Starting phenix.real_space_refine on Tue May 5 05:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553.map" model { file = "/net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pe4_71553/05_2026/9pe4_71553_trim.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 69 5.16 5 C 8581 2.51 5 N 2129 2.21 5 O 2270 1.98 5 H 12323 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25373 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1524, 24110 Classifications: {'peptide': 1524} Link IDs: {'PCIS': 2, 'PTRANS': 65, 'TRANS': 1456} Chain breaks: 11 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 12, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 165 Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 791 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 6, 'TRANS': 46} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 433 Unusual residues: {'3PE': 1, 'LMN': 2, 'Y01': 7} Classifications: {'undetermined': 10, 'water': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.22, per 1000 atoms: 0.17 Number of scatterers: 25373 At special positions: 0 Unit cell: (95.932, 112.472, 135.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 1 15.00 O 2270 8.00 N 2129 7.00 C 8581 6.00 H 12323 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A1849 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 638.2 milliseconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 3 sheets defined 67.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.885A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 4.215A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.748A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.617A pdb=" N LYS A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.789A pdb=" N LEU A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.545A pdb=" N GLU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.524A pdb=" N LEU A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.530A pdb=" N GLN A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 368 removed outlier: 4.009A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.692A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.509A pdb=" N HIS A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 3.560A pdb=" N TRP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 488 through 517 removed outlier: 4.660A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 553 removed outlier: 3.677A pdb=" N ARG A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 560 through 583 Processing helix chain 'A' and resid 615 through 640 removed outlier: 3.562A pdb=" N TRP A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 671 through 712 removed outlier: 3.688A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 764 removed outlier: 3.977A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 3.507A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 813 through 828 removed outlier: 3.622A pdb=" N SER A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.565A pdb=" N ARG A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 3.506A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1082 through 1091 removed outlier: 4.237A pdb=" N ILE A1091 " --> pdb=" O ASN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1113 Processing helix chain 'A' and resid 1114 through 1121 Processing helix chain 'A' and resid 1173 through 1179 removed outlier: 4.638A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1187 Processing helix chain 'A' and resid 1201 through 1207 Processing helix chain 'A' and resid 1226 through 1233 Processing helix chain 'A' and resid 1267 through 1272 Processing helix chain 'A' and resid 1272 through 1282 removed outlier: 3.565A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1325 removed outlier: 3.821A pdb=" N HIS A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) Proline residue: A1295 - end of helix removed outlier: 4.018A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1313 " --> pdb=" O GLN A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1353 through 1381 removed outlier: 3.528A pdb=" N ARG A1357 " --> pdb=" O ASP A1353 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A1369 " --> pdb=" O VAL A1365 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) Proline residue: A1372 - end of helix Processing helix chain 'A' and resid 1382 through 1397 Processing helix chain 'A' and resid 1437 through 1449 removed outlier: 4.902A pdb=" N GLY A1447 " --> pdb=" O SER A1443 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A1448 " --> pdb=" O ARG A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1467 Processing helix chain 'A' and resid 1471 through 1489 removed outlier: 4.126A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) Proline residue: A1486 - end of helix Processing helix chain 'A' and resid 