Starting phenix.real_space_refine on Mon May 12 07:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ia8_35298/05_2025/8ia8_35298_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ia8_35298/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ia8_35298/05_2025/8ia8_35298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ia8_35298/05_2025/8ia8_35298.map" model { file = "/net/cci-nas-00/data/ceres_data/8ia8_35298/05_2025/8ia8_35298_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ia8_35298/05_2025/8ia8_35298_neut.cif" } resolution = 2.86 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASP:plan': 3} 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: 5.30, per 1000 atoms: 0.60 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: 2.04 Conformation dependent library (CDL) restraints added in 993.2 milliseconds 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: 1.02 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: 2.39 Time building geometry restraints manager: 2.40 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.640 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (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 TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.002 PHE A 164 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.25228 ( 388) hydrogen bonds : angle 8.27846 ( 1116) SS BOND : bond 0.00573 ( 3) SS BOND : angle 1.48711 ( 6) covalent geometry : bond 0.00506 ( 8997) covalent geometry : angle 0.63156 (12190) *********************** 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 : 0.909 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: 1.7310 time to fit residues: 260.8862 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 : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.126799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.082674 restraints weight = 11320.048| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.55 r_work: 0.2722 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1221 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= 0.213 Angle : 0.642 7.260 12196 Z= 0.340 Chirality : 0.047 0.354 1390 Planarity : 0.005 0.062 1537 Dihedral : 4.734 25.842 1218 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.09 % Allowed : 8.79 % 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 (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: -0.59 (0.25), residues: 1114 helix: 0.47 (0.27), residues: 377 sheet: 0.14 (0.32), residues: 280 loop : -1.42 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.002 PHE S 29 TYR 0.018 0.002 TYR B 105 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 388) hydrogen bonds : angle 5.16830 ( 1116) SS BOND : bond 0.00726 ( 3) SS BOND : angle 1.55166 ( 6) covalent geometry : bond 0.00515 ( 8997) covalent geometry : angle 0.64118 (12190) *********************** 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 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.962 Fit side-chains REVERT: A 365 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7535 (ptm160) REVERT: C 330 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: B 42 ARG cc_start: 0.8117 (tpt170) cc_final: 0.7731 (tmt170) REVERT: B 46 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7145 (mmp80) REVERT: B 198 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 217 MET cc_start: 0.8327 (ptt) cc_final: 0.8076 (ptt) REVERT: G 42 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8076 (mm-30) REVERT: G 58 GLU cc_start: 0.8505 (pm20) cc_final: 0.7955 (pm20) REVERT: S 1 ASP cc_start: 0.7611 (t70) cc_final: 0.7260 (t0) outliers start: 20 outliers final: 7 residues processed: 126 average time/residue: 1.6630 time to fit residues: 219.8843 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 154 CYS 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 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.130395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086652 restraints weight = 11548.055| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.54 r_work: 0.2775 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9000 Z= 0.117 Angle : 0.547 9.095 12196 Z= 0.288 Chirality : 0.043 0.343 1390 Planarity : 0.004 0.066 1537 Dihedral : 4.307 21.732 1218 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.09 % Allowed : 10.67 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1114 helix: 0.98 (0.28), residues: 379 sheet: 0.25 (0.31), residues: 279 loop : -1.31 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE S 29 TYR 0.014 0.001 TYR S 190 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 388) hydrogen bonds : angle 4.59813 ( 1116) SS BOND : bond 0.00494 ( 3) SS BOND : angle 1.09821 ( 6) covalent geometry : bond 0.00266 ( 8997) covalent geometry : angle 