Starting phenix.real_space_refine on Mon May 4 17:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.map" model { file = "/net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9z_63973/05_2026/9u9z_63973.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 7194 2.51 5 N 1893 2.21 5 O 1958 1.98 5 H 11359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22452 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4059 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain: "B" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3995 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain: "C" Number of atoms: 10318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 10318 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 35, 'TRANS': 624} Chain: "D" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4080 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Time building chain proxies: 3.72, per 1000 atoms: 0.17 Number of scatterers: 22452 At special positions: 0 Unit cell: (88.81, 89.88, 151.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1958 8.00 N 1893 7.00 C 7194 6.00 H 11359 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.20 Conformation dependent library (CDL) restraints added in 773.4 milliseconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 57.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.704A pdb=" N ASN A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 114 removed outlier: 4.306A pdb=" N SER A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 145 removed outlier: 3.738A pdb=" N TRP A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 146 through 173 removed outlier: 3.616A pdb=" N THR A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.801A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.541A pdb=" N ARG A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 197 through 227 removed outlier: 3.533A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 4.011A pdb=" N ILE A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.636A pdb=" N TRP A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 275 Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 82 through 114 removed outlier: 4.269A pdb=" N ILE B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Proline residue: B 123 - end of helix removed outlier: 3.854A pdb=" N THR B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.608A pdb=" N TRP B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 152 through 160 removed outlier: 4.064A pdb=" N THR B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 173 removed outlier: 3.583A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 224 removed outlier: 4.561A pdb=" N ILE B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Proline residue: B 199 - end of helix Proline residue: B 203 - end of helix removed outlier: 3.672A pdb=" N LEU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 248 through 274 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.706A pdb=" N ALA C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.684A pdb=" N ASP C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 removed outlier: 3.830A pdb=" N VAL C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 188 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 241 through 266 removed outlier: 3.857A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.656A pdb=" N GLU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.605A pdb=" N ILE C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 4.710A pdb=" N MET C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 378 removed outlier: 3.741A pdb=" N TYR C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 406 through 419 removed outlier: 3.506A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.861A pdb=" N VAL C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 462 removed outlier: 3.557A pdb=" N ASN C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 Processing helix chain 'C' and resid 493 through 513 removed outlier: 3.725A pdb=" N ASP C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.511A pdb=" N SER C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.134A pdb=" N HIS C 538 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 584 removed outlier: 3.519A pdb=" N HIS C 574 " --> pdb=" O SER C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 602 through 614 removed outlier: 3.723A pdb=" N PHE C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.452A pdb=" N ARG C 622 " --> pdb=" O THR C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.587A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.601A pdb=" N ALA D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 removed outlier: 4.291A pdb=" N ILE D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.450A pdb=" N GLN D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 3.897A pdb=" N GLU D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.698A pdb=" N MET D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 11 removed outlier: 6.909A pdb=" N ASP C 8 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 29 " --> pdb=" O ASP C 8 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL C 10 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.352A