Starting phenix.real_space_refine on Mon Jul 28 19:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcr_44435/07_2025/9bcr_44435.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 49 5.16 5 C 6876 2.51 5 N 1796 2.21 5 O 1874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10595 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2613 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2210 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 269} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2876 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2896 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 20, 'TRANS': 352} Time building chain proxies: 7.14, per 1000 atoms: 0.67 Number of scatterers: 10595 At special positions: 0 Unit cell: (82.524, 94.162, 141.772, 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 49 16.00 O 1874 8.00 N 1796 7.00 C 6876 6.00 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: 3.72 Conformation dependent library (CDL) restraints added in 2.5 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 51.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'H' and resid 37 through 50 Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.578A pdb=" N PHE H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 79 removed outlier: 3.779A pdb=" N TYR H 67 " --> pdb=" O TYR H 63 " (cutoff:3.500A) Proline residue: H 70 - end of helix removed outlier: 6.336A pdb=" N GLY H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.785A pdb=" N PHE H 91 " --> pdb=" O ILE H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'H' and resid 261 through 270 removed outlier: 4.070A pdb=" N PHE H 268 " --> pdb=" O PHE H 264 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP H 270 " --> pdb=" O ARG H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 307 Processing helix chain 'H' and resid 313 through 327 Proline residue: H 324 - end of helix Processing helix chain 'H' and resid 328 through 340 Processing helix chain 'H' and resid 346 through 355 Processing helix chain 'H' and resid 364 through 395 Proline residue: H 382 - end of helix Processing helix chain 'H' and resid 397 through 407 Processing helix chain 'H' and resid 409 through 417 Processing helix chain 'H' and resid 417 through 439 removed outlier: 3.593A pdb=" N LEU H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS H 424 " --> pdb=" O PRO H 420 " (cutoff:3.500A) Proline residue: H 425 - end of helix Proline residue: H 428 - end of helix Processing helix chain 'H' and resid 440 through 448 removed outlier: 4.170A pdb=" N ILE H 444 " --> pdb=" O ASN H 440 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 446 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 447 " --> pdb=" O LEU H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 477 Processing helix chain 'H' and resid 478 through 481 removed outlier: 3.535A pdb=" N GLY H 481 " --> pdb=" O GLY H 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 478 through 481' Processing helix chain 'H' and resid 483 through 488 Processing helix chain 'H' and resid 489 through 510 removed outlier: 4.275A pdb=" N PHE H 495 " --> pdb=" O ALA H 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 40 removed outlier: 4.101A pdb=" N ALA I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 3.547A pdb=" N SER I 38 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU I 39 " --> pdb=" O VAL I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 Processing helix chain 'I' and resid 80 through 112 removed outlier: 4.659A pdb=" N THR I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 130 removed outlier: 4.311A pdb=" N MET I 130 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 149 removed outlier: 4.524A pdb=" N GLU I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 155 removed outlier: 3.720A pdb=" N ILE I 154 " --> pdb=" O ILE I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 167 removed outlier: 3.976A pdb=" N VAL I 162 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 184 removed outlier: 3.988A pdb=" N HIS I 173 " --> pdb=" O GLY I 169 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 176 " --> pdb=" O LEU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 196 removed outlier: 4.690A pdb=" N GLU I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 206 Processing helix chain 'I' and resid 206 through 211 removed outlier: 3.740A pdb=" N