Starting phenix.real_space_refine on Wed Jul 30 23:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz1_34387/07_2025/8gz1_34387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz1_34387/07_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_34387/07_2025/8gz1_34387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz1_34387/07_2025/8gz1_34387.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz1_34387/07_2025/8gz1_34387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz1_34387/07_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.69, per 1000 atoms: 0.65 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: 3.38 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: 1.20 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: 4.09 Time building geometry restraints manager: 3.81 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 30.780 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- 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 : 1.362 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: 0.2323 time to fit residues: 71.8757 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 : 1.891 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101986 restraints weight = 23270.484| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.54 r_work: 0.3442 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.7140 (ttm) cc_final: 0.6744 (ttt) REVERT: D 180 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6079 (t80) REVERT: B 1206 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6991 (t80) REVERT: B 1265 CYS cc_start: 0.8432 (m) cc_final: 0.7884 (m) REVERT: B 1286 TYR cc_start: 0.6806 (m-80) cc_final: 0.6282 (m-80) REVERT: B 1481 MET cc_start: 0.8097 (mtp) cc_final: 0.7779 (mtt) REVERT: B 1580 TYR cc_start: 0.6027 (m-10) cc_final: 0.5760 (m-10) REVERT: B 1670 MET cc_start: 0.8037 (mtt) cc_final: 0.7775 (mtt) REVERT: B 1691 PHE cc_start: 0.8061 (t80) cc_final: 0.7850 (t80) REVERT: C 82 GLN cc_start: 0.8233 (mt0) cc_final: 0.7751 (mm-40) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.2039 time to fit residues: 54.5483 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 : 1.284 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 338 GLN B 347 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.142419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102290 restraints weight = 23366.447| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.58 r_work: 0.3445 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1721 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= 0.139 Angle : 0.621 9.538 16602 Z= 0.309 Chirality : 0.042 0.188 1921 Planarity : 0.004 0.052 2019 Dihedral : 7.974 53.763 1894 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.19 % Allowed : 13.19 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.23), residues: 1435 helix: 1.63 (0.18), residues: 840 sheet: 0.09 (0.55), residues: 99 loop : -1.12 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1415 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 0.00269 ( 7) link_NAG-ASN : angle 2.22831 ( 21) link_BETA1-4 : bond 0.00597 ( 10) link_BETA1-4 : angle 2.59365 ( 30) hydrogen bonds : bond 0.03812 ( 734) hydrogen bonds : angle 4.41952 ( 2088) SS BOND : bond 0.00239 ( 10) SS BOND : angle 1.04101 ( 20) covalent geometry : bond 0.00311 (12200) covalent geometry : angle 0.60664 (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 197 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8374 (t80) cc_final: 0.8098 (t80) REVERT: B 388 MET cc_start: 0.8165 (tmm) cc_final: 0.7796 (tmm) REVERT: B 848 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8564 (mm) REVERT: B 858 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: B 1206 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7168 (t80) REVERT: B 1265 CYS cc_start: 0.8468 (m) cc_final: 0.7879 (m) REVERT: B 1286 TYR cc_start: 0.6796 (m-80) cc_final: 0.6271 (m-80) REVERT: B 1304 LEU cc_start: 0.8897 (mt) cc_final: 0.8622 (mt) REVERT: B 1580 TYR cc_start: 0.6009 (m-10) cc_final: 0.5770 (m-10) REVERT: C 82 GLN cc_start: 0.8249 (mt0) cc_final: 0.7436 (mm110) outliers start: 28 outliers final: 15 residues processed: 181 average time/residue: 0.2082 time to fit residues: 57.4900 Evaluate side-chains 174 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 1327 ILE Chi-restraints excluded: chain B residue 1332 LEU 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: 8.9990 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 417 GLN B 728 ASN B 774 HIS B1466 ASN ** B1727 HIS ** 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 = 0.4072 r_free = 0.4072 target = 0.137039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095913 restraints weight = 23426.050| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.54 r_work: 0.3349 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12227 Z= 0.274 Angle : 0.748 12.471 16602 Z= 0.376 Chirality : 0.046 0.222 1921 Planarity : 0.004 0.048 2019 Dihedral : 6.879 55.716 1894 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.43 % Allowed : 15.53 % 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: 0.49 (0.22), residues: 1435 helix: 1.26 (0.17), residues: 837 sheet: -0.18 (0.52), residues: 109 loop : -1.18 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 