pdb=" N GLY C 42 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER C 39 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU C 212 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 41 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE C 209 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 223 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET C 211 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 282 through 284 removed outlier: 7.146A pdb=" N ILE C 283 " --> pdb=" O VAL C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 333 through 337 removed outlier: 6.656A pdb=" N LYS C 481 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR C 360 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 399 through 400 removed outlier: 3.603A pdb=" N ALA C 367 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 3.544A pdb=" N GLU D 81 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL D 27 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 79 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.910A pdb=" N LEU D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 84 529 hydrogen bonds defined for protein. 1551 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: 4.80 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11347 1.03 - 1.23: 63 1.23 - 1.43: 4568 1.43 - 1.62: 6648 1.62 - 1.82: 84 Bond restraints: 22710 Sorted by residual: bond pdb=" CB PRO B 30 " pdb=" CG PRO B 30 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.18e+00 bond pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.89e+00 bond pdb=" CA GLU C 164 " pdb=" CB GLU C 164 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.31e+00 bond pdb=" CA ILE B 174 " pdb=" CB ILE B 174 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CA GLU C 164 " pdb=" C GLU C 164 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.29e-01 ... (remaining 22705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 41080 2.40 - 4.81: 179 4.81 - 7.21: 4 7.21 - 9.62: 0 9.62 - 12.02: 2 Bond angle restraints: 41265 Sorted by residual: angle pdb=" CA PRO B 30 " pdb=" N PRO B 30 " pdb=" CD PRO B 30 " ideal model delta sigma weight residual 112.00 99.98 12.02 1.40e+00 5.10e-01 7.37e+01 angle pdb=" N ILE C 464 " pdb=" CA ILE C 464 " pdb=" C ILE C 464 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" N LEU B 50 " pdb=" CA LEU B 50 " pdb=" CB LEU B 50 " ideal model delta sigma weight residual 114.17 110.39 3.78 1.14e+00 7.69e-01 1.10e+01 angle pdb=" CA LEU B 29 " pdb=" CB LEU B 29 " pdb=" CG LEU B 29 " ideal model delta sigma weight residual 116.30 127.36 -11.06 3.50e+00 8.16e-02 9.99e+00 angle pdb=" N THR D 153 " pdb=" CA THR D 153 " pdb=" C THR D 153 " ideal model delta sigma weight residual 113.18 108.98 4.20 1.33e+00 5.65e-01 9.98e+00 ... (remaining 41260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9129 17.95 - 35.91: 1016 35.91 - 53.86: 350 53.86 - 71.82: 78 71.82 - 89.77: 14 Dihedral angle restraints: 10587 sinusoidal: 5815 harmonic: 4772 Sorted by residual: dihedral pdb=" CA LEU B 29 " pdb=" C LEU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLY B 234 " pdb=" C GLY B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO C 231 " pdb=" C PRO C 231 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 10584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1185 0.031 - 0.061: 378 0.061 - 0.092: 131 0.092 - 0.122: 74 0.122 - 0.153: 14 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CG LEU B 29 " pdb=" CB LEU B 29 " pdb=" CD1 LEU B 29 " pdb=" CD2 LEU B 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE D 171 " pdb=" N ILE D 171 " pdb=" C ILE D 171 " pdb=" CB ILE D 171 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1779 not shown) Planarity restraints: 3295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 29 " 0.099 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO B 30 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 244 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR C 244 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR C 244 " 0.021 2.00e-02 2.50e+03 pdb=" N SER C 245 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 31 " -0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO D 32 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " -0.044 5.00e-02 4.00e+02 ... (remaining 3292 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1391 2.19 - 2.79: 45482 2.79 - 3.39: 63944 3.39 - 4.00: 82062 4.00 - 4.60: 128143 Nonbonded interactions: 321022 Sorted by model distance: nonbonded pdb=" O ILE B 109 " pdb=" HG1 THR B 113 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP C 471 " pdb=" HE2 HIS C 478 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASN A 114 " pdb=" H ILE A 117 " model vdw 1.596 2.450 nonbonded pdb=" H GLY C 365 " pdb=" OD2 ASP C 471 " model vdw 1.609 2.450 nonbonded pdb=" O ALA D 222 " pdb="HH12 ARG D 248 " model vdw 1.614 2.450 ... (remaining 321017 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 27 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name C \ Z2 or name CZ3 or name CH2 or name HA or name HB2 or name HB3 or name HD1 or nam \ e HE1 or name HE3 or name HZ2 or name HZ3 or name HH2)) or resid 28 through 274) \ ) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 