Starting phenix.real_space_refine on Thu May 15 07:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz1_34387/05_2025/8gz1_34387.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 957 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 101 5.16 5 Na 2 4.78 5 C 7818 2.51 5 N 1869 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11912 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1409 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 172} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 9307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9307 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 32, 'TRANS': 1119} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.26, per 1000 atoms: 0.61 Number of scatterers: 11912 At special positions: 0 Unit cell: (133.12, 141.44, 116.48, 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 101 16.00 Na 2 11.00 O 2122 8.00 N 1869 7.00 C 7818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS C 55 " distance=1.18 Simple disulfide: pdb=" SG CYS B 906 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 944 " - pdb=" SG CYS B 953 " distance=2.03 Simple disulfide: pdb=" SG CYS B1356 " - pdb=" SG CYS B1376 " distance=2.04 Simple disulfide: pdb=" SG CYS B1721 " - pdb=" SG CYS B1736 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 1 " - " ASN B 295 " " NAG B2001 " - " ASN B 289 " " NAG D 301 " - " ASN D 135 " " NAG E 1 " - " ASN B 308 " " NAG F 1 " - " ASN B 326 " " NAG G 1 " - " ASN B1358 " " NAG H 1 " - " ASN B1372 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 66.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'D' and resid 153 through 190 removed outlier: 3.557A pdb=" N ILE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.668A pdb=" N SER B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 158 through 179 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.742A pdb=" N TRP B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 223 through 234 removed outlier: 4.154A pdb=" N ALA B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 251 removed outlier: 3.618A pdb=" N ILE B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.661A pdb=" N SER B 291 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.602A pdb=" N PHE B 312 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 355 through 369 Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.034A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.695A pdb=" N PHE B 391 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 426 removed outlier: 3.540A pdb=" N GLU B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 731 removed outlier: 3.654A pdb=" N PHE B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 751 removed outlier: 4.397A pdb=" N MET B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 772 removed outlier: 4.019A pdb=" N MET B 772 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 807 Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 815 through 834 removed outlier: 3.955A pdb=" N LEU B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 857 removed outlier: 3.971A pdb=" N ARG B 847 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 removed outlier: 3.521A pdb=" N VAL B 872 " --> pdb=" O ILE B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 904 removed outlier: 5.580A pdb=" N LYS B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 902 " --> pdb=" O GLY B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 909 removed outlier: 4.062A pdb=" N ILE B 908 " --> pdb=" O CYS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 Processing helix chain 'B' and resid 937 through 949 removed outlier: 3.981A pdb=" N ASP B 943 " --> pdb=" O GLU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 3.981A pdb=" N CYS B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1197 Processing helix chain 'B' and resid 1197 through 1214 Processing helix chain 'B' and resid 1225 through 1255 removed outlier: 3.751A pdb=" N LYS B1237 " --> pdb=" O GLU B1233 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B1238 " --> pdb=" O TYR B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1261 Processing helix chain 'B' and resid 1262 through 1284 Processing helix chain 'B' and resid 1289 through 1297 removed outlier: 3.784A pdb=" N THR B1297 " --> pdb=" O LYS B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1298 