284 HIS 0.005 0.001 HIS B 783 PHE 0.030 0.002 PHE C 63 TYR 0.026 0.002 TYR B 376 ARG 0.004 0.001 ARG D 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 7) link_NAG-ASN : angle 2.67988 ( 21) link_BETA1-4 : bond 0.00531 ( 10) link_BETA1-4 : angle 2.95716 ( 30) hydrogen bonds : bond 0.04223 ( 734) hydrogen bonds : angle 4.61567 ( 2088) SS BOND : bond 0.00428 ( 10) SS BOND : angle 1.43923 ( 20) covalent geometry : bond 0.00647 (12200) covalent geometry : angle 0.73071 (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 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8648 (t80) cc_final: 0.8324 (t80) REVERT: D 180 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6056 (t80) REVERT: B 848 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 858 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: B 1189 LYS cc_start: 0.8282 (pttm) cc_final: 0.8076 (mtmm) REVERT: B 1206 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7333 (t80) REVERT: B 1265 CYS cc_start: 0.8735 (m) cc_final: 0.8397 (m) REVERT: B 1580 TYR cc_start: 0.6234 (m-10) cc_final: 0.5986 (m-10) REVERT: B 1714 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8695 (mp) outliers start: 44 outliers final: 25 residues processed: 182 average time/residue: 0.2059 time to fit residues: 57.2502 Evaluate side-chains 182 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain D residue 174 LEU 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 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 1564 PHE 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 56 TYR 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: 8.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100236 restraints weight = 23466.020| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.59 r_work: 0.3403 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12227 Z= 0.143 Angle : 0.628 11.077 16602 Z= 0.312 Chirality : 0.042 0.224 1921 Planarity : 0.004 0.047 2019 Dihedral : 5.941 54.398 1894 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.20 % Allowed : 16.47 % Favored : 80.33 % 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: 0.80 (0.23), residues: 1435 helix: 1.52 (0.18), residues: 843 sheet: 0.09 (0.53), residues: 99 loop : -1.11 (0.30), residues: 493 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 B1616 TYR 0.022 0.002 TYR B1749 ARG 0.005 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 7) link_NAG-ASN : angle 2.28092 ( 21) link_BETA1-4 : bond 0.00544 ( 10) link_BETA1-4 : angle 2.50602 ( 30) hydrogen bonds : bond 0.03764 ( 734) hydrogen bonds : angle 4.38229 ( 2088) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.13222 ( 20) covalent geometry : bond 0.00326 (12200) covalent geometry : angle 0.61312 (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 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8660 (t80) cc_final: 0.8289 (t80) REVERT: D 184 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8385 (mttt) REVERT: B 388 MET cc_start: 0.8467 (tmm) cc_final: 0.8256 (tmm) REVERT: B 829 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 848 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 858 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: B 954 LEU cc_start: 0.8094 (mt) cc_final: 0.7839 (tp) REVERT: B 1206 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7225 (t80) REVERT: B 1265 CYS cc_start: 0.8680 (m) cc_final: 0.8129 (m) REVERT: B 1286 TYR cc_start: 0.7040 (m-80) cc_final: 0.6352 (m-80) REVERT: B 1301 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 1304 LEU cc_start: 0.9010 (mt) cc_final: 0.8750 (mt) REVERT: B 1437 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8546 (t0) REVERT: B 1481 MET cc_start: 0.8337 (mtp) cc_final: 0.8135 (mtp) REVERT: B 1580 TYR cc_start: 0.6367 (m-10) cc_final: 0.5878 (m-80) outliers start: 41 outliers final: 20 residues processed: 185 average time/residue: 0.2056 time to fit residues: 58.6782 Evaluate side-chains 183 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 829 LEU 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 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 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 0.0010 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.141967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100898 restraints weight = 23700.426| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.64 r_work: 0.3418 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12227 Z= 0.137 Angle : 0.619 9.746 16602 Z= 0.308 Chirality : 0.042 0.207 1921 Planarity : 0.004 0.048 2019 Dihedral : 5.551 54.256 1894 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.12 % Allowed : 17.33 % Favored : 79.55 % 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: 0.92 (0.23), residues: 1435 helix: 1.60 (0.18), residues: 844 sheet: 0.12 (0.54), residues: 99 loop : -1.03 (0.30), residues: 492 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 0.026 0.002 TYR B 812 ARG 0.004 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 7) link_NAG-ASN : angle 2.23864 ( 21) link_BETA1-4 : bond 0.00514 ( 10) link_BETA1-4 : angle 2.40543 ( 30) hydrogen bonds : bond 0.03624 ( 734) hydrogen bonds : angle 4.30130 ( 2088) SS BOND : bond 0.00291 ( 10) SS BOND : angle 