11351 Z= 0.124 Angle : 0.595 12.020 15451 Z= 0.322 Chirality : 0.040 0.153 1782 Planarity : 0.005 0.140 1959 Dihedral : 17.732 89.773 4137 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.42 % Allowed : 28.98 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1409 helix: 0.87 (0.20), residues: 724 sheet: -1.44 (0.58), residues: 84 loop : -1.94 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 458 TYR 0.018 0.001 TYR C 252 PHE 0.014 0.001 PHE A 73 TRP 0.008 0.001 TRP C 92 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00274 (11351) covalent geometry : angle 0.59496 (15451) hydrogen bonds : bond 0.15807 ( 529) hydrogen bonds : angle 5.76603 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 165 average time/residue: 0.2219 time to fit residues: 53.0952 Evaluate side-chains 163 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 243 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107543 restraints weight = 50629.276| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.80 r_work: 0.3243 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11351 Z= 0.192 Angle : 0.593 9.939 15451 Z= 0.309 Chirality : 0.041 0.150 1782 Planarity : 0.005 0.076 1959 Dihedral : 4.899 53.415 1530 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.44 % Allowed : 25.53 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1409 helix: 0.64 (0.19), residues: 752 sheet: -1.82 (0.54), residues: 83 loop : -2.07 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 248 TYR 0.013 0.001 TYR D 259 PHE 0.014 0.001 PHE A 73 TRP 0.010 0.001 TRP C 343 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00433 (11351) covalent geometry : angle 0.59271 (15451) hydrogen bonds : bond 0.05013 ( 529) hydrogen bonds : angle 4.98615 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 463 ASN cc_start: 0.8308 (m-40) cc_final: 0.7447 (t0) REVERT: C 602 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7670 (mmm-85) outliers start: 29 outliers final: 18 residues processed: 189 average time/residue: 0.2160 time to fit residues: 59.3984 Evaluate side-chains 186 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107709 restraints weight = 50383.264| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.80 r_work: 0.3247 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11351 Z= 0.170 Angle : 0.574 9.077 15451 Z= 0.298 Chirality : 0.040 0.159 1782 Planarity : 0.005 0.063 1959 Dihedral : 4.874 52.025 1529 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.61 % Allowed : 25.02 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1409 helix: 0.59 (0.19), residues: 757 sheet: -1.84 (0.55), residues: 78 loop : -2.16 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 248 TYR 0.012 0.001 TYR A 204 PHE 0.015 0.001 PHE A 73 TRP 0.009 0.001 TRP C 343 HIS 0.003 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00388 (11351) covalent geometry : angle 0.57351 (15451) hydrogen bonds : bond 0.04609 ( 529) hydrogen bonds : angle 4.88175 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: B 59 MET cc_start: 0.7181 (ptt) cc_final: 0.6953 (ptt) REVERT: C 227 ASP cc_start: 0.8289 (t0) cc_final: 0.7978 (t0) REVERT: C 463 ASN cc_start: 0.8295 (m-40) cc_final: 0.7411 (t0) REVERT: C 602 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7675 (mmm-85) outliers start: 31 outliers final: 22 residues processed: 191 average time/residue: 0.2151 time to fit residues: 60.4146 Evaluate side-chains 187 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108451 restraints weight = 50344.985| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.80 r_work: 0.3254 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11351 Z= 0.138 Angle : 0.548 8.476 15451 Z= 0.282 Chirality : 0.040 0.144 1782 Planarity : 0.005 0.058 1959 Dihedral : 4.817 50.733 1529 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.70 % Allowed : 24.77 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.23), residues: 1409 helix: 0.69 (0.19), residues: 759 sheet: -1.83 (0.55), residues: 78 loop : -2.14 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.008 0.001 TYR A 204 PHE 0.014 0.001 PHE A 73 TRP 0.007 0.001 TRP C 343 HIS 0.003 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00317 (11351) covalent geometry : angle 0.54843 (15451) hydrogen bonds : bond 0.04081 ( 529) hydrogen bonds : angle 4.69250 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 ASP cc_start: 0.8491 (t0) cc_final: 0.8141 (t0) REVERT: C 230 ARG cc_start: 0.8470 (tpm170) cc_final: 0.8023 (tpm170) REVERT: C 463 ASN cc_start: 0.8381 (m-40) cc_final: 0.7455 (t0) REVERT: C 602 ARG cc_start: 0.8340 (mmm160) cc_final: 0.8025 (tpp80) outliers start: 32 outliers final: 26 residues processed: 198 average time/residue: 0.2272 time to fit residues: 65.0909 Evaluate side-chains 194 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN C 516 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108791 restraints weight = 49833.107| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.78 r_work: 0.3259 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11351 Z= 0.138 Angle : 0.550 8.097 15451 Z= 0.281 Chirality : 0.040 0.144 1782 Planarity : 0.004 0.053 1959 Dihedral : 4.632 48.087 1527 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.29 % Allowed : 23.76 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1409 helix: 0.72 (0.19), residues: 760 sheet: -1.83 (0.55), residues: 78 loop : -2.11 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 248 TYR 0.008 0.001 TYR C 252 PHE 0.014 0.001 PHE A 73 TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00317 (11351) covalent geometry : angle 0.55032 (15451) hydrogen bonds : bond 0.03949 ( 529) hydrogen bonds : angle 4.61396 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: C 227 ASP cc_start: 0.8507 (t0) cc_final: 0.8137 (t0) REVERT: C 230 ARG cc_start: 0.8439 (tpm170) cc_final: 0.7996 (tpm170) REVERT: C 463 ASN cc_start: 0.8437 (m-40) cc_final: 0.7535 (t0) REVERT: C 602 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7991 (tpp80) outliers start: 39 outliers final: 29 residues processed: 196 average time/residue: 0.2197 time to fit residues: 62.7741 Evaluate side-chains 197 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 120 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106891 restraints weight = 50339.637| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.78 r_work: 0.3235 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11351 Z= 0.185 Angle : 0.573 7.652 15451 Z= 0.296 Chirality : 0.041 0.147 1782 Planarity : 0.005 0.049 1959 Dihedral : 4.710 47.940 1527 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.12 % Allowed : 24.52 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1409 helix: 0.64 (0.19), residues: 762 sheet: -1.94 (0.55), residues: 78 loop : -2.17 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 248 TYR 0.017 0.001 TYR B 241 PHE 0.015 0.001 PHE A 73 TRP 0.008 0.001 TRP C 475 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00424 (11351) covalent geometry : angle 0.57332 (15451) hydrogen bonds : bond 0.04075 ( 529) hydrogen bonds : angle 4.66419 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7824 (mt0) cc_final: 0.7620 (mt0) REVERT: B 224 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: C 227 ASP cc_start: 0.8516 (t0) cc_final: 0.8121 (t0) REVERT: C 461 MET cc_start: 0.8126 (ptt) cc_final: 0.7904 (ptt) REVERT: C 463 ASN cc_start: 0.8403 (m-40) cc_final: 0.7478 (t0) REVERT: C 602 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7613 (mmm-85) outliers start: 37 outliers final: 29 residues processed: 191 average time/residue: 0.2387 time to fit residues: 65.0019 Evaluate side-chains 191 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 114 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108233 restraints weight = 50283.281| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.79 r_work: 0.3252 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11351 Z= 0.133 Angle : 0.550 7.705 15451 Z= 0.281 Chirality : 0.040 0.155 1782 Planarity : 0.004 0.047 1959 Dihedral : 4.657 46.820 1527 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.20 % Allowed : 24.18 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1409 helix: 0.72 (0.19), residues: 762 sheet: -1.95 (0.55), residues: 78 loop : -2.15 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 266 TYR 0.009 0.001 TYR B 241 PHE 0.015 0.001 PHE A 73 TRP 0.008 0.001 TRP C 92 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00309 (11351) covalent geometry : angle 0.54993 (15451) hydrogen bonds : bond 0.03874 ( 529) hydrogen bonds : angle 4.56196 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7725 (mt0) cc_final: 0.7507 (mt0) REVERT: B 224 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: C 230 ARG cc_start: 0.8395 (tpm170) cc_final: 0.7985 (tpm170) REVERT: C 461 MET cc_start: 0.8063 (ptt) cc_final: 0.7825 (ptt) REVERT: C 463 ASN cc_start: 0.8275 (m-40) cc_final: 0.7422 (t0) REVERT: C 602 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7983 (tpp80) outliers start: 38 outliers final: 30 residues processed: 193 average time/residue: 0.2465 time to fit residues: 69.3517 Evaluate side-chains 197 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 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 = 0.3845 r_free = 0.3845 target = 0.142680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109382 restraints weight = 49644.877| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.76 r_work: 0.3272 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11351 Z= 0.112 Angle : 0.538 7.960 15451 Z= 0.274 Chirality : 0.040 0.148 1782 Planarity : 0.004 0.046 1959 Dihedral : 4.580 45.964 1527 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.86 % Allowed : 24.85 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1409 helix: 0.83 (0.19), residues: 762 sheet: -1.97 (0.56), residues: 80 loop : -2.09 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 115 TYR 0.008 0.001 TYR C 252 PHE 0.014 0.001 PHE A 73 TRP 0.011 0.001 TRP C 475 HIS 0.002 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00260 (11351) covalent geometry : angle 0.53775 (15451) hydrogen bonds : bond 0.03696 ( 529) hydrogen bonds : angle 4.45633 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7717 (mt0) cc_final: 0.7487 (mt0) REVERT: B 224 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: C 230 ARG cc_start: 0.8486 (tpm170) cc_final: 0.8078 (tpm170) REVERT: C 399 MET cc_start: 