0.54694 (12190) *********************** 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 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.000 Fit side-chains REVERT: A 84 LEU cc_start: 0.8437 (mt) cc_final: 0.7921 (tp) REVERT: A 151 PHE cc_start: 0.8015 (t80) cc_final: 0.7773 (t80) REVERT: A 365 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7751 (ptm160) REVERT: A 442 PHE cc_start: 0.7508 (t80) cc_final: 0.7306 (t80) REVERT: C 313 ARG cc_start: 0.8164 (pmm-80) cc_final: 0.7813 (pmm-80) REVERT: B 23 LYS cc_start: 0.8487 (tttp) cc_final: 0.8040 (tppt) REVERT: B 42 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7761 (tmt170) REVERT: B 198 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 217 MET cc_start: 0.8334 (ptt) cc_final: 0.8115 (ptt) REVERT: G 42 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8104 (mm-30) REVERT: G 58 GLU cc_start: 0.8562 (pm20) cc_final: 0.7988 (pm20) REVERT: S 1 ASP cc_start: 0.7457 (t70) cc_final: 0.7067 (t0) outliers start: 20 outliers final: 7 residues processed: 129 average time/residue: 1.6688 time to fit residues: 225.8934 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 ARG Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087050 restraints weight = 11326.112| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.52 r_work: 0.2783 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9000 Z= 0.117 Angle : 0.535 8.199 12196 Z= 0.282 Chirality : 0.043 0.250 1390 Planarity : 0.004 0.064 1537 Dihedral : 4.144 20.687 1218 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.20 % Allowed : 12.13 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.04 (0.25), residues: 1114 helix: 1.23 (0.29), residues: 377 sheet: 0.27 (0.31), residues: 280 loop : -1.13 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 107 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 388) hydrogen bonds : angle 4.38532 ( 1116) SS BOND : bond 0.00563 ( 3) SS BOND : angle 1.20061 ( 6) covalent geometry : bond 0.00268 ( 8997) covalent geometry : angle 0.53483 (12190) *********************** 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 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.071 Fit side-chains REVERT: A 84 LEU cc_start: 0.8436 (mt) cc_final: 0.7940 (tp) REVERT: A 151 PHE cc_start: 0.8009 (t80) cc_final: 0.7795 (t80) REVERT: A 155 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6957 (mp) REVERT: A 365 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7789 (ptm160) REVERT: A 442 PHE cc_start: 0.7502 (t80) cc_final: 0.7278 (t80) REVERT: C 313 ARG cc_start: 0.8150 (pmm-80) cc_final: 0.7694 (pmm-80) REVERT: B 23 LYS cc_start: 0.8431 (tttp) cc_final: 0.7975 (tppt) REVERT: B 42 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7763 (tmt170) REVERT: B 198 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 217 MET cc_start: 0.8315 (ptt) cc_final: 0.8104 (ptt) REVERT: G 42 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8014 (mm-30) REVERT: G 58 GLU cc_start: 0.8576 (pm20) cc_final: 0.8000 (pm20) REVERT: S 1 ASP cc_start: 0.7187 (t70) cc_final: 0.6968 (t70) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 1.6056 time to fit residues: 222.8754 Evaluate side-chains 128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 52 GLN 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 C residue 347 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087167 restraints weight = 11345.685| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.54 r_work: 0.2790 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1908 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= 0.117 Angle : 0.536 8.209 12196 Z= 0.282 Chirality : 0.043 0.208 1390 Planarity : 0.004 0.039 1537 Dihedral : 4.077 20.370 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 : 2.72 % Allowed : 12.66 % 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 (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: 0.22 (0.25), residues: 1114 helix: 1.42 (0.29), residues: 376 sheet: 0.34 (0.31), residues: 281 loop : -1.05 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE A 107 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 388) hydrogen bonds : angle 4.27264 ( 1116) SS BOND : bond 0.00620 ( 3) SS BOND : angle 1.22950 ( 6) covalent geometry : bond 0.00271 ( 8997) covalent geometry : angle 0.53548 (12190) *********************** 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.882 Fit side-chains REVERT: A 84 LEU cc_start: 0.8451 (mt) cc_final: 0.7943 (tp) REVERT: A 98 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6664 (tt) REVERT: A 155 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7014 (mp) REVERT: A 365 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7867 (ptm160) REVERT: A 442 PHE cc_start: 0.7510 (t80) cc_final: 0.7289 (t80) REVERT: C 313 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7665 (pmm-80) REVERT: B 19 ARG cc_start: 0.8310 (tmm160) cc_final: 0.8101 (tmm160) REVERT: B 23 LYS cc_start: 0.8393 (tttp) cc_final: 0.7974 (tppt) REVERT: B 198 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8374 (pp) REVERT: B 217 MET cc_start: 0.8312 (ptt) cc_final: 0.8105 (ptt) REVERT: G 42 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8010 (mm-30) REVERT: G 58 GLU cc_start: 0.8571 (pm20) cc_final: 0.7982 (pm20) outliers start: 26 outliers final: 10 residues processed: 131 average time/residue: 1.6062 time to fit residues: 220.8349 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 : 0.958 ------------------------------------------------------------------------------- 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 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 313 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086008 restraints weight = 11403.827| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.56 r_work: 0.2776 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1976 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= 0.124 Angle : 0.531 8.506 12196 Z= 0.278 Chirality : 0.042 0.142 1390 Planarity : 0.004 0.039 1537 Dihedral : 4.073 20.593 1218 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.72 % Allowed : 13.18 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.29 (0.25), residues: 1114 helix: 1.48 (0.28), residues: 379 sheet: 0.35 (0.31), residues: 288 loop : -1.01 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE C 189 TYR 0.012 0.001 TYR S 190 ARG 0.006 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 388) hydrogen bonds : angle 4.25711 ( 1116) SS BOND : bond 0.00652 ( 3) SS BOND : angle 1.20500 ( 6) covalent geometry : bond 0.00294 ( 8997) covalent geometry : angle 0.53036 (12190) *********************** 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 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.999 Fit side-chains REVERT: A 84 LEU cc_start: 0.8484 (mt) cc_final: 0.7978 (tp) REVERT: A 98 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6646 (tt) REVERT: A 155 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7071 (mp) REVERT: A 365 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7914 (ptm160) REVERT: A 442 PHE cc_start: 0.7521 (t80) cc_final: 0.7318 (t80) REVERT: C 242 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7853 (ttm-80) REVERT: C 245 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7948 (mp0) REVERT: C 313 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7686 (pmm-80) REVERT: B 23 LYS cc_start: 0.8343 (tttp) cc_final: 0.7934 (tppt) REVERT: B 198 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (pp) REVERT: B 215 GLU cc_start: 0.8538 (mp0) cc_final: 0.7701 (mp0) REVERT: B 217 MET cc_start: 0.8320 (ptt) cc_final: 0.8104 (ptt) REVERT: G 42 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8004 (mm-30) REVERT: G 58 GLU cc_start: 0.8551 (pm20) cc_final: 0.7975 (pm20) outliers start: 26 outliers final: 11 residues processed: 129 average time/residue: 1.5996 time to fit residues: 216.6054 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 313 ARG 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 S residue 91 THR Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085584 restraints weight = 11456.581| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.56 r_work: 0.2770 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2022 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= 0.132 Angle : 0.546 8.747 12196 Z= 0.286 Chirality : 0.043 0.147 1390 Planarity : 0.004 0.039 1537 Dihedral : 4.092 20.904 1218 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.41 % Allowed : 14.12 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1114 helix: 1.50 (0.28), residues: 379 sheet: 0.38 (0.31), residues: 283 loop : -1.02 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE C 189 TYR 0.012 0.001 TYR S 190 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 388) hydrogen bonds : angle 4.24015 ( 1116) SS BOND : bond 0.00652 ( 3) SS BOND : angle 1.28339 ( 6) covalent geometry : bond 0.00316 ( 8997) covalent geometry : angle 0.54518 (12190) *********************** 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 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.321 Fit side-chains REVERT: A 84 LEU cc_start: 0.8545 (mt) cc_final: 0.8033 (tp) REVERT: A 98 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6649 (tt) REVERT: A 155 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 442 PHE cc_start: 0.7554 (t80) cc_final: 0.7347 (t80) REVERT: C 242 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.7917 (ttm-80) REVERT: C 245 