LEU I 210 " --> pdb=" O VAL I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 228 Processing helix chain 'I' and resid 230 through 236 Processing helix chain 'I' and resid 259 through 270 Processing helix chain 'I' and resid 271 through 281 Processing helix chain 'C' and resid 38 through 51 removed outlier: 4.059A pdb=" N LYS C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 91 through 104 removed outlier: 5.748A pdb=" N GLY C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 165 through 184 Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.656A pdb=" N ALA C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 91 through 104 removed outlier: 5.714A pdb=" N GLY D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 121 Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 22 removed outlier: 6.434A pdb=" N LYS C 11 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 9 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 22 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 7 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN C 8 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP C 59 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 80 removed outlier: 6.131A pdb=" N GLY C 78 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C 155 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 190 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 157 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 31 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL C 205 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 33 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU C 207 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 35 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 204 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 215 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 206 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.510A pdb=" N ILE C 62 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.899A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR C 249 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN C 255 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 292 removed outlier: 6.555A pdb=" N HIS C 317 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 25 removed outlier: 6.585A pdb=" N VAL D 18 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA D 12 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS D 20 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 10 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE D 22 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL D 9 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER D 57 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 77 through 80 removed outlier: 6.341A pdb=" N GLY D 78 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASP D 158 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 80 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE D 155 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL D 190 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 157 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 32 " --> pdb=" O TYR D 189 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE D 31 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL D 205 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 33 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU D 207 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 35 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN D 214 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP D 208 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 265 through 269 removed outlier: 4.380A pdb=" N ALA D 248 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU D 257 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 246 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 354 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 291 through 292 removed outlier: 3.612A pdb=" N ILE D 345 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N HIS D 317 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 307 " --> pdb=" O GLN D 315 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN D 315 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN D 309 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1530 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: 4.29 Time building