0.8790 (mtp) cc_final: 0.8311 (mtt) REVERT: C 461 MET cc_start: 0.8099 (ptt) cc_final: 0.7874 (ptt) REVERT: C 463 ASN cc_start: 0.8347 (m-40) cc_final: 0.7497 (t0) REVERT: C 602 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8017 (tpp80) outliers start: 34 outliers final: 30 residues processed: 194 average time/residue: 0.2303 time to fit residues: 65.0116 Evaluate side-chains 202 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 210 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 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 = 0.3847 r_free = 0.3847 target = 0.142808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109386 restraints weight = 49828.902| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.78 r_work: 0.3271 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11351 Z= 0.116 Angle : 0.534 7.832 15451 Z= 0.271 Chirality : 0.040 0.146 1782 Planarity : 0.004 0.045 1959 Dihedral : 4.552 45.756 1527 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.61 % Allowed : 25.02 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1409 helix: 0.86 (0.19), residues: 761 sheet: -1.94 (0.56), residues: 80 loop : -2.06 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.008 0.001 TYR C 252 PHE 0.016 0.001 PHE C 374 TRP 0.011 0.001 TRP C 475 HIS 0.003 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00269 (11351) covalent geometry : angle 0.53419 (15451) hydrogen bonds : bond 0.03666 ( 529) hydrogen bonds : angle 4.43664 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7725 (mt0) cc_final: 0.7485 (mt0) REVERT: B 190 GLN cc_start: 0.8034 (tt0) cc_final: 0.7794 (tm-30) REVERT: B 224 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: C 230 ARG cc_start: 0.8495 (tpm170) cc_final: 0.8086 (tpm170) REVERT: C 286 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8538 (m) REVERT: C 399 MET cc_start: 0.8757 (mtp) cc_final: 0.8257 (mtt) REVERT: C 461 MET cc_start: 0.8078 (ptt) cc_final: 0.7854 (ptt) REVERT: C 463 ASN cc_start: 0.8336 (m-40) cc_final: 0.7518 (t0) REVERT: C 602 ARG cc_start: 0.8363 (mmm160) cc_final: 0.8019 (tpp80) outliers start: 31 outliers final: 27 residues processed: 193 average time/residue: 0.2224 time to fit residues: 63.7480 Evaluate side-chains 198 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 52 optimal weight: 0.0010 chunk 90 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 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 = 0.3860 r_free = 0.3860 target = 0.143794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110473 restraints weight = 49950.224| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.79 r_work: 0.3288 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.002 0.027 11351 Z= 0.101 Angle : 0.528 7.944 15451 Z= 0.267 Chirality : 0.040 0.145 1782 Planarity : 0.004 0.045 1959 Dihedral : 4.485 45.027 1527 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.44 % Allowed : 25.19 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1409 helix: 0.95 (0.19), residues: 761 sheet: -1.86 (0.56), residues: 80 loop : -2.00 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.008 0.001 TYR C 252 PHE 0.013 0.001 PHE A 73 TRP 0.014 0.001 TRP C 475 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00233 (11351) covalent geometry : angle 0.52790 (15451) hydrogen bonds : bond 0.03525 ( 529) hydrogen bonds : angle 4.36310 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7649 (mt0) cc_final: 0.7400 (mt0) REVERT: B 119 LYS cc_start: 0.8859 (tppt) cc_final: 0.8605 (tppt) REVERT: B 224 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: C 230 ARG cc_start: 0.8408 (tpm170) cc_final: 0.8024 (tpm170) REVERT: C 399 MET cc_start: 0.8640 (mtp) cc_final: 0.8116 (mtt) REVERT: C 461 MET cc_start: 0.8054 (ptt) cc_final: 0.7830 (ptt) REVERT: C 463 ASN cc_start: 0.8177 (m-40) cc_final: 0.7495 (t0) REVERT: C 602 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7997 (tpp80) outliers start: 29 outliers final: 24 residues processed: 200 average time/residue: 0.2116 time to fit residues: 62.7808 Evaluate side-chains 199 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 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 = 0.3849 r_free = 0.3849 target = 0.142941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109705 restraints weight = 49885.071| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.75 r_work: 0.3275 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11351 Z= 0.125 Angle : 0.539 7.768 15451 Z= 0.274 Chirality : 0.040 0.152 1782 Planarity : 0.004 0.044 1959 Dihedral : 4.488 45.075 1527 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.53 % Allowed : 25.27 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1409 helix: 1.00 (0.19), residues: 755 sheet: -1.90 (0.56), residues: 80 loop : -1.98 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 248 TYR 0.024 0.001 TYR C 252 PHE 0.013 0.001 PHE A 73 TRP 0.014 0.001 TRP C 475 HIS 0.003 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00291 (11351) covalent geometry : angle 0.53924 (15451) hydrogen bonds : bond 0.03595 ( 529) hydrogen bonds : angle 4.38523 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4969.65 seconds wall clock time: 85 minutes 5.64 seconds (5105.64 seconds total)