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 313 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7712 (pmm-80) REVERT: B 23 LYS cc_start: 0.8344 (tttp) cc_final: 0.7936 (tppt) REVERT: B 198 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8374 (pp) REVERT: B 215 GLU cc_start: 0.8542 (mp0) cc_final: 0.7701 (mp0) REVERT: B 217 MET cc_start: 0.8333 (ptt) cc_final: 0.8102 (ptt) REVERT: B 254 ASP cc_start: 0.8229 (t70) cc_final: 0.7902 (t70) REVERT: G 42 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7992 (mm-30) REVERT: G 58 GLU cc_start: 0.8546 (pm20) cc_final: 0.7940 (pm20) REVERT: S 39 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8465 (tt0) outliers start: 23 outliers final: 11 residues processed: 126 average time/residue: 1.6344 time to fit residues: 216.9495 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 : 0.923 ------------------------------------------------------------------------------- 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 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 313 ARG 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 S residue 39 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.085812 restraints weight = 11496.888| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.57 r_work: 0.2774 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9000 Z= 0.125 Angle : 0.536 9.019 12196 Z= 0.280 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.048 1537 Dihedral : 4.059 20.643 1218 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.41 % Allowed : 15.17 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.36 (0.25), residues: 1114 helix: 1.54 (0.28), residues: 380 sheet: 0.47 (0.32), residues: 273 loop : -1.01 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE C 189 TYR 0.012 0.001 TYR S 190 ARG 0.013 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 388) hydrogen bonds : angle 4.21878 ( 1116) SS BOND : bond 0.00647 ( 3) SS BOND : angle 1.29789 ( 6) covalent geometry : bond 0.00298 ( 8997) covalent geometry : angle 0.53543 (12190) *********************** 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 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.057 Fit side-chains REVERT: A 84 LEU cc_start: 0.8550 (mt) cc_final: 0.8032 (tp) REVERT: A 98 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6645 (tt) REVERT: A 155 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7166 (mp) REVERT: A 442 PHE cc_start: 0.7547 (t80) cc_final: 0.7336 (t80) REVERT: C 242 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7944 (ttm-80) REVERT: C 245 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 313 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7746 (pmm-80) REVERT: B 23 LYS cc_start: 0.8350 (tttp) cc_final: 0.7935 (tppt) REVERT: B 198 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8369 (pp) REVERT: B 215 GLU cc_start: 0.8533 (mp0) cc_final: 0.7691 (mp0) REVERT: B 217 MET cc_start: 0.8321 (ptt) cc_final: 0.8074 (ptt) REVERT: B 234 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: B 254 ASP cc_start: 0.8237 (t70) cc_final: 0.7887 (t70) REVERT: G 42 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8055 (mm-30) REVERT: G 58 GLU cc_start: 0.8546 (pm20) cc_final: 0.7909 (pm20) REVERT: S 39 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: S 76 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7669 (pmtt) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 1.7110 time to fit residues: 232.9455 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 313 ARG 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 S residue 39 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085226 restraints weight = 11532.210| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.57 r_work: 0.2764 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9000 Z= 0.139 Angle : 0.556 9.148 12196 Z= 0.290 Chirality : 0.043 0.137 1390 Planarity : 0.004 0.052 1537 Dihedral : 4.101 21.302 1218 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.41 % Allowed : 15.59 % 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 (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: 0.37 (0.25), residues: 1114 helix: 1.57 (0.28), residues: 380 sheet: 0.46 (0.32), residues: 274 loop : -1.01 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE A 164 TYR 0.012 0.001 TYR S 190 ARG 0.015 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 388) hydrogen bonds : angle 4.22534 ( 1116) SS BOND : bond 0.00684 ( 3) SS BOND : angle 1.38700 ( 6) covalent geometry : bond 0.00336 ( 8997) covalent geometry : angle 0.55504 (12190) *********************** 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 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.012 Fit side-chains REVERT: A 84 LEU cc_start: 0.8552 (mt) cc_final: 