geometry restraints manager: 3.68 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: 2009 1.33 - 1.45: 2543 1.45 - 1.57: 6189 1.57 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 10830 Sorted by residual: bond pdb=" CG PRO I 273 " pdb=" CD PRO I 273 " ideal model delta sigma weight residual 1.503 1.207 0.296 3.40e-02 8.65e+02 7.56e+01 bond pdb=" N PRO I 273 " pdb=" CD PRO I 273 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.57e+01 bond pdb=" CB PRO I 273 " pdb=" CG PRO I 273 " ideal model delta sigma weight residual 1.492 1.679 -0.187 5.00e-02 4.00e+02 1.39e+01 bond pdb=" N PRO I 273 " pdb=" CA PRO I 273 " ideal model delta sigma weight residual 1.469 1.428 0.040 1.28e-02 6.10e+03 1.00e+01 bond pdb=" N VAL C 335 " pdb=" CA VAL C 335 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.22e-02 6.72e+03 7.47e+00 ... (remaining 10825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 14660 3.69 - 7.37: 67 7.37 - 11.06: 4 11.06 - 14.74: 2 14.74 - 18.43: 2 Bond angle restraints: 14735 Sorted by residual: angle pdb=" CA PRO I 273 " pdb=" N PRO I 273 " pdb=" CD PRO I 273 " ideal model delta sigma weight residual 112.00 93.57 18.43 1.40e+00 5.10e-01 1.73e+02 angle pdb=" N PRO I 273 " pdb=" CD PRO I 273 " pdb=" CG PRO I 273 " ideal model delta sigma weight residual 103.20 86.45 16.75 1.50e+00 4.44e-01 1.25e+02 angle pdb=" CA PRO I 273 " pdb=" CB PRO I 273 " pdb=" CG PRO I 273 " ideal model delta sigma weight residual 104.50 92.91 11.59 1.90e+00 2.77e-01 3.72e+01 angle pdb=" N PRO I 273 " pdb=" CA PRO I 273 " pdb=" CB PRO I 273 " ideal model delta sigma weight residual 103.25 97.74 5.51 1.05e+00 9.07e-01 2.76e+01 angle pdb=" N ARG H 454 " pdb=" CA ARG H 454 " pdb=" C ARG H 454 " ideal model delta sigma weight residual 110.59 104.56 6.03 1.45e+00 4.76e-01 1.73e+01 ... (remaining 14730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5583 17.95 - 35.90: 631 35.90 - 53.85: 165 53.85 - 71.80: 48 71.80 - 89.75: 11 Dihedral angle restraints: 6438 sinusoidal: 2509 harmonic: 3929 Sorted by residual: dihedral pdb=" CA MET C 260 " pdb=" C MET C 260 " pdb=" N PRO C 261 " pdb=" CA PRO C 261 " ideal model delta harmonic sigma weight residual -180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CD ARG H 454 " pdb=" NE ARG H 454 " pdb=" CZ ARG H 454 " pdb=" NH1 ARG H 454 " ideal model delta sinusoidal sigma weight residual 0.00 38.81 -38.81 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA GLN D 82 " pdb=" C GLN D 82 " pdb=" N SER D 83 " pdb=" CA SER D 83 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1224 0.041 - 0.083: 315 0.083 - 0.124: 157 0.124 - 0.165: 19 0.165 - 0.207: 6 Chirality restraints: 1721 Sorted by residual: chirality pdb=" CG LEU H 496 " pdb=" CB LEU H 496 " pdb=" CD1 LEU H 496 " pdb=" CD2 LEU H 496 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL D 335 " pdb=" N VAL D 335 " pdb=" C VAL D 335 " pdb=" CB VAL D 335 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA LEU H 466 " pdb=" N LEU H 466 " pdb=" C LEU H 466 " pdb=" CB LEU H 466 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1718 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 454 " 0.691 9.50e-02 1.11e+02 3.10e-01 5.84e+01 pdb=" NE ARG H 454 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG H 454 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 454 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 454 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 272 " -0.098 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO I 273 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO I 273 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO I 273 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 330 " 0.354 9.50e-02 1.11e+02 1.59e-01 1.54e+01 pdb=" NE ARG D 330 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 330 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 330 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 330 " 0.012 2.00e-02 2.50e+03 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 346 2.71 - 3.26: 10777 3.26 - 3.81: 17434 3.81 - 4.35: 20852 4.35 - 4.90: 35891 Nonbonded interactions: 85300 Sorted by model distance: nonbonded pdb=" O LEU C 164 " pdb=" NH1 ARG C 169 " model vdw 2.168 3.120 nonbonded pdb=" O LYS D 107 " pdb=" ND2 ASN D 111 " model vdw 2.212 3.120 nonbonded pdb=" N GLN H 99 " pdb=" OE1 GLN H 99 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR H 97 " pdb=" OD1 ASN H 98 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP I 71 " pdb=" N GLY I 72 " model vdw 2.293 3.120 ... (remaining 85295 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 'C' selection = (chain 'D' and resid 2 through 372) } 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: 48.420 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 10830 Z= 0.247 Angle : 0.736 18.430 14735 Z= 0.437 Chirality : 0.046 0.207 1721 Planarity : 0.010 0.310 1873 Dihedral : 17.055 89.746 3906 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 1.42 % Allowed : 23.64 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1358 helix: 1.47 (0.21), residues: 619 sheet: -0.16 (0.37), residues: 197 loop : -1.38 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 75 HIS 0.008 0.001 HIS C 192 PHE 0.014 0.001 PHE H 441 TYR 0.015 0.001 TYR H 69 ARG 0.008 0.001 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.15705 ( 531) hydrogen bonds : angle 5.97535 ( 1530) covalent geometry : bond 0.00504 (10830) covalent geometry : angle 0.73591 (14735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.115 Fit side-chains REVERT: H 99 GLN cc_start: 0.8172 (pm20) cc_final: 0.7728 (pm20) REVERT: H 309 GLU cc_start: 0.7856 (tp30) cc_final: 0.7559 (tp30) REVERT: H 406 ASP cc_start: 0.8219 (m-30) cc_final: 0.7991 (m-30) REVERT: I 28 MET cc_start: 0.8860 (mmp) cc_final: 0.8634 (mmm) REVERT: I 71 ASP cc_start: 0.8038 (t0) cc_final: 0.7286 (p0) REVERT: C 198 MET cc_start: 0.9347 (mmm) cc_final: 0.9127 (mmp) REVERT: D 168 LEU cc_start: 0.8926 (mm) cc_final: 0.8526 (mt) outliers start: 16 outliers final: 5 residues processed: 170 average time/residue: 0.2754 time to fit residues: 63.6859 Evaluate side-chains 134 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 453 ASP Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 439 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN C 112 GLN D 82 GLN D 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080157 restraints weight = 22547.341| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.33 r_work: 0.3000 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10830 Z= 0.156 Angle : 0.586 8.470 14735 Z= 0.299 Chirality : 0.044 0.162 1721 Planarity : 0.005 0.058 1873 Dihedral : 5.157 58.684 1473 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.29 % Allowed : 20.80 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1358 helix: 1.59 (0.21), residues: 631 sheet: -0.14 (0.35), residues: 200 loop : -1.30 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 75 HIS 0.004 0.001 HIS I 173 PHE 0.012 0.001 PHE D 31 TYR 0.012 0.001 TYR D 84 ARG 0.006 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 531) hydrogen bonds : angle 4.97546 ( 1530) covalent geometry : bond 0.00362 (10830) covalent geometry : angle 0.58598 (14735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: H 309 GLU cc_start: 0.8391 (tp30) cc_final: 0.8068 (tp30) REVERT: H 384 MET cc_start: 0.8665 (mmm) cc_final: 0.8087 (mmm) REVERT: H 406 ASP cc_start: 0.8292 (m-30) cc_final: 0.7926 (m-30) REVERT: H 433 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (t) REVERT: I 28 MET cc_start: 0.8819 (mmp) cc_final: 0.8528 (mmm) REVERT: I 50 TRP cc_start: 0.6289 (OUTLIER) cc_final: 0.6044 (p90) REVERT: I 71 ASP cc_start: 0.8384 (t0) cc_final: 0.7571 (p0) REVERT: I 149 GLU cc_start: 0.8723 (mp0) cc_final: 0.8343 (pm20) REVERT: I 195 ASP cc_start: 0.8971 (m-30) cc_final: 0.8737 (m-30) REVERT: I 198 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7883 (p) REVERT: I 269 MET cc_start: 0.8853 (ttp) cc_final: 0.8623 (ttm) REVERT: C 172 MET cc_start: 0.9096 (ttp) cc_final: 0.8895 (ttp) outliers start: 37 outliers final: 16 residues processed: 160 average time/residue: 0.2254 time to fit residues: 51.4356 Evaluate side-chains 145 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 291 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 120 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 GLN I 53 GLN ** D 171 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 = 0.3577 r_free = 0.3577 target = 0.104367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079249 restraints weight = 22672.576| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.35 r_work: 0.2981 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10830 Z= 0.140 Angle : 0.550 12.506 14735 Z= 0.278 Chirality : 0.043 0.161 1721 Planarity : 