through 1303 Proline residue: B1303 - end of helix Processing helix chain 'B' and resid 1304 through 1310 removed outlier: 3.880A pdb=" N SER B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1324 Processing helix chain 'B' and resid 1324 through 1350 removed outlier: 4.659A pdb=" N ASN B1329 " --> pdb=" O PRO B1325 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B1330 " --> pdb=" O SER B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1383 removed outlier: 3.693A pdb=" N CYS B1376 " --> pdb=" O ASN B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1411 Processing helix chain 'B' and resid 1414 through 1424 removed outlier: 3.649A pdb=" N ILE B1418 " --> pdb=" O GLY B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1439 No H-bonds generated for 'chain 'B' and resid 1437 through 1439' Processing helix chain 'B' and resid 1440 through 1452 removed outlier: 3.676A pdb=" N PHE B1444 " --> pdb=" O MET B1440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B1452 " --> pdb=" O ILE B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1453 through 1474 Processing helix chain 'B' and resid 1482 through 1496 Processing helix chain 'B' and resid 1509 through 1521 Processing helix chain 'B' and resid 1521 through 1541 removed outlier: 3.787A pdb=" N ASP B1525 " --> pdb=" O GLN B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1547 through 1581 removed outlier: 7.984A pdb=" N HIS B1578 " --> pdb=" O PHE B1574 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR B1579 " --> pdb=" O ALA B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1605 Processing helix chain 'B' and resid 1612 through 1622 Processing helix chain 'B' and resid 1623 through 1634 Processing helix chain 'B' and resid 1635 through 1674 Proline residue: B1649 - end of helix removed outlier: 3.902A pdb=" N ALA B1674 " --> pdb=" O MET B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1703 removed outlier: 3.910A pdb=" N THR B1703 " --> pdb=" O PHE B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1712 Processing helix chain 'B' and resid 1738 through 1772 removed outlier: 3.652A pdb=" N ASN B1759 " --> pdb=" O LEU B1755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B1767 " --> pdb=" O ALA B1763 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.103A pdb=" N ALA D 30 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN D 50 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR D 55 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG D 72 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP D 57 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.503A pdb=" N THR C 33 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.856A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.856A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 138 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 48 738 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3607 1.34 - 1.46: 3169 1.46 - 1.59: 5260 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 12200 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 12195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 15937 1.59 - 3.18: 470 3.18 - 4.76: 86 4.76 - 6.35: 33 6.35 - 7.94: 5 Bond angle restraints: 16531 Sorted by residual: angle pdb=" C GLU B1366 " pdb=" N ILE B1367 " pdb=" CA ILE B1367 " ideal model delta sigma weight residual 121.65 118.44 3.21 9.40e-01 1.13e+00 1.16e+01 angle pdb=" N SER B1452 " pdb=" CA SER B1452 " pdb=" C SER B1452 " ideal model delta sigma weight residual 114.56 110.67 3.89 1.27e+00 6.20e-01 9.39e+00 angle pdb=" N PRO B1718 " pdb=" CA PRO B1718 " pdb=" C PRO B1718 " ideal model delta sigma weight residual 110.70 114.21 -3.51 1.22e+00 6.72e-01 8.28e+00 angle pdb=" N TRP B 284 " pdb=" CA TRP B 284 " pdb=" C TRP B 284 " ideal model delta sigma weight residual 109.81 116.08 -6.27 2.21e+00 2.05e-01 8.04e+00 angle pdb=" N GLN B 246 " pdb=" CA GLN B 246 " pdb=" CB GLN B 246 " ideal model delta sigma weight residual 110.16 114.31 -4.15 1.48e+00 4.57e-01 7.85e+00 ... (remaining 16526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 6737 22.10 - 44.20: 521 44.20 - 66.30: 59 66.30 - 88.41: 41 88.41 - 110.51: 21 Dihedral angle restraints: 7379 sinusoidal: 3149 harmonic: 4230 Sorted by residual: dihedral pdb=" CB CYS B 944 " pdb=" SG CYS B 944 " pdb=" SG CYS B 953 " pdb=" CB CYS B 953 " ideal model