Starting phenix.real_space_refine on Fri Jul 3 14:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xve_33484/07_2026/7xve_33484.map" } resolution = 2.7 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= 0.005 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 100 5.16 5 C 9045 2.51 5 N 2047 2.21 5 O 2441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13659 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1276, 10198 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 41, 'TRANS': 1234} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 1276, 10198 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 41, 'TRANS': 1234} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 10436 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 911 Unusual residues: {'1PW': 1, 'CLR': 4, 'LPE': 17, 'NAG': 2, 'PCW': 6, 'Y01': 1} Classifications: {'peptide': 1, 'undetermined': 31} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1PW:plan-1': 1, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {'LPE': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 874 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 874 " occ=0.50 Time building chain proxies: 4.80, per 1000 atoms: 0.35 Number of scatterers: 13659 At special positions: 0 Unit cell: (136.395, 143.972, 127.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 26 15.00 O 2441 8.00 N 2047 7.00 C 9045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.05 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.00 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.04 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 E 1 " - " NAG E 2 " NAG-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 302 " - " ASN B 93 " " NAG B 303 " - " ASN B 110 " " NAG B 304 " - " ASN B 114 " " NAG B 305 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 8 sheets defined 64.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.983A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 4.088A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 175 removed outlier: 3.668A pdb=" N TYR A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.710A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.570A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 WARNING: missing atoms! Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.610A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.953A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 427 removed outlier: 3.960A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.559A pdb=" N ILE A 740 " --> pdb=" O CYS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 763 Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.809A pdb=" N LYS A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 805 removed outlier: 4.222A pdb=" N PHE A 804 " --> pdb=" O PRO A 800 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 824 removed outlier: 3.593A pdb=" N GLU A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.997A pdb=" N VAL A 833 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 removed outlier: 3.640A pdb=" N PHE A 843 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 888 removed outlier: 4.813A pdb=" N GLY A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 895 removed outlier: 3.787A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.535A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 957 Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.829A pdb=" N ILE A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.585A pdb=" N HIS A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1210 removed outlier: 3.843A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1248 removed outlier: 3.515A pdb=" N LYS A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1285 through 1292 removed outlier: 3.512A pdb=" N LEU A1289 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.697A pdb=" N ARG A1296 " --> pdb=" O ARG A1293 " (cutoff:3.500A) Proline residue: A1297 - end of helix No H-bonds generated for 'chain 'A' and resid 1293 through 1297' Processing helix chain 'A' and resid 1298 through 1304 removed outlier: 4.347A pdb=" N SER A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A1304 " --> pdb=" O ALA A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1298 through 1304' Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.713A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.904A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A1327 " --> pdb=" O ASN A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.578A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.906A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1445 Processing helix chain 'A' and resid 1447 through 1468 removed outlier: 3.557A pdb=" N ILE A1453 " --> pdb=" O LEU A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 3.728A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1487 " --> pdb=" O ASN A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 