( 6) hydrogen bonds : bond 0.03441 ( 388) hydrogen bonds : angle 4.10773 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.434 Fit side-chains REVERT: A 84 LEU cc_start: 0.8545 (mt) cc_final: 0.8026 (tp) REVERT: A 98 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6612 (tt) REVERT: A 155 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7226 (mp) REVERT: A 162 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5687 (pp20) REVERT: A 352 MET cc_start: 0.8888 (mtp) cc_final: 0.8604 (mtp) REVERT: C 245 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7897 (mp0) REVERT: B 23 LYS cc_start: 0.8342 (tttp) cc_final: 0.7915 (tppt) REVERT: B 198 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 215 GLU cc_start: 0.8522 (mp0) cc_final: 0.7708 (mp0) REVERT: B 234 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: B 254 ASP cc_start: 0.8257 (t70) cc_final: 0.7897 (t70) REVERT: G 42 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8034 (mm-30) REVERT: G 58 GLU cc_start: 0.8548 (pm20) cc_final: 0.7909 (pm20) REVERT: S 7 SER cc_start: 0.8933 (t) cc_final: 0.8473 (p) REVERT: S 76 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7703 (pmtt) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.8548 time to fit residues: 112.9564 Evaluate side-chains 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.087345 restraints weight = 11329.187| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.53 r_work: 0.2789 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9000 Z= 0.122 Angle : 0.536 9.261 12196 Z= 0.279 Chirality : 0.042 0.136 1390 Planarity : 0.004 0.069 1537 Dihedral : 4.002 20.453 1218 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.78 % Allowed : 16.11 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.48 (0.25), residues: 1114 helix: 1.65 (0.28), residues: 382 sheet: 0.49 (0.31), residues: 273 loop : -0.93 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 365 TYR 0.012 0.001 TYR S 190 PHE 0.012 0.001 PHE A 164 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8997) covalent geometry : angle 0.53551 (12190) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.19722 ( 6) hydrogen bonds : bond 0.03485 ( 388) hydrogen bonds : angle 4.10441 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.387 Fit side-chains REVERT: A 84 LEU cc_start: 0.8569 (mt) cc_final: 0.8032 (tp) REVERT: A 98 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6608 (tt) REVERT: A 155 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7190 (mp) REVERT: A 352 MET cc_start: 0.8899 (mtp) cc_final: 0.8611 (mtp) REVERT: C 24 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6580 (mtt90) REVERT: C 245 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7896 (mp0) REVERT: B 19 ARG cc_start: 0.8292 (tmm160) cc_final: 0.8041 (tmm160) REVERT: B 23 LYS cc_start: 0.8366 (tttp) cc_final: 0.7933 (tppt) REVERT: B 198 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 215 GLU cc_start: 0.8526 (mp0) cc_final: 0.7722 (mp0) REVERT: B 234 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: B 254 ASP cc_start: 0.8284 (t70) cc_final: 0.7902 (t70) REVERT: G 42 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8005 (mm-30) REVERT: G 58 GLU cc_start: 0.8549 (pm20) cc_final: 0.7908 (pm20) REVERT: S 7 SER cc_start: 0.8963 (t) cc_final: 0.8511 (p) REVERT: S 76 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7772 (pmtt) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.8342 time to fit residues: 107.5191 Evaluate side-chains 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086691 restraints weight = 11420.321| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.55 r_work: 0.2795 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9000 Z= 0.119 Angle : 0.538 9.171 12196 Z= 0.281 Chirality : 0.042 0.135 1390 Planarity : 0.004 0.054 1537 Dihedral : 3.971 20.166 1218 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.09 % Allowed : 15.90 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1114 helix: 1.71 (0.28), residues: 382 sheet: 0.50 (0.31), residues: 273 loop : -0.93 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 134 TYR 0.012 0.001 TYR S 190 PHE 0.013 0.001 PHE A 164 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8997) covalent geometry : angle 0.53771 (12190) SS BOND : bond 0.00552 ( 3) SS BOND : angle 1.14981 ( 6) hydrogen bonds : bond 0.03424 ( 388) hydrogen bonds : angle 4.08089 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.11 seconds wall clock time: 65 minutes 22.75 seconds (3922.75 seconds total)