delta sinusoidal sigma weight residual -86.00 -166.62 80.62 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS B1356 " pdb=" SG CYS B1356 " pdb=" SG CYS B1376 " pdb=" CB CYS B1376 " ideal model delta sinusoidal sigma weight residual -86.00 -148.42 62.42 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CA TYR B1580 " pdb=" C TYR B1580 " pdb=" N PHE B1581 " pdb=" CA PHE B1581 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 7376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1588 0.056 - 0.111: 287 0.111 - 0.167: 34 0.167 - 0.223: 3 0.223 - 0.278: 9 Chirality restraints: 1921 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B1358 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1918 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 736 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO B 737 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 737 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 737 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1718 " -0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO B1719 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B1719 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1719 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1415 " -0.014 2.00e-02 2.50e+03 1.45e-02 5.27e+00 pdb=" CG TRP B1415 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1415 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1415 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B1415 " -0.001 2.00e-02 2.50e+03 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 70 2.53 - 3.12: 9506 3.12 - 3.72: 18693 3.72 - 4.31: 24804 4.31 - 4.90: 41070 Nonbonded interactions: 94143 Sorted by model distance: nonbonded pdb=" SG CYS B 912 " pdb=" CD ARG C 135 " model vdw 1.940 3.800 nonbonded pdb=" SG CYS B 912 " pdb=" NE ARG C 135 " model vdw 2.024 3.480 nonbonded pdb=" N LYS B 907 " pdb=" OH TYR C 56 " model vdw 2.030 3.120 nonbonded pdb=" CA LYS B 907 " pdb=" OH TYR C 56 " model vdw 2.101 3.470 nonbonded pdb=" O ILE B 868 " pdb=" OG SER B 871 " model vdw 2.217 3.040 ... (remaining 94138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.710 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.009 0.855 12227 Z= 0.422 Angle : 0.816 47.023 16602 Z= 0.413 Chirality : 0.046 0.278 1921 Planarity : 0.004 0.070 2019 Dihedral : 17.164 110.508 4615 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1435 helix: 1.49 (0.18), residues: 827 sheet: -0.04 (0.54), residues: 97 loop : -1.25 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1415 HIS 0.011 0.001 HIS B 131 PHE 0.030 0.001 PHE B1581 TYR 0.018 0.002 TYR B1488 ARG 0.007 0.001 ARG B 344 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 2.87774 ( 21) link_BETA1-4 : bond 0.00538 ( 10) link_BETA1-4 : angle 2.26634 ( 30) hydrogen bonds : bond 0.13898 ( 734) hydrogen bonds : angle 5.71117 ( 2088) SS BOND : bond 0.27026 ( 10) SS BOND : angle 12.40266 ( 20) covalent geometry : bond 0.00354 (12200) covalent geometry : angle 0.68087 (16531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: D 154 MET cc_start: 0.7000 (ttm) cc_final: 0.6565 (ttt) REVERT: B 1265 CYS cc_start: 0.7722 (m) cc_final: 0.7204 (m) REVERT: B 1286 TYR cc_start: 0.6252 (m-80) cc_final: 0.6022 (m-80) REVERT: B 1735 ASP cc_start: 0.6243 (t70) cc_final: 0.5902 (t0) REVERT: C 65 LEU cc_start: 0.6511 (pp) cc_final: 0.6041 (pp) REVERT: C 82 GLN cc_start: 0.8539 (mt0) cc_final: 0.7991 (mm110) REVERT: C 84 ARG cc_start: 0.5827 (mpt-90) cc_final: 0.5503 (mmt90) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2149 time to fit residues: 66.3436 Evaluate side-chains 156 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN D 143 HIS ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1466 ASN C 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.142038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101992 restraints weight = 23270.486| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.54 r_work: 0.3443 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12227 Z= 0.171 Angle : 0.669 10.021 16602 Z= 0.337 Chirality : 0.043 0.201 1921 Planarity : 0.004 0.055 2019 Dihedral : 11.517 70.962 1894 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.64 % Allowed : 10.46 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1435 helix: 1.59 (0.18), residues: 832 sheet: -0.09 (0.53), residues: 