4.048A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1569 removed outlier: 3.515A pdb=" N THR A1544 " --> pdb=" O SER A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1574 removed outlier: 3.505A pdb=" N TYR A1573 " --> pdb=" O ARG A1570 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1570 through 1574' Processing helix chain 'A' and resid 1576 through 1597 Processing helix chain 'A' and resid 1605 through 1613 removed outlier: 3.568A pdb=" N PHE A1609 " --> pdb=" O SER A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1623 removed outlier: 3.682A pdb=" N ARG A1622 " --> pdb=" O ARG A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 Proline residue: A1642 - end of helix removed outlier: 3.637A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A1647 " --> pdb=" O ALA A1643 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1695 Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1706 through 1709 Processing helix chain 'A' and resid 1732 through 1751 Processing helix chain 'A' and resid 1751 through 1768 removed outlier: 3.551A pdb=" N SER A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.520A pdb=" N GLU B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.674A pdb=" N PHE A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 removed outlier: 3.557A pdb=" N SER A1357 " --> pdb=" O ASN A1352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.276A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.186A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.752A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 48 removed outlier: 5.513A pdb=" N SER C 44 " --> pdb=" O ASN C 116 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1935 1.25 - 1.40: 3444 1.40 - 1.54: 8221 1.54 - 1.69: 185 1.69 - 1.84: 164 Bond restraints: 13949 Sorted by residual: bond pdb=" CAK Y01 A2003 " pdb=" CBD Y01 A2003 " ideal model delta sigma weight residual 1.525 1.102 0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" CAS Y01 A2003 " pdb=" CAU Y01 A2003 " ideal model delta sigma weight residual 1.530 1.146 0.384 2.00e-02 2.50e+03 3.68e+02 bond pdb=" CBD Y01 A2003 " pdb=" CBG Y01 A2003 " ideal model delta sigma weight residual 1.520 1.155 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CAV Y01 A2003 " pdb=" CAZ Y01 A2003 " ideal model delta sigma weight residual 1.507 1.777 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" CAZ Y01 A2003 " pdb=" CBH Y01 A2003 " ideal model delta sigma weight residual 1.519 1.267 0.252 2.00e-02 2.50e+03 1.58e+02 ... (remaining 13944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 17987 3.01 - 6.01: 656 6.01 - 9.02: 148 9.02 - 12.03: 27 12.03 - 15.03: 8 Bond angle restraints: 18826 Sorted by residual: angle pdb=" N LEU A 231 " pdb=" CA LEU A 231 " pdb=" C LEU A 231 " ideal model delta sigma weight residual 113.23 100.88 12.35 1.24e+00 6.50e-01 9.92e+01 angle pdb=" N VAL A 178 " pdb=" CA VAL A 178 " pdb=" C VAL A 178 " ideal model delta sigma weight residual 110.36 118.48 -8.12 1.05e+00 9.07e-01 5.98e+01 angle pdb=" N SER C 76 " pdb=" CA SER C 76 " pdb=" C SER C 76 " ideal model delta sigma weight residual 110.55 120.76 -10.21 1.35e+00 5.49e-01 5.72e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 112.38 103.36 9.02 1.22e+00 6.72e-01 5.47e+01 angle pdb=" N ILE A 118 " pdb=" CA ILE A 118 " pdb=" C ILE A 118 " ideal model delta sigma weight residual 110.72 117.76 -7.04 1.01e+00 9.80e-01 4.85e+01 ... (remaining 18821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.73: 7657 27.73 - 55.45: 556 55.45 - 83.18: 69 83.18 - 110.90: 17 110.90 - 138.63: 10 Dihedral angle restraints: 8309 sinusoidal: 3701 harmonic: 4608 Sorted by residual: dihedral pdb=" CA PRO C 132 " pdb=" C PRO C 132 " pdb=" N PRO C 133 " pdb=" CA PRO C 133 " ideal model delta harmonic sigma weight residual 0.00 26.32 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 897 " pdb=" SG CYS A 897 " pdb=" SG CYS A 903 " pdb=" CB CYS A 903 " ideal model delta sinusoidal sigma weight residual 93.00 130.75 -37.75 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CAP 1PW A2007 " pdb=" CAR 1PW A2007 " pdb=" CAT 1PW A2007 " pdb=" CAU 1PW A2007 " ideal model delta sinusoidal sigma weight residual 167.53 -53.84 -138.63 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 8306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 2103 0.281 - 0.562: 9 0.562 - 0.844: 1 0.844 - 1.125: 0 1.125 - 1.406: 1 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CBD Y01 A2003 " pdb=" CAK Y01 A2003 " pdb=" CBF Y01 A2003 " pdb=" CBG Y01 A2003 " both_signs ideal model delta sigma weight residual False 2.70 1.29 1.41 2.00e-01 2.50e+01 4.94e+01 chirality pdb=" C1 NAG B 305 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 305 " pdb=" O5 NAG B 305 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.36e+01 ... (remaining 2111 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.327 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A2001 