0.8026 (tp) REVERT: A 98 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6647 (tt) REVERT: A 155 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7188 (mp) REVERT: C 242 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7957 (ttm-80) REVERT: C 245 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7920 (mp0) REVERT: C 313 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7778 (pmm-80) REVERT: B 23 LYS cc_start: 0.8358 (tttp) cc_final: 0.7941 (tppt) REVERT: B 198 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (pp) REVERT: B 215 GLU cc_start: 0.8536 (mp0) cc_final: 0.7692 (mp0) REVERT: B 234 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: B 254 ASP cc_start: 0.8286 (t70) cc_final: 0.7894 (t70) REVERT: G 42 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8056 (mm-30) REVERT: G 58 GLU cc_start: 0.8552 (pm20) cc_final: 0.7939 (pm20) REVERT: S 39 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8550 (tt0) outliers start: 23 outliers final: 14 residues processed: 126 average time/residue: 1.6612 time to fit residues: 219.5377 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 313 ARG 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 S residue 39 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 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 = 0.3525 r_free = 0.3525 target = 0.129833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.085774 restraints weight = 11498.494| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.56 r_work: 0.2771 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2112 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 : 0.545 9.255 12196 Z= 0.284 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.065 1537 Dihedral : 4.071 21.085 1218 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.41 % Allowed : 15.69 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.25), residues: 1114 helix: 1.60 (0.28), residues: 381 sheet: 0.49 (0.32), residues: 273 loop : -1.00 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 164 TYR 0.012 0.001 TYR S 190 ARG 0.016 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 388) hydrogen bonds : angle 4.20248 ( 1116) SS BOND : bond 0.00653 ( 3) SS BOND : angle 1.35510 ( 6) covalent geometry : bond 0.00309 ( 8997) covalent geometry : angle 0.54402 (12190) ********************** 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 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.992 Fit side-chains REVERT: A 84 LEU cc_start: 0.8541 (mt) cc_final: 0.8020 (tp) REVERT: A 98 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6601 (tt) REVERT: A 155 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 245 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7908 (mp0) REVERT: C 313 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7782 (pmm-80) REVERT: B 23 LYS cc_start: 0.8346 (tttp) cc_final: 0.7930 (tppt) REVERT: B 198 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (pp) REVERT: B 215 GLU cc_start: 0.8536 (mp0) cc_final: 0.7725 (mp0) REVERT: B 234 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: B 254 ASP cc_start: 0.8284 (t70) cc_final: 0.7910 (t70) REVERT: G 42 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8045 (mm-30) REVERT: G 58 GLU cc_start: 0.8548 (pm20) cc_final: 0.7930 (pm20) REVERT: S 39 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: S 116 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (t) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 1.6080 time to fit residues: 214.4713 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 313 ARG 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 S residue 39 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3520 r_free = 0.3520 target = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085288 restraints weight = 11526.661| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.56 r_work: 0.2767 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9000 Z= 0.141 Angle : 0.564 9.178 12196 Z= 0.294 Chirality : 0.043 0.138 1390 Planarity : 0.004 0.067 1537 Dihedral : 4.113 21.532 1218 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.51 % Allowed : 15.79 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1114 helix: 1.60 (0.28), residues: 381 sheet: 0.46 (0.32), residues: 274 loop : -1.02 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 164 TYR 0.012 0.001 TYR S 190 ARG 0.016 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 388) hydrogen bonds : angle 4.21356 ( 1116) SS BOND : bond 0.00677 ( 3) SS BOND : angle 1.36813 ( 6) covalent geometry : bond 0.00340 ( 8997) covalent geometry : angle 0.56295 (12190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7519.79 seconds wall clock time: 129 minutes 48.65 seconds (7788.65 seconds total)