99 loop : -1.17 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1415 HIS 0.005 0.001 HIS B 131 PHE 0.025 0.001 PHE C 63 TYR 0.022 0.002 TYR B1489 ARG 0.004 0.001 ARG D 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 7) link_NAG-ASN : angle 2.32475 ( 21) link_BETA1-4 : bond 0.00580 ( 10) link_BETA1-4 : angle 2.77804 ( 30) hydrogen bonds : bond 0.04256 ( 734) hydrogen bonds : angle 4.67723 ( 2088) SS BOND : bond 0.00373 ( 10) SS BOND : angle 1.13843 ( 20) covalent geometry : bond 0.00396 (12200) covalent geometry : angle 0.65326 (16531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.7229 (ttm) cc_final: 0.6838 (ttt) REVERT: D 180 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6019 (t80) REVERT: B 1206 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 1265 CYS cc_start: 0.8583 (m) cc_final: 0.8096 (m) REVERT: B 1286 TYR cc_start: 0.6869 (m-80) cc_final: 0.6290 (m-80) REVERT: B 1481 MET cc_start: 0.8206 (mtp) cc_final: 0.7902 (mtt) REVERT: B 1580 TYR cc_start: 0.6149 (m-10) cc_final: 0.5866 (m-10) REVERT: B 1670 MET cc_start: 0.8175 (mtt) cc_final: 0.7949 (mtt) REVERT: B 1691 PHE cc_start: 0.8252 (t80) cc_final: 0.7864 (t80) REVERT: C 82 GLN cc_start: 0.8212 (mt0) cc_final: 0.7737 (mm-40) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.2062 time to fit residues: 55.1648 Evaluate side-chains 175 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 139 optimal weight: 0.0670 chunk 113 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.0170 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 369 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1431 GLN C 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.143439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103606 restraints weight = 23362.823| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.59 r_work: 0.3465 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12227 Z= 0.124 Angle : 0.611 9.686 16602 Z= 0.303 Chirality : 0.042 0.188 1921 Planarity : 0.004 0.052 2019 Dihedral : 7.811 53.488 1894 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.03 % Allowed : 13.04 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1435 helix: 1.66 (0.18), residues: 840 sheet: 0.10 (0.55), residues: 99 loop : -1.09 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1185 HIS 0.004 0.001 HIS B 131 PHE 0.025 0.001 PHE C 63 TYR 0.020 0.002 TYR B 812 ARG 0.006 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 7) link_NAG-ASN : angle 2.18099 ( 21) link_BETA1-4 : bond 0.00616 ( 10) link_BETA1-4 : angle 2.56148 ( 30) hydrogen bonds : bond 0.03751 ( 734) hydrogen bonds : angle 4.39014 ( 2088) SS BOND : bond 0.00236 ( 10) SS BOND : angle 0.98143 ( 20) covalent geometry : bond 0.00271 (12200) covalent geometry : angle 0.59607 (16531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8330 (t80) cc_final: 0.8073 (t80) REVERT: D 154 MET cc_start: 0.7124 (ttm) cc_final: 0.6728 (ttt) REVERT: B 848 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 1206 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 1265 CYS cc_start: 0.8453 (m) cc_final: 0.7872 (m) REVERT: B 1286 TYR cc_start: 0.6748 (m-80) cc_final: 0.6243 (m-80) REVERT: B 1304 LEU cc_start: 0.8854 (mt) cc_final: 0.8588 (mt) REVERT: B 1580 TYR cc_start: 0.6016 (m-10) cc_final: 0.5776 (m-10) REVERT: B 1735 ASP cc_start: 0.6238 (t70) cc_final: 0.5878 (t0) REVERT: C 82 GLN cc_start: 0.8199 (mt0) cc_final: 0.7399 (mm-40) outliers start: 26 outliers final: 14 residues processed: 186 average time/residue: 0.2080 time to fit residues: 58.1470 Evaluate side-chains 175 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1327 ILE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 1 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 338 GLN B 369 GLN B 374 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1466 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101256 restraints weight = 23396.113| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.88 r_work: 0.3354 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12227 Z= 0.209 Angle : 0.682 11.199 16602 Z= 0.341 Chirality : 0.044 0.198 1921 Planarity : 0.004 0.048 2019 Dihedral : 6.328 55.013 1894 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.36 % Allowed : 14.91 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1435 helix: 1.53 (0.18), residues: 841 sheet: -0.13 (0.52), residues: 109 loop : -1.11 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.032 0.002 PHE C 63 TYR 0.023 0.002 TYR B1749 ARG 0.003 0.000 ARG C 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 7) link_NAG-ASN : angle 2.46039 ( 21) link_BETA1-4 : bond 0.00527 ( 10) link_BETA1-4 : angle 2.69577 ( 30) hydrogen bonds : bond 0.03871 ( 734) hydrogen bonds : angle 4.44781 ( 2088) SS BOND : bond 0.00351 ( 10) SS BOND : angle 1.29533 ( 20) covalent geometry : bond 0.00491 (12200) covalent geometry : angle 0.66676 (16531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8506 (t80) cc_final: 0.8217 (t80) REVERT: D 180 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6109 (t80) REVERT: B 388 MET cc_start: 0.8403 (tmm) cc_final: 0.8066 (tmm) REVERT: B 848 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8597 (mm) REVERT: B 858 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: B 1189 LYS cc_start: 0.8250 (pttm) cc_final: 0.7996 (mtmm) REVERT: B 1206 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7143 (t80) REVERT: B 1265 CYS cc_start: 0.8605 (m) cc_final: 0.8245 (m) REVERT: B 1580 TYR cc_start: 0.6126 (m-10) cc_final: 0.5886 (m-10) REVERT: B 1600 MET cc_start: 0.7781 (tmm) cc_final: 0.7137 (tmm) outliers start: 43 outliers final: 23 residues processed: 183 average time/residue: 0.2013 time to fit residues: 56.7129 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1452 SER Chi-restraints excluded: chain B residue 1564 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 93 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN B 774 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.141725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099908 restraints weight = 23443.635| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.66 r_work: 0.3408 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12227 Z= 0.161 Angle : 0.627 10.083 16602 Z= 0.312 Chirality : 0.042 0.224 1921 Planarity : 0.004 0.048 2019 Dihedral : 5.710 54.487 1894 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.97 % Allowed : 16.00 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1435 helix: 1.59 (0.18), residues: 841 sheet: 0.14 (0.54), residues: 99 loop : -1.08 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.017 0.001 PHE C 63 TYR 0.020 0.002 TYR B1749 ARG 0.002 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 2.26657 ( 21) link_BETA1-4 : bond 0.00531 ( 10) link_BETA1-4 : angle 2.40526 ( 30) hydrogen bonds : bond 0.03690 ( 734) hydrogen bonds : angle 4.34152 ( 2088) SS BOND : bond 0.00256 ( 10) SS BOND : angle 1.14985 ( 20) covalent geometry : bond 0.00375 (12200) covalent geometry : angle 0.61298 (16531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8531 (t80) cc_final: 0.8173 (t80) REVERT: D 184 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8413 (mttt) REVERT: B 388 MET cc_start: 0.8195 (tmm) cc_final: 0.7852 (tmm) REVERT: B 848 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 858 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 954 LEU cc_start: 0.8042 (mt) cc_final: 0.7770 (tp) REVERT: B 1206 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7221 (t80) REVERT: B 1220 ILE cc_start: 0.8749 (pt) cc_final: 0.8535 (mm) REVERT: B 1265 CYS cc_start: 0.8551 (m) cc_final: 0.7959 (m) REVERT: B 1437 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8469 (t0) REVERT: B 1580 TYR cc_start: 0.6157 (m-10) cc_final: 0.5775 (m-80) REVERT: B 1714 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8681 (mt) outliers start: 38 outliers final: 22 residues processed: 182 average time/residue: 0.2061 time to fit residues: 57.6557 Evaluate side-chains 176 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1714 ILE Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN B 369 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.143557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102106 restraints weight = 23605.546| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.67 r_work: 0.3440 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12227 Z= 0.123 Angle : 0.610 9.212 16602 Z= 0.301 Chirality : 0.041 0.212 1921 Planarity : 0.004 0.048 2019 Dihedral : 5.369 54.194 1894 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.50 % Allowed : 17.72 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1435 helix: 1.71 (0.18), residues: 842 