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.314 2.00e-02 2.50e+03 2.71e-01 9.17e+02 pdb=" C7 NAG E 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.293 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" C7 NAG B 304 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " 0.016 2.00e-02 2.50e+03 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1950 2.75 - 3.29: 13052 3.29 - 3.83: 22551 3.83 - 4.36: 27901 4.36 - 4.90: 45385 Nonbonded interactions: 110839 Sorted by model distance: nonbonded pdb=" O TYR A 157 " pdb=" OG1 THR A 160 " model vdw 2.214 3.040 nonbonded pdb=" O ASN A 154 " pdb=" OG1 THR A 158 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG A 30 " pdb=" OD2 ASP A 84 " model vdw 2.294 3.120 nonbonded pdb=" O3 NAG B 305 " pdb=" O7 NAG B 305 " model vdw 2.320 3.040 nonbonded pdb=" CD1 ILE A 750 " pdb=" OE1 GLU A 790 " model vdw 2.328 3.460 ... (remaining 110834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 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: 2.180 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.014 0.423 13970 Z= 0.778 Angle : 1.534 60.793 18879 Z= 0.815 Chirality : 0.076 1.406 2114 Planarity : 0.014 0.283 2197 Dihedral : 19.073 138.629 5299 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.09 % Favored : 94.53 % Rotamer: Outliers : 0.94 % Allowed : 18.62 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.19), residues: 1556 helix: -0.74 (0.16), residues: 891 sheet: -1.73 (0.41), residues: 138 loop : -2.34 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.026 0.003 TYR A 367 PHE 0.053 0.003 PHE A 15 TRP 0.018 0.002 TRP A1179 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.01428 / 0.78 (13949) covalent geometry : angle 1.40239 / 0.77 (18826) SS BOND : bond 0.01234 / 0.87 ( 10) SS BOND : angle 17.12575 / 10.53 ( 20) hydrogen bonds : bond 0.17789 / 11.69 ( 779) hydrogen bonds : angle 6.76026 / 4.77 ( 2221) link_BETA1-4 : bond 0.00440 / 0.25 ( 2) link_BETA1-4 : angle 3.65289 / 2.44 ( 6) link_NAG-ASN : bond 0.01737 / 1.13 ( 9) link_NAG-ASN : angle 7.31410 / 4.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8507 (mtpp) REVERT: A 1176 LYS cc_start: 0.6073 (mptt) cc_final: 0.4341 (ptpp) REVERT: A 1241 MET cc_start: 0.8464 (ttp) cc_final: 0.8040 (ttp) REVERT: A 1338 MET cc_start: 0.8092 (mtm) cc_final: 0.7672 (mtp) REVERT: A 1412 MET cc_start: 0.8659 (mtm) cc_final: 0.8412 (mtp) REVERT: A 1754 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: C 65 LEU cc_start: 0.8677 (pp) cc_final: 0.8392 (tt) outliers start: 13 outliers final: 0 residues processed: 241 average time/residue: 0.5999 time to fit residues: 158.3001 Evaluate side-chains 151 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 1754 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 139 ASN A 146 ASN A 147 ASN A 270 ASN A 395 ASN A 409 ASN A 765 HIS A 805 GLN A 861 ASN A 909 HIS A 961 ASN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1424 GLN A1528 ASN A1551 ASN A1676 ASN A1762 ASN C 73 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103946 restraints weight = 21994.456| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.46 r_work: 0.3167 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13970 Z= 0.148 Angle : 0.650 14.559 18879 Z= 0.328 Chirality : 0.044 0.461 2114 Planarity : 0.005 0.058 2197 Dihedral : 16.777 130.451 2362 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.70 % Allowed : 19.13 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1556 helix: 0.93 (0.17), residues: 914 sheet: -0.87 (0.43), residues: 139 loop : -1.68 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 84 TYR 0.027 0.002 TYR B 182 PHE 0.021 0.001 PHE A 878 TRP 0.025 0.001 TRP A 808 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (13949) covalent geometry : angle 0.62130 / 0.32 (18826) SS BOND : bond 0.00161 / 0.11 ( 10) SS BOND : angle 1.45929 / 0.98 ( 20) hydrogen bonds : bond 0.05837 / 3.81 ( 779) hydrogen bonds : angle 4.85194 / 3.42 ( 2221) link_BETA1-4 : bond 0.00215 / 0.12 ( 2) link_BETA1-4 : angle 3.74176 / 2.57 ( 6) link_NAG-ASN : bond 0.00566 / 0.41 ( 9) link_NAG-ASN : angle 4.67204 / 3.01 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5999 (tt0) REVERT: A 798 MET cc_start: 0.5058 (ppp) cc_final: 0.4564 (ppp) REVERT: A 803 TYR cc_start: 0.6741 (p90) cc_final: 0.5709 (p90) REVERT: A 1176 LYS cc_start: 0.6457 (mptt) cc_final: 0.3418 (ptpp) REVERT: A 1241 MET cc_start: 0.8717 (ttp) cc_final: 0.8388 (ttp) REVERT: A 1374 MET cc_start: 0.8436 (mtp) cc_final: 0.8232 (mtp) REVERT: A 1412 MET cc_start: 0.8931 (mtm) cc_final: 0.8653 (mtp) REVERT: B 152 ARG cc_start: 0.9097 (mtp-110) cc_final: 0.8795 (mtm180) REVERT: B 154 MET cc_start: 0.7343 (tpt) cc_final: 0.7095 (tpp) REVERT: C 38 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5917 (mm) REVERT: C 65 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7819 (tt) REVERT: C 118 GLN cc_start: 0.6014 (mp-120) cc_final: 0.5605 (mt0) REVERT: C 122 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5252 (pm20) outliers start: 51 outliers final: 11 residues processed: 198 average time/residue: 0.6030 time to fit residues: 131.1514 Evaluate side-chains 161 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100154 restraints weight = 26448.763| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.82 r_work: 0.3118 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13970 Z= 0.142 Angle : 0.583 13.322 18879 Z= 0.293 Chirality : 0.042 0.405 2114 Planarity : 0.005 0.064 2197 Dihedral : 15.207 134.424 2355 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.97 % Allowed : 20.80 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1556 helix: 1.57 (0.17), residues: 913 sheet: -0.58 (0.43), residues: 141 loop : -1.45 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 835 TYR 0.024 0.001 TYR B 182 PHE 0.019 0.001 PHE A1440 TRP 0.016 0.001 TRP A 808 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13949) covalent geometry : angle 0.55568 / 0.29 (18826) SS BOND : bond 0.00157 / 0.12 ( 10) SS BOND : angle 1.33896 / 0.90 ( 20) hydrogen bonds : bond 0.05127 / 3.32 ( 779) hydrogen bonds : angle 4.50458 / 3.17 ( 2221) link_BETA1-4 : bond 0.00310 / 0.19 ( 2) link_BETA1-4 : angle 3.25818 / 2.16 ( 6) link_NAG-ASN : bond 0.00480 / 0.35 ( 9) link_NAG-ASN : angle 4.27403 / 2.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: A 415 GLU cc_start: 0.7509 (tp30) cc_final: 0.7262 (tt0) REVERT: A 418 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: A 773 LYS cc_start: 0.7383 (ttmt) cc_final: 0.7035 (mtmt) REVERT: A 798 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.4305 (ppp) REVERT: A 803 TYR cc_start: 0.6731 (p90) cc_final: 0.5643 (p90) REVERT: A 950 MET cc_start: 0.8137 (mtp) cc_final: 0.7917 (mtm) REVERT: A 1176 LYS cc_start: 0.6047 (mptt) cc_final: 0.3210 (ptpp) REVERT: A 1241 MET cc_start: 0.8521 (ttp) cc_final: 0.8239 (ttp) REVERT: A 1412 MET cc_start: 0.8852 (mtm) cc_final: 0.8602 (mtp) REVERT: B 152 ARG cc_start: 0.9100 (mtp-110) cc_final: 0.8801 (mtm180) REVERT: B 184 LYS cc_start: 0.7056 (ttmm) cc_final: 0.6795 (mtpp) REVERT: C 65 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7771 (tt) REVERT: C 122 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5247 (pm20) REVERT: C 128 TYR cc_start: 0.7919 (m-80) cc_final: 0.7419 (m-80) outliers start: 41 outliers final: 11 residues processed: 191 average time/residue: 0.6245 time to fit residues: 130.4114 Evaluate side-chains 167 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 809 ASN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098782 restraints weight = 24713.288| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.62 r_work: 0.3101 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13970 Z= 0.174 Angle : 0.588 12.860 18879 Z= 0.296 Chirality : 0.043 0.438 2114 Planarity : 0.005 0.062 2197 Dihedral : 14.462 133.307 2355 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.48 % Allowed : 20.65 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1556 helix: 1.70 (0.17), residues: 913 sheet: -0.41 (0.43), residues: 139 loop : -1.28 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 84 TYR 0.022 0.001 TYR B 182 PHE 0.021 0.002 PHE A1440 TRP 0.014 0.001 TRP A 808 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13949) covalent geometry : angle 0.56521 / 0.29 (18826) SS BOND : bond 0.00172 / 0.12 ( 10) SS BOND : angle 1.09572 / 0.75 ( 20) hydrogen bonds : bond 0.05304 / 3.43 ( 779) hydrogen bonds : angle 4.46774 / 3.14 ( 2221) link_BETA1-4 : bond 0.00208 / 0.12 ( 2) link_BETA1-4 : angle 3.23937 / 2.20 ( 6) link_NAG-ASN : bond 0.00403 / 0.30 ( 9) link_NAG-ASN : angle 3.94289 / 2.59 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 415 GLU cc_start: 0.7562 (tp30) cc_final: 0.7272 (tt0) REVERT: A 747 ASP cc_start: 0.6728 (t0) cc_final: 0.6424 (t0) REVERT: A 773 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7213 (mtmt) REVERT: A 798 MET cc_start: 0.4578 (OUTLIER) cc_final: 0.4252 (ppp) REVERT: A 803 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5741 (p90) REVERT: A 842 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8174 (m) REVERT: A 1176 LYS cc_start: 0.6178 (mptt) cc_final: 0.3289 (ptpp) REVERT: A 1241 MET cc_start: 0.8557 (ttp) cc_final: 0.8298 (ttp) REVERT: A 1278 LEU cc_start: 0.8025 (tp) cc_final: 0.7485 (tt) REVERT: A 1412 MET cc_start: 0.8870 (mtm) cc_final: 0.8622 (mtp) REVERT: A 1494 GLN cc_start: 0.7306 (mp10) cc_final: 0.6914 (mp10) REVERT: A 1545 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: B 75 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7703 (p0) REVERT: B 96 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8123 (mtp85) REVERT: B 152 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8846 (mtm180) REVERT: B 166 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7215 (mm) REVERT: C 65 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7928 (tt) REVERT: C 92 LEU cc_start: 0.5746 (mp) cc_final: 0.5512 (mp) REVERT: C 122 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5304 (pm20) REVERT: C 128 TYR cc_start: 0.7932 (m-80) cc_final: 0.7441 (m-80) REVERT: C 148 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.5555 (tpp) outliers start: 48 outliers final: 16 residues processed: 185 average time/residue: 0.6028 time to fit residues: 122.5004 Evaluate side-chains 175 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099363 restraints weight = 21269.199| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.36 r_work: 0.3116 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13970 Z= 0.155 Angle : 0.560 12.714 18879 Z= 0.282 Chirality : 0.042 0.410 2114 Planarity : 0.004 0.048 2197 Dihedral : 13.965 132.035 2355 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.68 % Allowed : 21.38 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.01 (0.21), residues: 1556 helix: 1.84 (0.17), residues: 911 sheet: -0.34 (0.43), residues: 139 loop : -1.23 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.023 0.001 TYR B 182 PHE 0.018 0.001 PHE A1440 TRP 0.009 0.001 TRP A1700 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (13949) covalent geometry : angle 0.53787 / 0.28 (18826) SS BOND : bond 0.00211 / 0.15 ( 10) SS BOND : angle 1.01046 / 0.69 ( 20) hydrogen bonds : bond 0.05031 / 3.25 ( 779) hydrogen bonds : angle 4.36776 / 3.07 ( 2221) link_BETA1-4 : bond 0.00210 / 0.13 ( 2) link_BETA1-4 : angle 3.31410 / 2.23 ( 6) link_NAG-ASN : bond 0.00388 / 0.29 ( 9) link_NAG-ASN : angle 3.76496 / 2.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.507 Fit side-chains REVERT: A 145 MET cc_start: 0.8094 (mtm) cc_final: 0.7769 (ttp) REVERT: A 281 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8295 (mm-30) REVERT: A 747 ASP cc_start: 0.6969 (t0) cc_final: 0.6652 (t0) REVERT: A 773 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7179 (mtmt) REVERT: A 798 MET cc_start: 0.4820 (OUTLIER) cc_final: 0.4494 (ppp) REVERT: A 803 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.5854 (p90) REVERT: A 1176 LYS cc_start: 0.6597 (mptt) cc_final: 0.3563 (ptpp) REVERT: A 1241 MET cc_start: 0.8671 (ttp) cc_final: 0.8433 (ttp) REVERT: A 1278 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 1412 MET cc_start: 0.8943 (mtm) cc_final: 0.8711 (mtp) REVERT: A 1471 ASP cc_start: 0.8803 (t0) cc_final: 0.8394 (t0) REVERT: A 1494 GLN cc_start: 0.7275 (mp10) cc_final: 0.6839 (mp10) REVERT: A 1545 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: B 96 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8134 (mtp85) REVERT: B 113 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: B 152 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8791 (mtm180) REVERT: B 166 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7217 (mm) REVERT: B 184 LYS cc_start: 0.7117 (ttmm) cc_final: 0.6781 (mtpp) REVERT: C 65 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8059 (tt) REVERT: C 122 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: C 128 TYR cc_start: 0.8153 (m-80) cc_final: 0.7566 (m-80) REVERT: C 148 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.5895 (tpp) outliers start: 37 outliers final: 22 residues processed: 178 average time/residue: 0.6275 time to fit residues: 122.1955 Evaluate side-chains 181 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1761 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098948 restraints weight = 29593.938| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.92 r_work: 0.3092 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13970 Z= 0.133 Angle : 0.540 12.640 18879 Z= 0.272 Chirality : 0.041 0.391 2114 Planarity : 0.004 0.047 2197 Dihedral : 13.641 128.904 2355 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.97 % Allowed : 21.01 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.13 (0.21), residues: 1556 helix: 1.93 (0.17), residues: 912 sheet: -0.29 (0.43), residues: 142 loop : -1.17 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 84 TYR 0.014 0.001 TYR B 182 PHE 0.018 0.001 PHE A1440 TRP 0.009 0.001 TRP A1700 HIS 0.009 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13949) covalent geometry : angle 0.51366 / 0.27 (18826) SS BOND : bond 0.00192 / 0.13 ( 10) SS BOND : angle 0.92867 / 0.64 ( 20) hydrogen bonds : bond 0.04764 / 3.07 ( 779) hydrogen bonds : angle 4.30831 / 3.03 ( 2221) link_BETA1-4 : bond 0.00216 / 0.13 ( 2) link_BETA1-4 : angle 3.24573 / 2.20 ( 6) link_NAG-ASN : bond 0.00400 / 0.29 ( 9) link_NAG-ASN : angle 4.07220 / 2.69 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.5228 (tpt) cc_final: 0.4756 (mmt) REVERT: A 145 MET cc_start: 0.7965 (mtm) cc_final: 0.7630 (ttp) REVERT: A 747 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6465 (t0) REVERT: A 773 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7199 (mtmt) REVERT: A 798 MET cc_start: 0.4323 (OUTLIER) cc_final: 0.4047 (ppp) REVERT: A 