0.004 0.053 1873 Dihedral : 4.268 41.759 1464 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.67 % Allowed : 21.87 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1358 helix: 1.70 (0.21), residues: 631 sheet: -0.11 (0.36), residues: 200 loop : -1.30 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 75 HIS 0.003 0.001 HIS I 173 PHE 0.010 0.001 PHE I 153 TYR 0.010 0.001 TYR C 189 ARG 0.004 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 531) hydrogen bonds : angle 4.73649 ( 1530) covalent geometry : bond 0.00329 (10830) covalent geometry : angle 0.55023 (14735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: H 309 GLU cc_start: 0.8376 (tp30) cc_final: 0.8051 (tp30) REVERT: H 384 MET cc_start: 0.8688 (mmm) cc_final: 0.8159 (mmm) REVERT: H 406 ASP cc_start: 0.8289 (m-30) cc_final: 0.7893 (m-30) REVERT: H 433 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8672 (t) REVERT: I 28 MET cc_start: 0.8822 (mmp) cc_final: 0.8505 (mmm) REVERT: I 33 MET cc_start: 0.9091 (mmm) cc_final: 0.8601 (mmt) REVERT: I 50 TRP cc_start: 0.6292 (OUTLIER) cc_final: 0.6000 (p90) REVERT: I 71 ASP cc_start: 0.8397 (t0) cc_final: 0.7548 (p0) REVERT: I 149 GLU cc_start: 0.8731 (mp0) cc_final: 0.8315 (pm20) REVERT: I 182 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8721 (mm-30) REVERT: I 195 ASP cc_start: 0.9063 (m-30) cc_final: 0.8718 (m-30) REVERT: I 198 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7901 (p) REVERT: I 210 LEU cc_start: 0.9449 (mt) cc_final: 0.9227 (mt) REVERT: I 269 MET cc_start: 0.8832 (ttp) cc_final: 0.8614 (ttm) REVERT: C 13 TRP cc_start: 0.7671 (t-100) cc_final: 0.6910 (m-90) REVERT: C 172 MET cc_start: 0.9137 (ttp) cc_final: 0.8935 (ttp) outliers start: 30 outliers final: 20 residues processed: 152 average time/residue: 0.2170 time to fit residues: 47.6102 Evaluate side-chains 151 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.104284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078883 restraints weight = 22433.278| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.32 r_work: 0.2972 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10830 Z= 0.135 Angle : 0.543 12.523 14735 Z= 0.273 Chirality : 0.043 0.158 1721 Planarity : 0.004 0.051 1873 Dihedral : 4.209 37.891 1464 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.02 % Allowed : 22.13 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1358 helix: 1.74 (0.21), residues: 628 sheet: -0.05 (0.36), residues: 199 loop : -1.32 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 175 HIS 0.003 0.001 HIS I 173 PHE 0.010 0.001 PHE H 42 TYR 0.010 0.001 TYR C 189 ARG 0.004 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 531) hydrogen bonds : angle 4.62058 ( 1530) covalent geometry : bond 0.00314 (10830) covalent geometry : angle 0.54349 (14735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: H 274 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7809 (tp40) REVERT: H 309 GLU cc_start: 0.8328 (tp30) cc_final: 0.8018 (tp30) REVERT: H 384 MET cc_start: 0.8693 (mmm) cc_final: 0.8178 (mmm) REVERT: H 406 ASP cc_start: 0.8308 (m-30) cc_final: 0.7918 (m-30) REVERT: H 433 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8693 (t) REVERT: H 448 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.9006 (p) REVERT: I 28 MET cc_start: 0.8844 (mmp) cc_final: 0.8522 (mmm) REVERT: I 50 TRP cc_start: 0.6221 (OUTLIER) cc_final: 0.5946 (p90) REVERT: I 149 GLU cc_start: 0.8747 (mp0) cc_final: 0.8338 (pm20) REVERT: I 198 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7964 (p) REVERT: I 210 LEU cc_start: 0.9481 (mt) cc_final: 0.9256 (mt) REVERT: C 13 TRP cc_start: 0.7727 (t-100) cc_final: 0.6978 (m-90) REVERT: C 172 MET cc_start: 0.9119 (ttp) cc_final: 0.8902 (ttp) outliers start: 34 outliers final: 19 residues processed: 157 average time/residue: 0.2174 time to fit residues: 49.3533 Evaluate side-chains 150 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** D 171 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 = 0.3578 r_free = 0.3578 target = 0.104417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079528 restraints weight = 22330.581| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.32 r_work: 0.2983 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10830 Z= 0.121 Angle : 0.536 9.396 14735 Z= 0.271 Chirality : 0.042 0.155 1721 Planarity : 0.004 0.051 1873 Dihedral : 4.134 32.276 1464 