sheet: 0.14 (0.54), residues: 99 loop : -0.99 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.017 0.001 PHE B1616 TYR 0.024 0.001 TYR B 812 ARG 0.002 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 7) link_NAG-ASN : angle 2.19102 ( 21) link_BETA1-4 : bond 0.00533 ( 10) link_BETA1-4 : angle 2.27386 ( 30) hydrogen bonds : bond 0.03503 ( 734) hydrogen bonds : angle 4.24559 ( 2088) SS BOND : bond 0.00190 ( 10) SS BOND : angle 1.00709 ( 20) covalent geometry : bond 0.00273 (12200) covalent geometry : angle 0.59741 (16531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8521 (t80) cc_final: 0.8152 (t80) REVERT: D 154 MET cc_start: 0.7259 (ttm) cc_final: 0.6915 (ttt) REVERT: D 184 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8379 (mttt) REVERT: B 388 MET cc_start: 0.8114 (tmm) cc_final: 0.7764 (tmm) REVERT: B 845 SER cc_start: 0.9025 (t) cc_final: 0.8476 (t) REVERT: B 848 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8598 (mm) REVERT: B 858 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: B 1206 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7071 (t80) REVERT: B 1265 CYS cc_start: 0.8546 (m) cc_final: 0.7952 (m) REVERT: B 1286 TYR cc_start: 0.6865 (m-80) cc_final: 0.6302 (m-80) REVERT: B 1301 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8437 (mm) REVERT: B 1304 LEU cc_start: 0.8848 (mt) cc_final: 0.8606 (mt) REVERT: B 1375 GLU cc_start: 0.7702 (tp30) cc_final: 0.7348 (tp30) REVERT: B 1437 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8452 (t0) REVERT: B 1536 MET cc_start: 0.8274 (tmm) cc_final: 0.7881 (tmm) REVERT: B 1559 LEU cc_start: 0.8600 (mt) cc_final: 0.8260 (pp) outliers start: 32 outliers final: 21 residues processed: 177 average time/residue: 0.2016 time to fit residues: 54.7023 Evaluate side-chains 176 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102139 restraints weight = 23583.369| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.67 r_work: 0.3443 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12227 Z= 0.127 Angle : 0.610 9.560 16602 Z= 0.302 Chirality : 0.041 0.191 1921 Planarity : 0.004 0.049 2019 Dihedral : 5.236 54.261 1894 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.73 % Allowed : 18.11 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1435 helix: 1.79 (0.18), residues: 834 sheet: 0.23 (0.54), residues: 99 loop : -1.04 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.017 0.001 PHE B1616 TYR 0.025 0.001 TYR C 69 ARG 0.002 0.000 ARG B1617 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 7) link_NAG-ASN : angle 2.19282 ( 21) link_BETA1-4 : bond 0.00501 ( 10) link_BETA1-4 : angle 2.20040 ( 30) hydrogen bonds : bond 0.03445 ( 734) hydrogen bonds : angle 4.16584 ( 2088) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.95633 ( 20) covalent geometry : bond 0.00285 (12200) covalent geometry : angle 0.59814 (16531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8524 (t80) cc_final: 0.8158 (t80) REVERT: D 154 MET cc_start: 0.7273 (ttm) cc_final: 0.6930 (ttt) REVERT: D 184 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8371 (mttt) REVERT: B 388 MET cc_start: 0.8056 (tmm) cc_final: 0.7727 (tmm) REVERT: B 845 SER cc_start: 0.9024 (t) cc_final: 0.8459 (t) REVERT: B 848 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8624 (mm) REVERT: B 858 TRP cc_start: 0.8063 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: B 954 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (mm) REVERT: B 1206 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7240 (t80) REVERT: B 1265 CYS cc_start: 0.8496 (m) cc_final: 0.7890 (m) REVERT: B 1286 TYR cc_start: 0.6845 (m-80) cc_final: 0.6309 (m-80) REVERT: B 1301 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8445 (mm) REVERT: B 1304 LEU cc_start: 0.8836 (mt) cc_final: 0.8601 (mt) REVERT: B 1437 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8411 (t0) REVERT: B 1536 MET cc_start: 0.8316 (tmm) cc_final: 0.7963 (tmm) REVERT: B 1559 LEU cc_start: 0.8634 (mt) cc_final: 0.8280 (pp) outliers start: 35 outliers final: 22 residues processed: 174 average time/residue: 0.2043 time to fit residues: 54.7121 Evaluate side-chains 177 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.140833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098865 restraints weight = 23837.991| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.65 r_work: 0.3396 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12227 Z= 0.193 Angle : 0.667 10.400 16602 Z= 0.331 Chirality : 0.043 0.197 1921 Planarity : 0.004 0.049 2019 Dihedral : 5.396 55.160 1894 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.43 % Allowed : 18.