803 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5892 (p90) REVERT: A 835 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7940 (ttp-110) REVERT: A 842 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 1176 LYS cc_start: 0.6211 (mptt) cc_final: 0.3367 (ptpp) REVERT: A 1241 MET cc_start: 0.8534 (ttp) cc_final: 0.8272 (ttp) REVERT: A 1412 MET cc_start: 0.8853 (mtm) cc_final: 0.8623 (mtp) REVERT: A 1471 ASP cc_start: 0.8700 (t0) cc_final: 0.8387 (t0) REVERT: A 1494 GLN cc_start: 0.7245 (mp10) cc_final: 0.6785 (mp10) REVERT: A 1545 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 62 LYS cc_start: 0.9035 (ttpm) cc_final: 0.8830 (ttpp) REVERT: B 96 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8036 (mtp85) REVERT: B 166 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7007 (mm) REVERT: B 184 LYS cc_start: 0.6954 (ttmm) cc_final: 0.6661 (mtpp) REVERT: C 65 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 122 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5475 (pm20) REVERT: C 128 TYR cc_start: 0.8022 (m-80) cc_final: 0.7428 (m-80) outliers start: 41 outliers final: 18 residues processed: 184 average time/residue: 0.6288 time to fit residues: 126.5311 Evaluate side-chains 174 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101101 restraints weight = 24760.432| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.65 r_work: 0.3130 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13970 Z= 0.121 Angle : 0.524 12.213 18879 Z= 0.265 Chirality : 0.040 0.359 2114 Planarity : 0.004 0.051 2197 Dihedral : 13.157 120.978 2355 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 21.88 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.24 (0.21), residues: 1556 helix: 2.02 (0.17), residues: 912 sheet: -0.24 (0.43), residues: 142 loop : -1.14 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 84 TYR 0.014 0.001 TYR B 182 PHE 0.016 0.001 PHE A1440 TRP 0.015 0.001 TRP A 808 HIS 0.010 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13949) covalent geometry : angle 0.50166 / 0.26 (18826) SS BOND : bond 0.00188 / 0.13 ( 10) SS BOND : angle 0.88682 / 0.61 ( 20) hydrogen bonds : bond 0.04465 / 2.89 ( 779) hydrogen bonds : angle 4.22832 / 2.97 ( 2221) link_BETA1-4 : bond 0.00283 / 0.16 ( 2) link_BETA1-4 : angle 3.15199 / 2.14 ( 6) link_NAG-ASN : bond 0.00416 / 0.31 ( 9) link_NAG-ASN : angle 3.66839 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.5224 (tpt) cc_final: 0.4782 (mmt) REVERT: A 145 MET cc_start: 0.8052 (mtm) cc_final: 0.7712 (ttp) REVERT: A 747 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 773 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7163 (mtmt) REVERT: A 798 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.4314 (ppp) REVERT: A 803 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5925 (p90) REVERT: A 835 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7975 (ttp-110) REVERT: A 1176 LYS cc_start: 0.6681 (mptt) cc_final: 0.3629 (ptpp) REVERT: A 1241 MET cc_start: 0.8647 (ttp) cc_final: 0.8363 (ttp) REVERT: A 1412 MET cc_start: 0.8922 (mtm) cc_final: 0.8704 (mtp) REVERT: A 1471 ASP cc_start: 0.8764 (t0) cc_final: 0.8517 (t0) REVERT: A 1494 GLN cc_start: 0.7309 (mp10) cc_final: 0.6838 (mp10) REVERT: A 1545 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: A 1761 GLU cc_start: 0.8103 (tp30) cc_final: 0.7881 (tp30) REVERT: B 62 LYS cc_start: 0.9089 (ttpm) cc_final: 0.8875 (ttpp) REVERT: B 96 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: B 113 TYR cc_start: 0.8556 (m-10) cc_final: 0.8108 (m-10) REVERT: B 154 MET cc_start: 0.7165 (tpt) cc_final: 0.6929 (tpp) REVERT: B 166 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7126 (mm) REVERT: B 182 TYR cc_start: 0.7389 (t80) cc_final: 0.6965 (t80) REVERT: B 184 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6792 (mtpp) REVERT: C 53 ASN cc_start: 0.8511 (t0) cc_final: 0.8188 (t0) REVERT: C 65 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8207 (tt) REVERT: C 122 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.5291 (pm20) REVERT: C 128 TYR cc_start: 0.8187 (m-80) cc_final: 0.7560 (m-80) outliers start: 30 outliers final: 15 residues processed: 173 average time/residue: 0.6197 time to fit residues: 117.6886 Evaluate side-chains 174 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101750 restraints weight = 17914.769| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.13 r_work: 0.3148 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13970 Z= 0.126 Angle : 0.519 12.374 18879 Z= 0.263 Chirality : 0.040 0.362 2114 Planarity : 0.004 0.062 2197 Dihedral : 12.844 113.322 2355 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.88 % Allowed : 22.61 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.30 (0.21), residues: 1556 helix: 2.08 (0.17), residues: 912 sheet: -0.28 (0.42), residues: 142 loop : -1.10 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 84 TYR 0.015 0.001 TYR B 182 PHE 