1495 through 1512 Processing helix chain 'A' and resid 1521 through 1530 removed outlier: 3.712A pdb=" N ARG A1530 " --> pdb=" O VAL A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1565 Processing helix chain 'A' and resid 1565 through 1584 Processing helix chain 'A' and resid 1598 through 1621 removed outlier: 3.529A pdb=" N ILE A1602 " --> pdb=" O SER A1598 " (cutoff:3.500A) Proline residue: A1609 - end of helix Processing helix chain 'A' and resid 1640 through 1665 Processing helix chain 'A' and resid 1668 through 1696 Processing helix chain 'A' and resid 1726 through 1754 removed outlier: 3.508A pdb=" N GLN A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 Processing helix chain 'A' and resid 1762 through 1775 removed outlier: 3.591A pdb=" N PHE A1766 " --> pdb=" O LYS A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1825 Proline residue: A1818 - end of helix removed outlier: 3.680A pdb=" N ALA A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1838 removed outlier: 3.986A pdb=" N VAL A1837 " --> pdb=" O ASP A1834 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 118 Processing helix chain 'G' and resid 120 through 125 removed outlier: 4.200A pdb=" N GLN G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 120 through 125' Processing helix chain 'G' and resid 127 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 781 Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1072 removed outlier: 3.670A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A1047 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A1148 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS A1237 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A1150 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N CYS A1239 " --> pdb=" O ILE A1150 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY A1152 " --> pdb=" O CYS A1239 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR A1241 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A1154 " --> pdb=" O TYR A1241 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN A1243 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR A1156 " --> pdb=" O GLN A1243 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A1245 " --> pdb=" O TYR A1156 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A1158 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY A1247 " --> pdb=" O PHE A1158 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2151 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: 5.04 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 12299 0.99 - 1.20: 1 1.20 - 1.40: 5532 1.40 - 1.61: 7792 1.61 - 1.81: 113 Bond restraints: 25737 Sorted by residual: bond pdb=" ND2 ASN A1849 " pdb="HD22 ASN A1849 " ideal model delta sigma weight residual 0.860 0.967 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" CAY Y01 A2001 " pdb=" OAW Y01 A2001 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" CAY Y01 A2007 " pdb=" OAW Y01 A2007 " ideal model delta sigma weight residual 1.332 1.432 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CAY Y01 A2004 " pdb=" OAW Y01 A2004 " ideal model delta sigma weight residual 1.332 1.432 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CAY Y01 A2002 " pdb=" OAW Y01 A2002 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 25732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 45919 3.12 - 6.24: 190 6.24 - 9.36: 30 9.36 - 12.48: 14 12.48 - 15.60: 4 Bond angle restraints: 46157 Sorted by residual: angle pdb="HD21 ASN A1849 " pdb=" ND2 ASN A1849 " pdb="HD22 ASN A1849 " ideal model delta sigma weight residual 120.00 104.40 15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" CAT Y01 A2007 " pdb=" CBH Y01 A2007 " pdb=" CBF Y01 A2007 " ideal model delta sigma weight residual 108.46 94.75 13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CA THR A1851 " pdb=" C THR A1851 " pdb=" O THR A1851 " ideal model delta sigma weight residual 121.87 116.91 4.96 1.16e+00 7.43e-01 1.83e+01 angle pdb=" CAT Y01 A2001 " pdb=" CBH Y01 A2001 " pdb=" CBF Y01 A2001 " ideal model delta sigma weight residual 108.46 95.75 12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CAI Y01 A2002 " pdb=" CAZ Y01 A2002 " pdb=" CAV Y01 A2002 " ideal model delta sigma weight residual 120.03 132.64 -12.61 3.00e+00 1.11e-01 1.77e+01 ... (remaining 46152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 12271 25.81 - 51.63: 425 51.63 - 77.44: 93 77.44 - 103.26: 13 103.26 - 129.07: 29 Dihedral angle restraints: 12831 sinusoidal: 7090 harmonic: 5741 Sorted by residual: dihedral pdb=" CAB LMN A2010 " pdb=" CAX LMN A2010 " pdb=" CAZ LMN A2010 " pdb=" CBB LMN A2010 " ideal model delta sinusoidal sigma weight residual 180.03 50.96 129.07 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CBG LMN A2009 " pdb=" CBI LMN A2009 " pdb=" CBK LMN A2009 " pdb=" CBQ LMN A2009 " ideal model delta sinusoidal sigma weight residual 181.33 53.52 127.81 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CAZ LMN A2010 " pdb=" CBB LMN A2010 " pdb=" CBD LMN A2010 " pdb=" CBF LMN A2010 " ideal model delta sinusoidal sigma weight residual 180.29 56.78 123.51 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 12828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1980 0.114 - 0.228: 49 0.228 - 0.341: 15 0.341 - 0.455: 13 0.455 - 0.569: 2 Chirality restraints: 2059 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.03e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1849 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CBH Y01 A2002 " pdb=" CAT Y01 A2002 " pdb=" CAZ Y01 A2002 " pdb=" CBF Y01 A2002 " both_signs ideal model delta sigma weight residual False -2.85 -3.31 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2056 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1849 " 0.151 2.00e-02 2.50e+03 3.93e-01 2.32e+03 pdb=" CG ASN A1849 " -0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN A1849 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A1849 " -0.159 2.00e-02 2.50e+03 pdb="HD21 ASN A1849 " -0.565 2.00e-02 2.50e+03 pdb="HD22 ASN A1849 " 0.739 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1849 " -0.017 2.00e-02 2.50e+03 1.08e-01 1.76e+02 pdb=" CG ASN A1849 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A1849 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A1849 " 0.226 2.00e-02 2.50e+03 pdb="HD21 ASN A1849 " -0.128 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1847 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C THR A1847 " -0.050 2.00e-02 2.50e+03 pdb=" O THR A1847 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A1848 " 0.017 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1648 2.22 - 2.81: 53292 2.81 - 3.41: 70931 3.41 - 4.00: 94407 4.00 - 4.60: 146185 Nonbonded interactions: 366463 Sorted by model distance: nonbonded pdb=" OE2 GLU A 165 " pdb=" H LEU G 106 " model vdw 1.622 2.450 nonbonded pdb=" OD1 ASN A 184 " pdb="HH22 ARG A1094 " model vdw 1.631 2.450 nonbonded pdb=" O PRO A 933 " pdb=" HG1 THR A 936 " model vdw 1.635 2.450 nonbonded pdb=" OE2 GLU A 514 " pdb=" HH TYR A1276 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLU A 514 " pdb="HH22 ARG A 531 " model vdw 1.652 2.450 ... (remaining 366458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.090 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 0.163 13419 Z= 0.242 Angle : 0.790 13.714 18267 Z= 0.343 Chirality : 0.060 0.569 2059 Planarity : 0.004 0.039 2230 Dihedral : 15.861 129.073 5441 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 0.31 % Allowed : 3.99 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.21), residues: 1551 helix: 1.97 (0.17), residues: 952 sheet: 0.64 (0.64), residues: 66 loop : 0.10 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.011 0.001 TYR A1800 PHE 0.018 0.001 PHE A1297 TRP 0.009 0.001 TRP A 625 HIS 0.004 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00450 (13414) covalent geometry : angle 0.78192 (18254) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.37991 ( 4) hydrogen bonds : bond 0.16042 ( 732) hydrogen bonds : angle 6.09949 ( 2151) link_BETA1-4 : bond 0.01177 ( 2) link_BETA1-4 : angle 1.63613 ( 6) link_NAG-ASN : bond 0.16262 ( 1) link_NAG-ASN : angle 8.88941 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ARG cc_start: 0.6307 (mtm180) cc_final: 0.5931 (mmm160) REVERT: A 491 TYR cc_start: 0.7725 (m-80) cc_final: 0.7477 (m-80) REVERT: A 1571 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7894 (t80) outliers start: 4 outliers final: 2 residues processed: 227 average time/residue: 1.2004 time to fit residues: 298.5976 Evaluate side-chains 148 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 779 GLN A1305 GLN A1845 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088574 restraints weight = 50154.258| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.44 r_work: 0.2956 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13419 Z= 0.140 Angle : 0.556 8.457 18267 Z= 0.282 Chirality : 0.039 0.219 2059 Planarity : 0.004 0.045 2230 Dihedral : 12.869 109.812 2593 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.26 % Rotamer: Outliers : 0.84 % Allowed : 11.05 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.21), residues: 1551 helix: 2.34 (0.16), residues: 944 sheet: 1.10 (0.72), residues: 56 loop : 0.15 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.013 0.001 TYR A1800 PHE 0.016 0.001 PHE A1363 TRP 0.012 0.001 TRP A 625 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00298 (13414) covalent geometry : angle 0.55488 (18254) SS BOND : bond 0.00297 ( 2) SS BOND : angle 0.34793 ( 4) hydrogen bonds : bond 0.05385 ( 732) hydrogen bonds : angle 