Starting phenix.real_space_refine on Thu Mar 13 03:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.map" model { file = "/net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id4_35357/03_2025/8id4_35357.cif" } resolution = 3.1 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= 0.016 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 58 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1761 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2572 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 404 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1733 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.45, per 1000 atoms: 0.63 Number of scatterers: 8665 At special positions: 0 Unit cell: (106.47, 127.764, 113.568, 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 58 16.00 O 1590 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'R' and resid 38 through 69 removed outlier: 3.619A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 90 removed outlier: 3.635A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 4.018A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 112 removed outlier: 3.691A pdb=" N HIS R 112 " --> pdb=" O VAL R 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 109 through 112' Processing helix chain 'R' and resid 113 through 142 Processing helix chain 'R' and resid 152 through 171 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 201 through 216 removed outlier: 3.662A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR R 213 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.663A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 294 removed outlier: 3.864A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.849A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 321 removed outlier: 3.867A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.546A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.681A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.198A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.613A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.655A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.938A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.546A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.636A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.093A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.638A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.850A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A 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: 6.516A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.937A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.557A 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: 6.420A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.692A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 removed outlier: 3.522A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.792A pdb=" N GLU S 247 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1191 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: 2.64 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2378 1.33 - 1.45: 1616 1.45 - 1.57: 4759 1.57 - 1.70: 2 1.70 - 1.82: 83 Bond restraints: 8838 Sorted by residual: bond pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA PHE R 88 " pdb=" C PHE R 88 " ideal model delta sigma weight residual 1.524 1.584 -0.061 1.27e-02 6.20e+03 2.28e+01 bond pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.20e-02 6.94e+03 1.55e+01 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.23e-02 6.61e+03 8.84e+00 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11810 2.46 - 4.92: 147 4.92 - 7.38: 31 7.38 - 9.84: 2 9.84 - 12.29: 2 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ALA A 326 " pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 108.38 120.67 -12.29 1.35e+00 5.49e-01 8.29e+01 angle pdb=" N SER R 244 " pdb=" CA SER R 244 " pdb=" C SER R 244 " ideal model delta sigma weight residual 110.28 100.09 10.19 1.48e+00 4.57e-01 4.74e+01 angle pdb=" N ARG R 69 " pdb=" CA ARG R 69 " pdb=" C ARG R 69 " ideal model delta sigma weight residual 112.90 106.20 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" N SER R 90 " pdb=" CA SER R 90 " pdb=" C SER R 90 " ideal model delta sigma weight residual 112.34 105.71 6.63 1.30e+00 5.92e-01 2.60e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 111.44 117.93 -6.49 1.34e+00 5.57e-01 2.34e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4753 16.82 - 33.64: 377 33.64 - 50.46: 68 50.46 - 67.29: 10 67.29 - 84.11: 9 Dihedral angle restraints: 5217 sinusoidal: 1934 harmonic: 3283 Sorted by residual: dihedral pdb=" C THR A 327 " pdb=" N THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual -122.00 -145.78 23.78 0 2.50e+00 1.60e-01 9.05e+01 dihedral pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N TRP R 299 " pdb=" CA TRP R 299 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 1391 0.171 - 0.342: 8 0.342 - 0.514: 0 0.514 - 0.685: 0 0.685 - 0.856: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 1.67 0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" CB ILE R 197 " pdb=" CA ILE R 197 " pdb=" CG1 ILE R 197 " pdb=" CG2 ILE R 197 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER R 244 " pdb=" N SER R 244 " pdb=" C SER R 244 " pdb=" CB SER R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1397 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO R 172 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 324 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C THR A 324 " -0.054 2.00e-02 2.50e+03 pdb=" O THR A 324 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO S 14 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.041 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1199 2.75 - 3.29: 8068 3.29 - 3.83: 13913 3.83 - 4.36: 16869 4.36 - 4.90: 30336 Nonbonded interactions: 70385 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 176 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 3.040 ... (remaining 70380 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: 0.390 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.004 0.095 8838 Z= 0.275 Angle : 0.732 12.295 11992 Z= 0.427 Chirality : 0.053 0.856 1400 Planarity : 0.005 0.078 1508 Dihedral : 12.922 84.108 3088 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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: -1.06 (0.25), residues: 1112 helix: 0.33 (0.28), residues: 370 sheet: -0.43 (0.31), residues: 276 loop : -1.68 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.002 PHE R 25 TYR 0.024 0.001 TYR S 176 ARG 0.012 0.001 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.907 Fit side-chains REVERT: A 28 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 134 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7575 (ptt-90) REVERT: B 221 THR cc_start: 0.8845 (t) cc_final: 0.8308 (m) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2583 time to fit residues: 45.6070 Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 0.4980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 ASN A 306 GLN B 17 GLN B 91 HIS S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132494 restraints weight = 9276.671| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.28 r_work: 0.3061 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8838 Z= 0.181 Angle : 0.552 7.948 11992 Z= 0.296 Chirality : 0.042 0.233 1400 Planarity : 0.004 0.063 1508 Dihedral : 5.476 70.342 1227 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 1.10 % Allowed : 6.91 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.62 (0.25), residues: 1112 helix: 0.83 (0.28), residues: 376 sheet: -0.18 (0.29), residues: 278 loop : -1.60 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 207 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.001 PHE R 25 TYR 0.016 0.001 TYR S 176 ARG 0.005 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.895 Fit side-chains REVERT: A 28 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 29 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7545 (tttp) REVERT: A 197 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8057 (mmtt) REVERT: B 17 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7219 (pp30) REVERT: B 217 MET cc_start: 0.8304 (ppp) cc_final: 0.8078 (ppp) REVERT: S 82 GLN cc_start: 0.7716 (tp40) cc_final: 0.6385 (mp10) outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.2482 time to fit residues: 44.0047 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 0.0020 chunk 24 optimal weight: 6.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125857 restraints weight = 9497.373| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.74 r_work: 0.2979 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8838 Z= 0.329 Angle : 0.604 7.855 11992 Z= 0.322 Chirality : 0.045 0.224 1400 Planarity : 0.005 0.064 1508 Dihedral : 5.543 70.220 1227 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 1.54 % Allowed : 9.87 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.65 (0.24), residues: 1112 helix: 0.81 (0.27), residues: 375 sheet: -0.22 (0.29), residues: 285 loop : -1.61 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.002 TYR S 176 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.893 Fit side-chains REVERT: A 28 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 17 GLN cc_start: 0.7895 (pp30) cc_final: 0.7633 (pp30) REVERT: B 217 MET cc_start: 0.8304 (ppp) cc_final: 0.7918 (ptm) REVERT: B 325 MET cc_start: 0.8974 (mtt) cc_final: 0.8587 (mtm) REVERT: S 82 GLN cc_start: 0.7816 (tp40) cc_final: 0.6438 (mp10) outliers start: 14 outliers final: 11 residues processed: 131 average time/residue: 0.2419 time to fit residues: 41.9922 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.169244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128752 restraints weight = 9390.931| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.97 r_work: 0.3019 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8838 Z= 0.158 Angle : 0.505 6.933 11992 Z= 0.271 Chirality : 0.041 0.232 1400 Planarity : 0.004 0.056 1508 Dihedral : 5.184 70.434 1227 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 1.75 % Allowed : 11.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.26 (0.25), residues: 1112 helix: 1.27 (0.28), residues: 373 sheet: 0.02 (0.29), residues: 277 loop : -1.51 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 207 HIS 0.003 0.001 HIS A 188 PHE 0.021 0.001 PHE R 25 TYR 0.012 0.001 TYR S 191 ARG 0.004 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.895 Fit side-chains REVERT: A 28 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 217 MET cc_start: 0.8316 (ppp) cc_final: 0.7848 (ptm) REVERT: S 46 GLU cc_start: 0.8415 (tt0) cc_final: 0.8215 (tt0) REVERT: S 82 GLN cc_start: 0.7853 (tp40) cc_final: 0.6555 (mp10) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.2965 time to fit residues: 49.5580 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129705 restraints weight = 9304.787| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.82 r_work: 0.2984 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8838 Z= 0.209 Angle : 0.520 6.673 11992 Z= 0.279 Chirality : 0.042 0.237 1400 Planarity : 0.004 0.057 1508 Dihedral : 5.208 70.703 1227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 1.86 % Allowed : 12.28 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.25), residues: 1112 helix: 1.26 (0.27), residues: 377 sheet: 0.02 (0.29), residues: 285 loop : -1.38 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.020 0.001 PHE R 25 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.887 Fit side-chains REVERT: A 28 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8073 (mt-10) REVERT: B 217 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7899 (ptm) REVERT: S 46 GLU cc_start: 0.8441 (tt0) cc_final: 0.8241 (tt0) REVERT: S 82 GLN cc_start: 0.7736 (tp40) cc_final: 0.6413 (mp10) outliers start: 17 outliers final: 13 residues processed: 127 average time/residue: 0.2433 time to fit residues: 41.6239 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125987 restraints weight = 9321.675| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.03 r_work: 0.2967 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8838 Z= 0.275 Angle : 0.549 6.142 11992 Z= 0.295 Chirality : 0.043 0.250 1400 Planarity : 0.004 0.060 1508 Dihedral : 5.317 70.695 1227 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.41 % Allowed : 12.94 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.25), residues: 1112 helix: 1.22 (0.27), residues: 377 sheet: 0.10 (0.29), residues: 280 loop : -1.40 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.002 PHE B 151 TYR 0.011 0.001 TYR S 191 ARG 0.006 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8120 (mt-10) REVERT: A 197 LYS cc_start: 0.8540 (mttm) cc_final: 0.8189 (mttp) REVERT: A 309 ASP cc_start: 0.7885 (m-30) cc_final: 0.7669 (m-30) REVERT: S 82 GLN cc_start: 0.7759 (tp40) cc_final: 0.6408 (mp10) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.2255 time to fit residues: 39.8329 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132973 restraints weight = 9352.373| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.59 r_work: 0.3070 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8838 Z= 0.136 Angle : 0.483 6.137 11992 Z= 0.260 Chirality : 0.041 0.268 1400 Planarity : 0.004 0.053 1508 Dihedral : 5.024 70.911 1227 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.12 (0.25), residues: 1112 helix: 1.56 (0.28), residues: 378 sheet: 0.15 (0.29), residues: 283 loop : -1.25 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE R 25 TYR 0.012 0.001 TYR S 191 ARG 0.008 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.990 Fit side-chains REVERT: A 28 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 197 LYS cc_start: 0.8536 (mttm) cc_final: 0.8198 (mttp) REVERT: A 270 LYS cc_start: 0.8677 (mttt) cc_final: 0.8422 (mtmm) REVERT: B 221 THR cc_start: 0.8976 (t) cc_final: 0.8316 (m) REVERT: B 258 ASP cc_start: 0.6847 (t70) cc_final: 0.6584 (t70) REVERT: S 82 GLN cc_start: 0.7835 (tp40) cc_final: 0.6608 (mp10) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.2556 time to fit residues: 42.7121 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.167310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126717 restraints weight = 9456.336| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.06 r_work: 0.2955 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8838 Z= 0.364 Angle : 0.599 7.558 11992 Z= 0.320 Chirality : 0.045 0.226 1400 Planarity : 0.005 0.063 1508 Dihedral : 5.428 71.542 1227 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.75 % Allowed : 14.14 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.25), residues: 1112 helix: 1.28 (0.27), residues: 376 sheet: 0.09 (0.29), residues: 286 loop : -1.38 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.002 PHE S 29 TYR 0.011 0.002 TYR B 85 ARG 0.008 0.001 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.985 Fit side-chains REVERT: A 28 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8122 (mt-10) REVERT: A 197 LYS cc_start: 0.8513 (mttm) cc_final: 0.8181 (mttp) REVERT: A 309 ASP cc_start: 0.7890 (m-30) cc_final: 0.7687 (m-30) REVERT: B 217 MET cc_start: 0.8273 (ptp) cc_final: 0.7881 (ptm) REVERT: S 82 GLN cc_start: 0.7756 (tp40) cc_final: 0.6423 (mp10) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.2200 time to fit residues: 37.4725 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128671 restraints weight = 9375.680| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.15 r_work: 0.3025 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8838 Z= 0.157 Angle : 0.497 6.896 11992 Z= 0.268 Chirality : 0.041 0.287 1400 Planarity : 0.004 0.056 1508 Dihedral : 5.110 71.822 1227 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.32 % Allowed : 14.91 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.10 (0.25), residues: 1112 helix: 1.57 (0.28), residues: 378 sheet: 0.17 (0.30), residues: 281 loop : -1.30 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.023 0.001 PHE R 25 TYR 0.011 0.001 TYR S 191 ARG 0.009 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.946 Fit side-chains REVERT: A 28 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 197 LYS cc_start: 0.8472 (mttm) cc_final: 0.8145 (mttp) REVERT: A 270 LYS cc_start: 0.8668 (mttt) cc_final: 0.8458 (mttm) REVERT: B 258 ASP cc_start: 0.6852 (t70) cc_final: 0.6579 (t70) REVERT: S 82 GLN cc_start: 0.7712 (tp40) cc_final: 0.6426 (mp10) outliers start: 12 outliers final: 11 residues processed: 122 average time/residue: 0.2453 time to fit residues: 39.9417 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 6.9990 chunk 23 optimal weight: 0.0060 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130421 restraints weight = 9393.518| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.09 r_work: 0.3032 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8838 Z= 0.187 Angle : 0.508 7.110 11992 Z= 0.273 Chirality : 0.042 0.272 1400 Planarity : 0.004 0.056 1508 Dihedral : 5.101 72.296 1227 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.43 % Allowed : 14.69 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.25), residues: 1112 helix: 1.62 (0.27), residues: 378 sheet: 0.19 (0.29), residues: 287 loop : -1.23 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.023 0.001 PHE R 25 TYR 0.011 0.001 TYR S 191 ARG 0.009 0.000 ARG R 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.973 Fit side-chains REVERT: A 28 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 197 LYS cc_start: 0.8498 (mttm) cc_final: 0.8168 (mttp) REVERT: A 270 LYS cc_start: 0.8692 (mttt) cc_final: 0.8421 (mtmm) REVERT: B 221 THR cc_start: 0.8979 (t) cc_final: 0.8378 (m) REVERT: B 258 ASP cc_start: 0.6872 (t70) cc_final: 0.6611 (t70) REVERT: S 82 GLN cc_start: 0.7830 (tp40) cc_final: 0.6426 (mp10) outliers start: 13 outliers final: 11 residues processed: 126 average time/residue: 0.2540 time to fit residues: 43.0548 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131251 restraints weight = 9367.327| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.67 r_work: 0.3140 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8838 Z= 0.213 Angle : 0.519 7.217 11992 Z= 0.278 Chirality : 0.042 0.260 1400 Planarity : 0.004 0.057 1508 Dihedral : 5.129 72.562 1227 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.43 % Allowed : 15.13 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1112 helix: 1.61 (0.27), residues: 378 sheet: 0.19 (0.29), residues: 289 loop : -1.23 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.023 0.001 PHE R 25 TYR 0.011 0.001 TYR S 191 ARG 0.009 0.000 ARG R 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.92 seconds wall clock time: 77 minutes 29.45 seconds (4649.45 seconds total)