0.022 0.001 PHE A 963 TRP 0.008 0.001 TRP A1700 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13949) covalent geometry : angle 0.49821 / 0.26 (18826) SS BOND : bond 0.00188 / 0.13 ( 10) SS BOND : angle 0.87812 / 0.60 ( 20) hydrogen bonds : bond 0.04505 / 2.91 ( 779) hydrogen bonds : angle 4.20046 / 2.94 ( 2221) link_BETA1-4 : bond 0.00217 / 0.13 ( 2) link_BETA1-4 : angle 3.16526 / 2.15 ( 6) link_NAG-ASN : bond 0.00375 / 0.28 ( 9) link_NAG-ASN : angle 3.54976 / 2.34 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.5211 (tpt) cc_final: 0.4785 (mmt) REVERT: A 145 MET cc_start: 0.8015 (mtm) cc_final: 0.7694 (ttp) REVERT: A 147 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7827 (p0) REVERT: A 747 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6576 (t0) REVERT: A 773 LYS cc_start: 0.7438 (ttmt) cc_final: 0.7102 (mtmt) REVERT: A 798 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.4205 (ppp) REVERT: A 803 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.5918 (p90) REVERT: A 835 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7915 (ttp-110) REVERT: A 1176 LYS cc_start: 0.6580 (mptt) cc_final: 0.3524 (ptpp) REVERT: A 1241 MET cc_start: 0.8593 (ttp) cc_final: 0.8307 (ttp) REVERT: A 1412 MET cc_start: 0.8888 (mtm) cc_final: 0.8663 (mtp) REVERT: A 1471 ASP cc_start: 0.8748 (t0) cc_final: 0.8431 (t0) REVERT: A 1494 GLN cc_start: 0.7355 (mp10) cc_final: 0.6879 (mp10) REVERT: A 1545 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: A 1761 GLU cc_start: 0.7994 (tp30) cc_final: 0.7767 (tp30) REVERT: B 96 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7891 (mtp85) REVERT: B 113 TYR cc_start: 0.8564 (m-10) cc_final: 0.8239 (m-10) REVERT: B 154 MET cc_start: 0.7103 (tpt) cc_final: 0.6867 (tpp) REVERT: B 182 TYR cc_start: 0.7356 (t80) cc_final: 0.7002 (t80) REVERT: B 184 LYS cc_start: 0.6996 (ttmm) cc_final: 0.6751 (mtpp) REVERT: C 53 ASN cc_start: 0.8477 (t0) cc_final: 0.8178 (t0) REVERT: C 65 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 122 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4538 (pm20) REVERT: C 128 TYR cc_start: 0.8165 (m-80) cc_final: 0.7515 (m-80) outliers start: 26 outliers final: 15 residues processed: 168 average time/residue: 0.6229 time to fit residues: 114.3014 Evaluate side-chains 171 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098941 restraints weight = 30443.177| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.94 r_work: 0.3108 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13970 Z= 0.121 Angle : 0.517 12.327 18879 Z= 0.262 Chirality : 0.040 0.355 2114 Planarity : 0.004 0.065 2197 Dihedral : 12.688 108.112 2355 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.81 % Allowed : 22.54 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.34 (0.21), residues: 1556 helix: 2.10 (0.17), residues: 914 sheet: -0.29 (0.42), residues: 142 loop : -1.08 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 84 TYR 0.013 0.001 TYR B 182 PHE 0.023 0.001 PHE A 963 TRP 0.009 0.001 TRP A1700 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13949) covalent geometry : angle 0.49647 / 0.26 (18826) SS BOND : bond 0.00192 / 0.14 ( 10) SS BOND : angle 0.86402 / 0.60 ( 20) hydrogen bonds : bond 0.04419 / 2.85 ( 779) hydrogen bonds : angle 4.17708 / 2.92 ( 2221) link_BETA1-4 : bond 0.00251 / 0.15 ( 2) link_BETA1-4 : angle 3.14952 / 2.14 ( 6) link_NAG-ASN : bond 0.00380 / 0.28 ( 9) link_NAG-ASN : angle 3.52555 / 2.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.5180 (tpt) cc_final: 0.4762 (mmt) REVERT: A 145 MET cc_start: 0.8019 (mtm) cc_final: 0.7616 (ttp) REVERT: A 747 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6493 (t0) REVERT: A 763 MET cc_start: 0.8624 (mtm) cc_final: 0.8424 (mtm) REVERT: A 773 LYS cc_start: 0.7413 (ttmt) cc_final: 0.7077 (mtmt) REVERT: A 798 MET cc_start: 0.4076 (OUTLIER) cc_final: 0.3790 (ppp) REVERT: A 803 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.5865 (p90) REVERT: A 835 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7896 (ttp-110) REVERT: A 1176 LYS cc_start: 0.6253 (mptt) cc_final: 0.3378 (ptpp) REVERT: A 1241 MET cc_start: 0.8526 (ttp) cc_final: 0.8233 (ttp) REVERT: A 1412 MET cc_start: 0.8852 (mtm) cc_final: 0.8631 (mtp) REVERT: A 1471 ASP cc_start: 0.8666 (t0) cc_final: 0.8346 (t0) REVERT: A 1494 GLN cc_start: 0.7346 (mp10) cc_final: 0.6875 (mp10) REVERT: A 1545 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 1761 GLU cc_start: 0.7846 (tp30) cc_final: 0.7604 (tp30) REVERT: B 96 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: B 113 TYR cc_start: 0.8434 (m-10) cc_final: 0.8130 (m-10) REVERT: B 154 MET cc_start: 0.6987 (tpt) cc_final: 0.6756 (tpp) REVERT: B 182 TYR cc_start: 0.7275 (t80) cc_final: 0.6982 (t80) REVERT: B 184 LYS cc_start: 0.6916 (ttmm) cc_final: 0.6674 (mtpp) REVERT: C 53 ASN cc_start: 0.8415 (t0) cc_final: 0.8111 (t0) REVERT: C 65 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (tt) REVERT: C 81 LEU cc_start: 0.7390 (tp) cc_final: 0.6948 (mt) REVERT: C 122 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.4525 (pm20) REVERT: C 128 TYR cc_start: 0.8100 (m-80) cc_final: 0.7511 (m-80) outliers start: 25 outliers final: 15 residues processed: 165 average time/residue: 0.6495 time to fit residues: 117.0560 Evaluate side-chains 169 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 140 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100803 restraints weight = 26683.328| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.74 r_work: 0.3134 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13970 Z= 0.114 Angle : 0.510 12.192 18879 Z= 0.258 Chirality : 0.040 0.340 2114 Planarity : 0.004 0.065 2197 Dihedral : 12.306 102.786 2355 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.59 % Allowed : 22.83 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.43 (0.22), residues: 1556 helix: 2.17 (0.17), residues: 914 sheet: -0.27 (0.42), residues: 142 loop : -1.01 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 84 TYR 0.014 0.001 TYR B 182 PHE 0.022 0.001 PHE A 963 TRP 0.009 0.001 TRP A 808 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13949) covalent geometry : angle 0.49081 / 0.25 (18826) SS BOND : bond 0.00194 / 0.14 ( 10) SS BOND : angle 0.86100 / 0.59 ( 20) hydrogen bonds : bond 0.04250 / 2.74 ( 779) hydrogen bonds : angle 4.13316 / 2.89 ( 2221) link_BETA1-4 : bond 0.00285 / 0.17 ( 2) link_BETA1-4 : angle 3.09766 / 2.11 ( 6) link_NAG-ASN : bond 0.00424 / 0.32 ( 9) link_NAG-ASN : angle 3.33178 / 2.17 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.4864 (tpt) cc_final: 0.4524 (mmt) REVERT: A 145 MET cc_start: 0.8033 (mtm) cc_final: 0.7709 (ttp) REVERT: A 147 ASN cc_start: 0.8261 (p0) cc_final: 0.7856 (p0) REVERT: A 151 TRP cc_start: 0.7017 (p-90) cc_final: 0.6743 (p-90) REVERT: A 747 ASP cc_start: 0.6720 (t0) cc_final: 0.6480 (t0) REVERT: A 773 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7083 (mtmt) REVERT: A 798 MET cc_start: 0.3911 (OUTLIER) cc_final: 0.3642 (ppp) REVERT: A 803 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5869 (p90) REVERT: A 835 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7892 (ttp-110) REVERT: A 842 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 1176 LYS cc_start: 0.6198 (mptt) cc_final: 0.3362 (ptpp) REVERT: A 1241 MET cc_start: 0.8505 (ttp) cc_final: 0.8196 (ttp) REVERT: A 1412 MET cc_start: 0.8840 (mtm) cc_final: 0.8631 (mtp) REVERT: A 1471 ASP cc_start: 0.8640 (t0) cc_final: 0.8330 (t0) REVERT: A 1494 GLN cc_start: 0.7447 (mp10) cc_final: 0.6973 (mp10) REVERT: A 1545 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: A 1761 GLU cc_start: 0.7825 (tp30) cc_final: 0.7591 (tp30) REVERT: B 96 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7797 (mtp85) REVERT: B 113 TYR cc_start: 0.8376 (m-10) cc_final: 0.8073 (m-10) REVERT: B 154 MET cc_start: 0.7032 (tpt) cc_final: 0.6794 (tpp) REVERT: B 182 TYR cc_start: 0.7316 (t80) cc_final: 0.7040 (t80) REVERT: B 184 LYS cc_start: 0.6940 (ttmm) cc_final: 0.6710 (mtpp) REVERT: C 53 ASN cc_start: 0.8393 (t0) cc_final: 0.8122 (t0) REVERT: C 65 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8161 (tt) REVERT: C 81 LEU cc_start: 0.7371 (tp) cc_final: 0.6948 (mt) REVERT: C 122 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.4498 (pm20) REVERT: C 128 TYR cc_start: 0.8052 (m-80) cc_final: 0.7377 (m-80) outliers start: 22 outliers final: 14 residues processed: 166 average time/residue: 0.6178 time to fit residues: 112.2915 Evaluate side-chains 169 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 119 optimal weight: 0.3980 chunk 102 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100959 restraints weight = 36479.027| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.25 r_work: 0.3094 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13970 Z= 0.109 Angle : 0.504 11.959 18879 Z= 0.255 Chirality : 0.039 0.330 2114 Planarity : 0.004 0.064 2197 Dihedral : 12.079 103.777 2355 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.81 % Allowed : 22.54 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.47 (0.22), residues: 1556 helix: 2.20 (0.17), residues: 916 sheet: -0.25 (0.41), residues: 142 loop : -1.01 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 84 TYR 0.013 0.001 TYR B 182 PHE 0.025 0.001 PHE A 963 TRP 0.008 0.001 TRP A1700 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13949) covalent geometry : angle 0.48519 / 0.25 (18826) SS BOND : bond 0.00194 / 0.14 ( 10) SS BOND : angle 0.84523 / 0.58 ( 20) hydrogen bonds : bond 0.04147 / 2.68 ( 779) hydrogen bonds : angle 4.09841 / 2.87 ( 2221) link_BETA1-4 : bond 0.00279 / 0.16 ( 2) link_BETA1-4 : angle 3.05586 / 2.08 ( 6) link_NAG-ASN : bond 0.00381 / 0.29 ( 9) link_NAG-ASN : angle 3.27044 / 2.15 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6269.44 seconds wall clock time: 107 minutes 41.84 seconds (6461.84 seconds total)