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.29 % Allowed : 22.40 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1358 helix: 1.80 (0.21), residues: 630 sheet: 0.04 (0.37), residues: 198 loop : -1.26 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 75 HIS 0.003 0.001 HIS D 373 PHE 0.013 0.001 PHE H 42 TYR 0.009 0.001 TYR C 189 ARG 0.006 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 531) hydrogen bonds : angle 4.52945 ( 1530) covalent geometry : bond 0.00278 (10830) covalent geometry : angle 0.53616 (14735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: H 274 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7601 (tp40) REVERT: H 309 GLU cc_start: 0.8338 (tp30) cc_final: 0.8035 (tp30) REVERT: H 384 MET cc_start: 0.8639 (mmm) cc_final: 0.8140 (mmm) REVERT: H 406 ASP cc_start: 0.8310 (m-30) cc_final: 0.7917 (m-30) REVERT: H 433 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8674 (t) REVERT: H 448 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8957 (p) REVERT: I 28 MET cc_start: 0.8832 (mmp) cc_final: 0.8598 (mmm) REVERT: I 50 TRP cc_start: 0.6201 (OUTLIER) cc_final: 0.5925 (p90) REVERT: I 149 GLU cc_start: 0.8751 (mp0) cc_final: 0.8325 (pm20) REVERT: I 198 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7966 (p) REVERT: I 210 LEU cc_start: 0.9467 (mt) cc_final: 0.9233 (mt) REVERT: C 13 TRP cc_start: 0.7855 (t-100) cc_final: 0.7046 (m-90) REVERT: C 172 MET cc_start: 0.9109 (ttp) cc_final: 0.8877 (ttp) outliers start: 37 outliers final: 25 residues processed: 157 average time/residue: 0.2330 time to fit residues: 52.0284 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 124 optimal weight: 0.0370 chunk 69 optimal weight: 0.1980 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.104763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080131 restraints weight = 22531.718| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.31 r_work: 0.2996 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10830 Z= 0.110 Angle : 0.550 15.791 14735 Z= 0.273 Chirality : 0.042 0.153 1721 Planarity : 0.004 0.049 1873 Dihedral : 4.053 26.009 1464 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.38 % Allowed : 22.84 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1358 helix: 1.84 (0.21), residues: 630 sheet: 0.13 (0.37), residues: 198 loop : -1.24 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 75 HIS 0.003 0.001 HIS D 373 PHE 0.029 0.001 PHE H 344 TYR 0.009 0.001 TYR H 381 ARG 0.007 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 531) hydrogen bonds : angle 4.44405 ( 1530) covalent geometry : bond 0.00244 (10830) covalent geometry : angle 0.54957 (14735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: H 274 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: H 309 GLU cc_start: 0.8269 (tp30) cc_final: 0.8006 (tp30) REVERT: H 350 MET cc_start: 0.8782 (mtt) cc_final: 0.8562 (mtp) REVERT: H 384 MET cc_start: 0.8590 (mmm) cc_final: 0.8159 (mmm) REVERT: H 406 ASP cc_start: 0.8319 (m-30) cc_final: 0.7935 (m-30) REVERT: I 28 MET cc_start: 0.8804 (mmp) cc_final: 0.8570 (mmm) REVERT: I 50 TRP cc_start: 0.6121 (OUTLIER) cc_final: 0.5740 (p90) REVERT: I 149 GLU cc_start: 0.8747 (mp0) cc_final: 0.8280 (pm20) REVERT: I 198 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7978 (p) REVERT: I 210 LEU cc_start: 0.9476 (mt) cc_final: 0.9253 (mt) REVERT: C 13 TRP cc_start: 0.7821 (t-100) cc_final: 0.6949 (m-90) REVERT: C 172 MET cc_start: 0.9088 (ttp) cc_final: 0.8848 (ttp) outliers start: 38 outliers final: 24 residues processed: 157 average time/residue: 0.2279 time to fit residues: 51.5490 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 69 GLN ** I 157 ASN ** 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 = 0.3568 r_free = 0.3568 target = 0.103777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078723 restraints weight = 22875.993| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.37 r_work: 0.2969 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10830 Z= 0.142 Angle : 0.552 14.574 14735 Z= 0.276 Chirality : 0.043 0.155 1721 Planarity : 0.004 0.049 1873 Dihedral : 3.988 19.569 1463 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.11 % Allowed : 22.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1358 helix: 1.83 (0.21), residues: 629 sheet: 0.14 (0.37), residues: 198 loop : -1.