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1435 helix: 1.63 (0.18), residues: 835 sheet: 0.24 (0.54), residues: 99 loop : -1.08 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1185 HIS 0.006 0.001 HIS B1727 PHE 0.016 0.001 PHE B1616 TYR 0.025 0.002 TYR B 812 ARG 0.003 0.000 ARG B1388 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 7) link_NAG-ASN : angle 2.34299 ( 21) link_BETA1-4 : bond 0.00495 ( 10) link_BETA1-4 : angle 2.27410 ( 30) hydrogen bonds : bond 0.03668 ( 734) hydrogen bonds : angle 4.27136 ( 2088) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.10113 ( 20) covalent geometry : bond 0.00454 (12200) covalent geometry : angle 0.65496 (16531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8730 (t80) cc_final: 0.8321 (t80) REVERT: D 93 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6650 (m-40) REVERT: D 154 MET cc_start: 0.7435 (ttm) cc_final: 0.7070 (ttt) REVERT: D 184 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8370 (mttt) REVERT: B 139 MET cc_start: 0.6823 (tpp) cc_final: 0.5811 (ttm) REVERT: B 388 MET cc_start: 0.8507 (tmm) cc_final: 0.8242 (tmm) REVERT: B 845 SER cc_start: 0.9161 (t) cc_final: 0.8596 (t) REVERT: B 848 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8518 (mm) REVERT: B 858 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: B 954 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 1206 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7325 (t80) REVERT: B 1265 CYS cc_start: 0.8651 (m) cc_final: 0.8293 (m) REVERT: B 1286 TYR cc_start: 0.7037 (m-80) cc_final: 0.6395 (m-80) REVERT: B 1301 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8594 (mm) REVERT: B 1304 LEU cc_start: 0.8954 (mt) cc_final: 0.8713 (mt) REVERT: B 1437 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8683 (t0) REVERT: B 1559 LEU cc_start: 0.8736 (mt) cc_final: 0.8460 (pp) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 0.2065 time to fit residues: 56.3953 Evaluate side-chains 182 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1452 SER Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1695 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100678 restraints weight = 23490.066| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.77 r_work: 0.3345 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12227 Z= 0.215 Angle : 0.692 11.133 16602 Z= 0.346 Chirality : 0.044 0.215 1921 Planarity : 0.004 0.049 2019 Dihedral : 5.617 55.195 1894 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.51 % Allowed : 18.58 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1435 helix: 1.46 (0.18), residues: 832 sheet: 0.23 (0.54), residues: 99 loop : -1.11 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B1185 HIS 0.006 0.001 HIS B1727 PHE 0.017 0.002 PHE B 148 TYR 0.028 0.002 TYR B 812 ARG 0.004 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 7) link_NAG-ASN : angle 2.41989 ( 21) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.30732 ( 30) hydrogen bonds : bond 0.03860 ( 734) hydrogen bonds : angle 4.37497 ( 2088) SS BOND : bond 0.00565 ( 10) SS BOND : angle 1.70615 ( 20) covalent geometry : bond 0.00506 (12200) covalent geometry : angle 0.67854 (16531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8627 (t80) cc_final: 0.8226 (t80) REVERT: D 184 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8276 (mttt) REVERT: B 139 MET cc_start: 0.6682 (tpp) cc_final: 0.5672 (ttm) REVERT: B 829 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 848 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 858 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: B 954 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8231 (mm) REVERT: B 1206 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 1265 CYS cc_start: 0.8613 (m) cc_final: 0.8240 (m) REVERT: B 1286 TYR cc_start: 0.7058 (m-80) cc_final: 0.6440 (m-80) REVERT: B 1301 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 1304 LEU cc_start: 0.8977 (mt) cc_final: 0.8763 (mt) REVERT: B 1559 LEU cc_start: 0.8774 (mt) cc_final: 0.8550 (pp) REVERT: C 80 PHE cc_start: 