4.47589 ( 2151) link_BETA1-4 : bond 0.00536 ( 2) link_BETA1-4 : angle 2.29717 ( 6) link_NAG-ASN : bond 0.02056 ( 1) link_NAG-ASN : angle 0.78956 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8503 (mm110) cc_final: 0.8144 (tm-30) REVERT: A 443 ARG cc_start: 0.6637 (mtm180) cc_final: 0.6107 (mmm160) REVERT: A 691 ASP cc_start: 0.8444 (t0) cc_final: 0.8214 (t0) REVERT: A 1498 ASP cc_start: 0.8842 (m-30) cc_final: 0.8604 (m-30) REVERT: A 1528 MET cc_start: 0.7762 (mtt) cc_final: 0.7457 (mtm) outliers start: 11 outliers final: 3 residues processed: 151 average time/residue: 1.4412 time to fit residues: 235.7345 Evaluate side-chains 136 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085318 restraints weight = 50715.271| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.42 r_work: 0.2904 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13419 Z= 0.224 Angle : 0.560 7.273 18267 Z= 0.287 Chirality : 0.041 0.345 2059 Planarity : 0.004 0.047 2230 Dihedral : 10.824 113.075 2588 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.77 % Allowed : 11.20 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.21), residues: 1551 helix: 2.15 (0.16), residues: 961 sheet: 1.17 (0.69), residues: 62 loop : 0.14 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1357 TYR 0.013 0.001 TYR A1800 PHE 0.018 0.002 PHE A1657 TRP 0.015 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00524 (13414) covalent geometry : angle 0.55775 (18254) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.32349 ( 4) hydrogen bonds : bond 0.05626 ( 732) hydrogen bonds : angle 4.33716 ( 2151) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 2.54311 ( 6) link_NAG-ASN : bond 0.00696 ( 1) link_NAG-ASN : angle 0.81641 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8405 (m-40) cc_final: 0.7919 (OUTLIER) REVERT: A 295 GLN cc_start: 0.8523 (mm110) cc_final: 0.8206 (tm-30) REVERT: A 443 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6362 (mmm160) REVERT: A 779 GLN cc_start: 0.8150 (mt0) cc_final: 0.7901 (mt0) REVERT: A 1498 ASP cc_start: 0.8867 (m-30) cc_final: 0.8629 (m-30) REVERT: A 1528 MET cc_start: 0.7757 (mtt) cc_final: 0.7454 (mtm) REVERT: A 1571 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.7905 (t80) outliers start: 10 outliers final: 5 residues processed: 142 average time/residue: 1.4534 time to fit residues: 223.4855 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A1305 GLN A1845 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.085771 restraints weight = 50228.399| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.44 r_work: 0.2923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13419 Z= 0.143 Angle : 0.508 8.192 18267 Z= 0.259 Chirality : 0.038 0.301 2059 Planarity : 0.004 0.039 2230 Dihedral : 10.001 111.589 2588 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.69 % Allowed : 11.13 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.21), residues: 1551 helix: 2.33 (0.16), residues: 949 sheet: 1.02 (0.70), residues: 57 loop : 0.11 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1357 TYR 0.014 0.001 TYR A1800 PHE 0.015 0.001 PHE A1657 TRP 0.013 0.001 TRP A 625 HIS 0.006 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00323 (13414) covalent geometry : angle 0.50668 (18254) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.41867 ( 4) hydrogen bonds : bond 0.04851 ( 732) hydrogen bonds : angle 4.17509 ( 2151) link_BETA1-4 : bond 0.00168 ( 2) link_BETA1-4 : angle 2.11767 ( 6) link_NAG-ASN : bond 0.00551 ( 1) link_NAG-ASN : angle 0.85432 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8402 (m-40) cc_final: 0.7918 (OUTLIER) REVERT: A 295 GLN cc_start: 0.8493 (mm110) cc_final: 0.8172 (tm-30) REVERT: A 421 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8554 (mt-10) REVERT: A 443 ARG cc_start: 0.6939 (mtm180) cc_final: 0.6293 (mmm160) REVERT: A 593 MET cc_start: 0.6201 (ptm) cc_final: 0.5952 (ptp) REVERT: A 691 ASP cc_start: 0.8676 (t0) cc_final: 0.8424 (t0) REVERT: A 878 GLN cc_start: 0.7821 (tt0) cc_final: 0.7602 (tt0) REVERT: A 936 THR cc_start: 0.8373 (p) cc_final: 0.8170 (t) REVERT: A 1498 ASP cc_start: 0.8856 (m-30) cc_final: 0.8603 (m-30) REVERT: A 1528 MET cc_start: 0.7771 (mtt) cc_final: 0.7459 (mtm) REVERT: A 1571 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7901 (t80) outliers start: 9 outliers final: 5 residues processed: 142 average time/residue: 1.4109 time to fit residues: 217.2492 Evaluate side-chains 139 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1845 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083918 restraints weight = 50390.003| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.43 r_work: 0.2879 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13419 Z= 0.227 Angle : 0.535 6.142 18267 Z= 0.276 Chirality : 0.040 0.236 2059 Planarity : 0.004 0.039 2230 Dihedral : 9.736 106.725 2588 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.84 % Allowed : 10.90 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.21), residues: 1551 helix: 2.24 (0.16), residues: 951 sheet: 1.22 (0.68), residues: 62 loop : 0.02 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.016 0.001 TYR A1800 PHE 0.017 0.001 PHE A1657 TRP 0.015 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00540 (13414) covalent geometry : angle 0.53345 (18254) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.39041 ( 4) hydrogen bonds : bond 0.05220 ( 732) hydrogen bonds : angle 4.19074 ( 2151) link_BETA1-4 : bond 0.00217 ( 2) link_BETA1-4 : angle 1.95452 ( 6) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 1.14743 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8429 (m-40) cc_final: 0.7928 (p0) REVERT: A 295 GLN cc_start: 0.8463 (mm110) cc_final: 0.8127 (tm-30) REVERT: A 421 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 443 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6372 (mmm160) REVERT: A 691 ASP cc_start: 0.8699 (t0) cc_final: 0.8481 (t0) REVERT: A 791 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7745 (ttp-110) REVERT: A 936 THR cc_start: 0.8376 (p) cc_final: 0.8176 (t) REVERT: A 1498 ASP cc_start: 0.8869 (m-30) cc_final: 0.8615 (m-30) REVERT: A 1528 MET cc_start: 0.7731 (mtt) cc_final: 0.7423 (mtm) REVERT: A 1571 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 1794 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7948 (tptp) outliers start: 11 outliers final: 3 residues processed: 143 average time/residue: 1.4882 time to fit residues: 229.8118 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1571 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 22 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A1305 GLN A1845 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084768 restraints weight = 50401.612| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.45 r_work: 0.2906 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13419 Z= 0.147 Angle : 0.497 5.577 18267 Z= 0.255 Chirality : 0.038 0.184 2059 Planarity : 0.004 0.040 2230 Dihedral : 9.382 102.723 2588 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.00 % Allowed : 11.59 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.21), residues: 1551 helix: 2.38 (0.16), residues: 947 sheet: 1.03 (0.69), residues: 57 loop : 0.02 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.013 0.001 TYR A1800 PHE 0.015 0.001 PHE A1657 TRP 0.013 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00335 (13414) covalent geometry : angle 0.49564 (18254) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.42169 ( 4) hydrogen bonds : bond 0.04697 ( 732) hydrogen bonds : angle 4.09760 ( 2151) link_BETA1-4 : bond 0.00460 ( 2) link_BETA1-4 : angle 1.76822 ( 6) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 1.15336 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8426 (m-40) cc_final: 0.7915 (p0) REVERT: A 295 GLN cc_start: 0.8454 (mm110) cc_final: 0.8120 (tm-30) REVERT: A 421 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8579 (mt-10) REVERT: A 443 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6333 (mmm160) REVERT: A 530 ARG cc_start: 0.7409 (mtp85) cc_final: 0.7208 (ttt90) REVERT: A 691 ASP cc_start: 0.8702 (t0) cc_final: 0.8461 (t0) REVERT: A 936 THR cc_start: 0.8359 (p) cc_final: 0.8146 (t) REVERT: A 1498 ASP cc_start: 0.8864 (m-30) cc_final: 0.8619 (m-30) REVERT: A 1528 MET cc_start: 0.7743 (mtt) cc_final: 0.7421 (mtm) REVERT: A 1571 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 1794 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7931 (tptp) outliers start: 13 outliers final: 4 residues processed: 145 average time/residue: 1.4320 time to fit residues: 224.5893 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1845 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.084271 restraints weight = 50386.069| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.43 r_work: 0.2886 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13419 Z= 0.180 Angle : 0.509 5.718 18267 Z= 0.262 Chirality : 0.038 0.170 2059 Planarity : 0.004 0.039 2230 Dihedral : 9.213 92.227 2588 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.77 % Allowed : 11.97 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.21), residues: 1551 helix: 2.37 (0.16), residues: 947 sheet: 1.03 (0.70), residues: 57 loop : -0.01 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 862 TYR 0.014 0.001 TYR A1800 PHE 0.015 0.001 PHE A1363 TRP 0.014 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00424 (13414) covalent geometry : angle 0.50822 (18254) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.35002 ( 4) hydrogen bonds : bond 0.04821 ( 732) hydrogen bonds : angle 4.08200 ( 