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 175 HIS 0.003 0.001 HIS I 173 PHE 0.021 0.001 PHE H 344 TYR 0.010 0.001 TYR C 189 ARG 0.004 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 531) hydrogen bonds : angle 4.44637 ( 1530) covalent geometry : bond 0.00338 (10830) covalent geometry : angle 0.55230 (14735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: H 274 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7566 (tp40) REVERT: H 309 GLU cc_start: 0.8260 (tp30) cc_final: 0.7999 (tp30) REVERT: H 350 MET cc_start: 0.8800 (mtt) cc_final: 0.8566 (mtp) REVERT: H 384 MET cc_start: 0.8687 (mmm) cc_final: 0.8244 (mmm) REVERT: H 406 ASP cc_start: 0.8353 (m-30) cc_final: 0.7989 (m-30) REVERT: I 28 MET cc_start: 0.8840 (mmp) cc_final: 0.8605 (mmm) REVERT: I 50 TRP cc_start: 0.6198 (OUTLIER) cc_final: 0.5828 (p90) REVERT: I 149 GLU cc_start: 0.8766 (mp0) cc_final: 0.8293 (pm20) REVERT: I 182 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8649 (mm-30) REVERT: I 198 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7992 (p) REVERT: C 13 TRP cc_start: 0.7869 (t-100) cc_final: 0.7050 (m-90) outliers start: 35 outliers final: 24 residues processed: 153 average time/residue: 0.2280 time to fit residues: 50.1590 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 69 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 274 GLN ** I 157 ASN ** 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 = 0.3577 r_free = 0.3577 target = 0.104333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079461 restraints weight = 22547.288| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.32 r_work: 0.2987 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10830 Z= 0.112 Angle : 0.550 14.232 14735 Z= 0.273 Chirality : 0.042 0.216 1721 Planarity : 0.004 0.049 1873 Dihedral : 3.975 19.889 1463 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.58 % Allowed : 23.64 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1358 helix: 1.87 (0.21), residues: 628 sheet: 0.18 (0.37), residues: 198 loop : -1.25 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 246 HIS 0.003 0.001 HIS D 373 PHE 0.017 0.001 PHE H 344 TYR 0.010 0.001 TYR D 222 ARG 0.005 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 531) hydrogen bonds : angle 4.38837 ( 1530) covalent geometry : bond 0.00252 (10830) covalent geometry : angle 0.55013 (14735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: H 274 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7470 (tp40) REVERT: H 309 GLU cc_start: 0.8197 (tp30) cc_final: 0.7954 (tp30) REVERT: H 384 MET cc_start: 0.8621 (mmm) cc_final: 0.8179 (mmm) REVERT: H 406 ASP cc_start: 0.8368 (m-30) cc_final: 0.7986 (m-30) REVERT: I 28 MET cc_start: 0.8805 (mmp) cc_final: 0.8570 (mmm) REVERT: I 50 TRP cc_start: 0.6150 (OUTLIER) cc_final: 0.5749 (p90) REVERT: I 68 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6824 (mm-30) REVERT: I 149 GLU cc_start: 0.8773 (mp0) cc_final: 0.8283 (pm20) REVERT: I 198 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.7969 (p) REVERT: I 210 LEU cc_start: 0.9455 (mt) cc_final: 0.9193 (mt) REVERT: C 13 TRP cc_start: 0.7857 (t-100) cc_final: 0.7005 (m-90) outliers start: 29 outliers final: 22 residues processed: 152 average time/residue: 0.2177 time to fit residues: 47.3271 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 46 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: H 274 GLN ** I 157 ASN ** 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 = 0.3568 r_free = 0.3568 target = 0.103805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078622 restraints weight = 22639.029| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.34 r_work: 0.2972 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10830 Z= 0.138 Angle : 0.566 13.939 14735 Z= 0.281 Chirality : 0.043 0.154 1721 Planarity : 0.004 0.049 1873 Dihedral : 3.984 19.594 1463 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.84 % Allowed : 23.29 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1358 helix: 1.83 (0.21), residues: 629 sheet: 0.18 (0.37), residues: 198 loop : -1.27 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 246 HIS 0.003 0.001 HIS I 173 PHE 0.030 0.001 PHE I 44 TYR 0.010 0.001 TYR C 189 ARG 0.003 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 531) hydrogen bonds : angle 4.39249 ( 1530) covalent geometry : bond 0.00325 (10830) covalent geometry : angle 0.56616 (14735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: H 104 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5844 (ttt180) REVERT: H 274 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7635 (tp40) REVERT: H 309 GLU cc_start: 0.8187 (tp30) cc_final: 0.7870 (tp30) REVERT: H 384 MET cc_start: 0.8677 (mmm) cc_final: 0.8197 (mmm) REVERT: H 406 ASP cc_start: 0.8388 (m-30) cc_final: 0.8031 (m-30) REVERT: H 433 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8685 (t) REVERT: I 28 MET cc_start: 0.8822 (mmp) cc_final: 0.8582 (mmm) REVERT: I 50 TRP cc_start: 0.6186 (OUTLIER) cc_final: 0.5788 (p90) REVERT: I 68 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6740 (mm-30) REVERT: I 149 GLU cc_start: 0.8780 (mp0) cc_final: 0.8274 (pm20) REVERT: I 198 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 13 TRP cc_start: 0.7897 (t-100) cc_final: 0.7059 (m-90) REVERT: D 67 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8796 (mtp) outliers start: 32 outliers final: 24 residues processed: 150 average time/residue: 0.2326 time to fit residues: 50.8958 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 274 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079544 restraints weight = 22421.565| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.32 r_work: 0.2986 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10830 Z= 0.118 Angle : 0.560 13.801 14735 Z= 0.279 Chirality : 0.043 0.154 1721 Planarity : 0.004 0.049 1873 Dihedral : 3.967 19.823 1463 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.11 % Allowed : 22.76 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1358 helix: 1.84 (0.21), residues: 628 sheet: 0.23 (0.37), residues: 198 loop : -1.27 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 246 HIS 0.003 0.001 HIS C 125 PHE 0.010 0.001 PHE H 330 TYR 0.011 0.001 TYR D 222 ARG 0.004 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 531) hydrogen bonds : angle 4.36409 ( 1530) covalent geometry : bond 0.00269 (10830) covalent geometry : angle 0.55981 (14735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: H 60 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7928 (mmp80) REVERT: H 99 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: H 104 ARG cc_start: 0.6126 (ttt180) cc_final: 0.5601 (ttm170) REVERT: H 274 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: H 309 GLU cc_start: 0.8171 (tp30) cc_final: 0.7862 (tp30) REVERT: H 384 MET cc_start: 0.8630 (mmm) cc_final: 0.8199 (mmm) REVERT: H 406 ASP cc_start: 0.8387 (m-30) cc_final: 0.7997 (m-30) REVERT: I 28 MET cc_start: 0.8804 (mmp) cc_final: 0.8562 (mmm) REVERT: I 50 TRP cc_start: 0.6125 (OUTLIER) cc_final: 0.5714 (p90) REVERT: I 68 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6704 (mm-30) REVERT: I 71 ASP cc_start: 0.8639 (t0) cc_final: 0.8400 (m-30) REVERT: I 149 GLU cc_start: 0.8756 (mp0) cc_final: 0.8226 (pm20) REVERT: I 198 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 13 TRP cc_start: 0.7848 (t-100) cc_final: 0.6950 (m-90) REVERT: C 169 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7736 (tpp80) REVERT: D 67 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8790 (mtp) outliers start: 35 outliers final: 27 residues processed: 155 average time/residue: 0.2254 time to fit residues: 49.9680 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 355 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 274 GLN D 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078457 restraints weight = 22446.799| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.32 r_work: 0.2968 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10830 Z= 0.149 Angle : 0.573 13.728 14735 Z= 0.287 Chirality : 0.043 0.154 1721 Planarity : 0.004 0.049 1873 Dihedral : 3.976 19.500 1463 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.93 % Allowed : 23.29 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1358 helix: 1.82 (0.21), residues: 627 sheet: 0.23 (0.37), residues: 198 loop : -1.26 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 246 HIS 0.003 0.001 HIS I 173 PHE 0.010 0.001 PHE I 153 TYR 0.010 0.001 TYR C 189 ARG 0.004 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 531) hydrogen bonds : angle 4.38915 ( 1530) covalent geometry : bond 0.00353 (10830) covalent geometry : angle 0.57289 (14735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4994.87 seconds wall clock time: 86 minutes 57.51 seconds (5217.51 seconds total)