0.4702 (p90) cc_final: 0.4501 (p90) outliers start: 45 outliers final: 30 residues processed: 176 average time/residue: 0.1964 time to fit residues: 52.8446 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1452 SER Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1621 LEU Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1695 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 137 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.141572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100149 restraints weight = 23415.044| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.62 r_work: 0.3417 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12227 Z= 0.147 Angle : 0.657 10.000 16602 Z= 0.325 Chirality : 0.042 0.204 1921 Planarity : 0.004 0.049 2019 Dihedral : 5.393 54.363 1894 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.42 % Allowed : 19.59 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1435 helix: 1.61 (0.18), residues: 836 sheet: 0.35 (0.55), residues: 99 loop : -1.04 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.021 0.001 PHE B1616 TYR 0.028 0.002 TYR B 812 ARG 0.003 0.000 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 7) link_NAG-ASN : angle 2.25451 ( 21) link_BETA1-4 : bond 0.00483 ( 10) link_BETA1-4 : angle 2.18067 ( 30) hydrogen bonds : bond 0.03622 ( 734) hydrogen bonds : angle 4.27789 ( 2088) SS BOND : bond 0.00287 ( 10) SS BOND : angle 1.74687 ( 20) covalent geometry : bond 0.00338 (12200) covalent geometry : angle 0.64432 (16531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8541 (t80) cc_final: 0.8092 (t80) REVERT: D 184 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8345 (mttt) REVERT: B 139 MET cc_start: 0.6607 (tpp) cc_final: 0.5622 (ttm) REVERT: B 388 MET cc_start: 0.8121 (tmm) cc_final: 0.7775 (tmm) REVERT: B 829 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 845 SER cc_start: 0.9057 (t) cc_final: 0.8458 (t) REVERT: B 848 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8619 (mm) REVERT: B 858 TRP cc_start: 0.8347 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: B 954 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 1206 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7110 (t80) REVERT: B 1265 CYS cc_start: 0.8539 (m) cc_final: 0.7936 (m) REVERT: B 1286 TYR cc_start: 0.6965 (m-80) cc_final: 0.6433 (m-80) REVERT: B 1301 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8564 (mm) REVERT: B 1304 LEU cc_start: 0.8875 (mt) cc_final: 0.8665 (mt) REVERT: B 1375 GLU cc_start: 0.7725 (tp30) cc_final: 0.7419 (tp30) REVERT: B 1536 MET cc_start: 0.8392 (tmm) cc_final: 0.8007 (tmm) REVERT: B 1559 LEU cc_start: 0.8752 (mt) cc_final: 0.8536 (pp) REVERT: C 79 MET cc_start: 0.7277 (pmm) cc_final: 0.6403 (tmm) REVERT: C 130 MET cc_start: 0.3512 (mmt) cc_final: 0.2886 (mmt) outliers start: 31 outliers final: 25 residues processed: 173 average time/residue: 0.2001 time to fit residues: 52.3598 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1307 LEU Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1621 LEU Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.142916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.101940 restraints weight = 23639.710| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.64 r_work: 0.3445 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12227 Z= 0.127 Angle : 0.626 9.724 16602 Z= 0.311 Chirality : 0.041 0.191 1921 Planarity : 0.004 0.050 2019 Dihedral : 5.195 54.097 1894 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.42 % Allowed : 19.05 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1435 helix: 1.68 (0.18), residues: 837 sheet: 0.53 (0.55), residues: 99 loop : -0.94 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B1415 HIS 0.004 0.001 HIS B1727 PHE 0.020 0.001 PHE B1616 TYR 0.020 0.002 TYR B 812 ARG 0.002 0.000 ARG B1617 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 7) link_NAG-ASN : angle 2.18453 ( 21) link_BETA1-4 : bond 0.00483 ( 10) link_BETA1-4 : angle 2.13903 ( 30) hydrogen bonds : bond 0.03450 ( 734) hydrogen bonds : angle 4.19651 ( 2088) SS BOND : bond 0.00254 ( 10) SS BOND : angle 1.29570 ( 20) covalent geometry : bond 0.00285 (12200) covalent geometry : angle 0.61434 (16531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6140.35 seconds wall clock time: 106 minutes 46.90 seconds (6406.90 seconds total)