2151) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 1.73956 ( 6) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.23497 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8418 (m-40) cc_final: 0.7942 (p0) REVERT: A 295 GLN cc_start: 0.8465 (mm110) cc_final: 0.8125 (tm-30) REVERT: A 443 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6358 (mmm-85) REVERT: A 530 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7085 (ttt90) REVERT: A 691 ASP cc_start: 0.8706 (t0) cc_final: 0.8491 (t0) REVERT: A 936 THR cc_start: 0.8351 (p) cc_final: 0.8137 (t) REVERT: A 1498 ASP cc_start: 0.8847 (m-30) cc_final: 0.8602 (m-30) REVERT: A 1528 MET cc_start: 0.7739 (mtt) cc_final: 0.7427 (mtm) REVERT: A 1571 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 1794 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7926 (tptp) outliers start: 10 outliers final: 5 residues processed: 143 average time/residue: 1.4101 time to fit residues: 218.3868 Evaluate side-chains 136 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1571 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1845 ASN 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 = 0.124381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083289 restraints weight = 50294.313| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.44 r_work: 0.2876 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13419 Z= 0.174 Angle : 0.506 5.760 18267 Z= 0.260 Chirality : 0.038 0.167 2059 Planarity : 0.004 0.039 2230 Dihedral : 9.054 87.883 2588 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.92 % Allowed : 11.97 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.21), residues: 1551 helix: 2.39 (0.16), residues: 946 sheet: 1.00 (0.70), residues: 57 loop : -0.04 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 862 TYR 0.014 0.001 TYR A1800 PHE 0.016 0.001 PHE A1657 TRP 0.014 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00408 (13414) covalent geometry : angle 0.50540 (18254) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.37370 ( 4) hydrogen bonds : bond 0.04773 ( 732) hydrogen bonds : angle 4.07097 ( 2151) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 1.69558 ( 6) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.29866 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8432 (m-40) cc_final: 0.7944 (p0) REVERT: A 295 GLN cc_start: 0.8426 (mm110) cc_final: 0.8059 (tm-30) REVERT: A 443 ARG cc_start: 0.6941 (mtm180) cc_final: 0.6259 (mmm160) REVERT: A 520 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7599 (mtt180) REVERT: A 691 ASP cc_start: 0.8689 (t0) cc_final: 0.8463 (t0) REVERT: A 936 THR cc_start: 0.8322 (p) cc_final: 0.8108 (t) REVERT: A 1448 SER cc_start: 0.8893 (t) cc_final: 0.8595 (m) REVERT: A 1498 ASP cc_start: 0.8830 (m-30) cc_final: 0.8574 (m-30) REVERT: A 1528 MET cc_start: 0.7729 (mtt) cc_final: 0.7419 (mtm) REVERT: A 1571 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 1618 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: A 1798 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7811 (tppt) outliers start: 12 outliers final: 5 residues processed: 142 average time/residue: 1.5383 time to fit residues: 235.8520 Evaluate side-chains 137 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1618 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1305 GLN A1845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083690 restraints weight = 50607.688| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.43 r_work: 0.2878 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13419 Z= 0.158 Angle : 0.502 5.696 18267 Z= 0.256 Chirality : 0.037 0.169 2059 Planarity : 0.004 0.058 2230 Dihedral : 8.895 86.603 2588 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.69 % Allowed : 12.28 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.21), residues: 1551 helix: 2.45 (0.16), residues: 946 sheet: 1.06 (0.69), residues: 57 loop : -0.04 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 530 TYR 0.013 0.001 TYR A1800 PHE 0.015 0.001 PHE A1657 TRP 0.013 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00368 (13414) covalent geometry : angle 0.50118 (18254) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.38392 ( 4) hydrogen bonds : bond 0.04639 ( 732) hydrogen bonds : angle 4.03463 ( 2151) link_BETA1-4 : bond 0.00248 ( 2) link_BETA1-4 : angle 1.66325 ( 6) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 1.33013 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8423 (m-40) cc_final: 0.7952 (p0) REVERT: A 295 GLN cc_start: 0.8422 (mm110) cc_final: 0.8048 (tm-30) REVERT: A 443 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6185 (mmm-85) REVERT: A 520 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7681 (mtt180) REVERT: A 691 ASP cc_start: 0.8657 (t0) cc_final: 0.8427 (t0) REVERT: A 861 ILE cc_start: 0.7952 (tt) cc_final: 0.7489 (pp) REVERT: A 936 THR cc_start: 0.8297 (p) cc_final: 0.8076 (t) REVERT: A 1448 SER cc_start: 0.8869 (t) cc_final: 0.8568 (m) REVERT: A 1498 ASP cc_start: 0.8841 (m-30) cc_final: 0.8574 (m-30) REVERT: A 1504 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7838 (ttt180) REVERT: A 1528 MET cc_start: 0.7687 (mtt) cc_final: 0.7374 (mtm) REVERT: A 1571 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7828 (t80) REVERT: A 1618 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: A 1690 MET cc_start: 0.7706 (mtm) cc_final: 0.7490 (mtp) REVERT: A 1798 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7817 (tppt) outliers start: 9 outliers final: 5 residues processed: 139 average time/residue: 1.5024 time to fit residues: 225.9113 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1618 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1845 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082960 restraints weight = 50296.130| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.43 r_work: 0.2870 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13419 Z= 0.190 Angle : 0.516 5.831 18267 Z= 0.264 Chirality : 0.038 0.164 2059 Planarity : 0.004 0.064 2230 Dihedral : 8.888 86.914 2588 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.61 % Allowed : 12.28 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.21), residues: 1551 helix: 2.41 (0.16), residues: 946 sheet: 1.05 (0.70), residues: 57 loop : -0.08 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 530 TYR 0.015 0.001 TYR A1800 PHE 0.016 0.001 PHE A1657 TRP 0.014 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00450 (13414) covalent geometry : angle 0.51444 (18254) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.39742 ( 4) hydrogen bonds : bond 0.04820 ( 732) hydrogen bonds : angle 4.06865 ( 2151) link_BETA1-4 : bond 0.00218 ( 2) link_BETA1-4 : angle 1.69256 ( 6) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 1.43957 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue MET 141 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue VAL 1168 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LEU 1219 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LEU 1397 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue THR 1696 is missing expected H atoms. Skipping. Residue LYS 1733 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8422 (m-40) cc_final: 0.7992 (p0) REVERT: A 295 GLN cc_start: 0.8446 (mm110) cc_final: 0.8067 (tm-30) REVERT: A 443 ARG cc_start: 0.6956 (mtm180) cc_final: 0.6254 (mmm160) REVERT: A 520 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7712 (mtt180) REVERT: A 530 ARG cc_start: 0.7345 (mtp85) cc_final: 0.7077 (ttt90) REVERT: A 691 ASP cc_start: 0.8683 (t0) cc_final: 0.8456 (t0) REVERT: A 936 THR cc_start: 0.8315 (p) cc_final: 0.8095 (t) REVERT: A 1448 SER cc_start: 0.8893 (t) cc_final: 0.8577 (m) REVERT: A 1498 ASP cc_start: 0.8845 (m-30) cc_final: 0.8577 (m-30) REVERT: A 1504 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7865 (ttt180) REVERT: A 1508 ARG cc_start: 0.8531 (ttp-170) cc_final: 0.8269 (mtm-85) REVERT: A 1618 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: A 1690 MET cc_start: 0.7789 (mtm) cc_final: 0.7583 (mtp) REVERT: A 1794 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7814 (tptp) REVERT: A 1798 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7725 (tppt) outliers start: 8 outliers final: 5 residues processed: 139 average time/residue: 1.6034 time to fit residues: 240.9033 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1618 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083598 restraints weight = 50241.495| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.43 r_work: 0.2879 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13419 Z= 0.154 Angle : 0.499 5.545 18267 Z= 0.255 Chirality : 0.037 0.168 2059 Planarity : 0.004 0.039 2230 Dihedral : 8.773 87.806 2588 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.54 % Allowed : 12.59 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.21), residues: 1551 helix: 2.46 (0.16), residues: 946 sheet: 1.04 (0.69), residues: 57 loop : -0.10 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 530 TYR 0.013 0.001 TYR A1800 PHE 0.015 0.001 PHE A1657 TRP 0.013 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00358 (13414) covalent geometry : angle 0.49780 (18254) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.39896 ( 4) hydrogen bonds : bond 0.04600 ( 732) hydrogen bonds : angle 4.03240 ( 2151) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.64276 ( 6) link_NAG-ASN : bond 0.00217 ( 1) link_NAG-ASN : angle 1.42377 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9105.96 seconds wall clock time: 154 minutes 30.09 seconds (9270.09 seconds total)