1.05188 ( 20) covalent geometry : bond 0.00311 (12200) covalent geometry : angle 0.60508 (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 199 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8664 (t80) cc_final: 0.8289 (t80) REVERT: D 154 MET cc_start: 0.7348 (ttm) cc_final: 0.6995 (ttt) REVERT: D 184 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8365 (mttt) REVERT: B 388 MET cc_start: 0.8395 (tmm) cc_final: 0.8074 (tmm) REVERT: B 848 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8582 (mm) REVERT: B 858 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: B 954 LEU cc_start: 0.8107 (mt) cc_final: 0.7869 (tp) REVERT: B 1206 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 1265 CYS cc_start: 0.8682 (m) cc_final: 0.8143 (m) REVERT: B 1286 TYR cc_start: 0.7011 (m-80) cc_final: 0.6344 (m-80) REVERT: B 1301 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 1304 LEU cc_start: 0.8930 (mt) cc_final: 0.8693 (mt) REVERT: B 1437 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8598 (t0) REVERT: B 1481 MET cc_start: 0.8348 (mtp) cc_final: 0.8141 (mtp) REVERT: B 1536 MET cc_start: 0.8452 (tmm) cc_final: 0.8090 (tmm) REVERT: B 1559 LEU cc_start: 0.8723 (mt) cc_final: 0.8424 (pp) outliers start: 40 outliers final: 26 residues processed: 183 average time/residue: 0.2040 time to fit residues: 57.0541 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 871 SER 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 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 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN B1759 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.142604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101544 restraints weight = 23581.181| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.59 r_work: 0.3441 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2565 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= 0.126 Angle : 0.622 9.267 16602 Z= 0.306 Chirality : 0.041 0.219 1921 Planarity : 0.004 0.049 2019 Dihedral : 5.329 54.294 1894 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 18.35 % Favored : 78.53 % 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: 1.04 (0.23), residues: 1435 helix: 1.73 (0.18), residues: 838 sheet: 0.15 (0.54), residues: 99 loop : -1.00 (0.30), residues: 498 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 0.025 0.001 TYR C 69 ARG 0.004 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 7) link_NAG-ASN : angle 2.20129 ( 21) link_BETA1-4 : bond 0.00528 ( 10) link_BETA1-4 : angle 2.26608 ( 30) hydrogen bonds : bond 0.03486 ( 734) hydrogen bonds : angle 4.21670 ( 2088) SS BOND : bond 0.00229 ( 10) SS BOND : angle 0.94719 ( 20) covalent geometry : bond 0.00281 (12200) covalent geometry : angle 0.61028 (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 200 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8543 (t80) cc_final: 0.8211 (t80) REVERT: D 154 MET cc_start: 0.7338 (ttm) cc_final: 0.6990 (ttt) REVERT: D 184 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8393 (mttt) REVERT: B 388 MET cc_start: 0.8114 (tmm) cc_final: 0.7784 (tmm) REVERT: B 845 SER cc_start: 0.9038 (t) cc_final: 0.8489 (t) REVERT: B 848 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 858 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.6769 (m-10) REVERT: B 1206 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7091 (t80) REVERT: B 1265 CYS cc_start: 0.8543 (m) cc_final: 0.7947 (m) REVERT: B 1286 TYR cc_start: 0.6823 (m-80) cc_final: 0.6309 (m-80) REVERT: B 1301 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8454 (mm) REVERT: B 1304 LEU cc_start: 0.8845 (mt) cc_final: 0.8617 (mt) REVERT: B 1375 GLU cc_start: 0.7653 (tp30) cc_final: 0.7354 (tp30) REVERT: B 1437 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8463 (t0) REVERT: B 1536 MET cc_start: 0.8350 (tmm) cc_final: 0.8001 (tmm) REVERT: B 1559 LEU cc_start: 0.8689 (mt) cc_final: 0.8403 (pp) outliers start: 40 outliers final: 23 residues processed: 186 average time/residue: 0.2042 time to fit residues: 58.1993 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 871 SER 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 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 58 optimal weight: 0.0670 chunk 107 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 40.0000 overall best weight: 1.5722 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.142292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100896 restraints weight = 23751.760| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.62 r_work: 0.3420 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12227 Z= 0.146 Angle : 0.640 9.493 16602 Z= 0.316 Chirality : 0.042 0.199 1921 Planarity : 0.004 0.050 2019 Dihedral : 5.295 54.470 1894 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.97 % Allowed : 18.42 % Favored : 78.61 % 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: 1.01 (0.23), residues: 1435 helix: 1.69 (0.18), residues: 838 sheet: 0.27 (0.54), residues: 99 loop : -1.01 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1415 HIS 0.005 0.001 HIS B1727 PHE 0.025 0.001 PHE B1616 TYR 0.037 0.002 TYR C 69 ARG 0.003 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 7) link_NAG-ASN : angle 2.24233 ( 21) link_BETA1-4 : bond 0.00486 ( 10) link_BETA1-4 : angle 2.25083 ( 30) hydrogen bonds : bond 0.03554 ( 734) hydrogen bonds : angle 4.22963 ( 2088) SS BOND : bond 0.00257 ( 10) SS BOND : angle 1.00317 ( 20) covalent geometry : bond 0.00335 (12200) covalent geometry : angle 0.62781 (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 188 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8563 (t80) cc_final: 0.8242 (t80) REVERT: D 154 MET cc_start: 0.7350 (ttm) cc_final: 0.6999 (ttt) REVERT: D 184 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8370 (mttt) REVERT: B 388 MET cc_start: 0.8136 (tmm) cc_final: 0.7870 (tmm) REVERT: B 812 TYR cc_start: 0.6815 (t80) cc_final: 0.6495 (t80) REVERT: B 845 SER cc_start: 0.9055 (t) cc_final: 0.8509 (t) REVERT: B 848 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (mm) REVERT: B 858 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: B 954 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8287 (mm) REVERT: B 1206 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 1265 CYS cc_start: 0.8524 (m) cc_final: 0.7914 (m) REVERT: B 1286 TYR cc_start: 0.6878 (m-80) cc_final: 0.6337 (m-80) REVERT: B 1301 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 1304 LEU cc_start: 0.8856 (mt) cc_final: 0.8630 (mt) REVERT: B 1437 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8501 (t0) REVERT: B 1559 LEU cc_start: 0.8761 (mt) cc_final: 0.8493 (pp) outliers start: 38 outliers final: 28 residues processed: 175 average time/residue: 0.2164 time to fit residues: 57.6959 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 : 1.471 ------------------------------------------------------------------------------- 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 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 871 SER 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 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 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: 0.9980 chunk 112 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.0040 chunk 39 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.145267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104427 restraints weight = 23656.093| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.68 r_work: 0.3475 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12227 Z= 0.113 Angle : 0.609 10.200 16602 Z= 0.300 Chirality : 0.041 0.196 1921 Planarity : 0.004 0.050 2019 Dihedral : 5.029 53.653 1894 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.26 % Allowed : 19.67 % Favored : 78.06 % 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: 1.15 (0.23), residues: 1435 helix: 1.80 (0.18), residues: 840 sheet: 0.34 (0.55), residues: 99 loop : -0.96 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1415 HIS 0.003 0.001 HIS D 122 PHE 0.022 0.001 PHE B1616 TYR 0.037 0.001 TYR B1580 ARG 0.005 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 7) link_NAG-ASN : angle 2.09170 ( 21) link_BETA1-4 : bond 0.00517 ( 10) link_BETA1-4 : angle 2.10411 ( 30) hydrogen bonds : bond 0.03345 ( 734) hydrogen bonds : angle 4.11470 ( 2088) SS BOND : bond 0.00251 ( 10) SS BOND : angle 0.85780 ( 20) covalent geometry : bond 0.00241 (12200) covalent geometry : angle 0.59795 (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 190 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8560 (t80) cc_final: 0.8217 (t80) REVERT: D 154 MET cc_start: 0.7329 (ttm) cc_final: 0.6991 (ttt) REVERT: D 184 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8336 (mttt) REVERT: B 139 MET cc_start: 0.6484 (tpp) cc_final: 0.5595 (ttm) REVERT: B 388 MET cc_start: 0.8081 (tmm) cc_final: 0.7742 (tmm) REVERT: B 845 SER cc_start: 0.9021 (t) cc_final: 0.8479 (t) REVERT: B 848 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 858 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.6848 (m-10) REVERT: B 1206 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7094 (t80) REVERT: B 1265 CYS cc_start: 0.8498 (m) cc_final: 0.7894 (m) REVERT: B 1286 TYR cc_start: 0.6698 (m-80) cc_final: 0.6319 (m-80) REVERT: B 1304 LEU cc_start: 0.8747 (mt) cc_final: 0.8517 (mt) REVERT: B 1375 GLU cc_start: 0.7635 (tp30) cc_final: 0.7330 (tp30) REVERT: B 1437 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (t0) REVERT: B 1536 MET cc_start: 0.8454 (tmm) cc_final: 0.8044 (tmm) REVERT: C 66 ASN cc_start: 0.5460 (OUTLIER) cc_final: 0.5196 (m-40) REVERT: C 79 MET cc_start: 0.7271 (pmm) cc_final: 0.6445 (tmm) outliers start: 29 outliers final: 18 residues processed: 178 average time/residue: 0.2034 time to fit residues: 55.4010 Evaluate side-chains 174 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 292 TYR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE 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 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1646 MET Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 ASN 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 120 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.137890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098618 restraints weight = 23342.642| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.89 r_work: 0.3354 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12227 Z= 0.250 Angle : 0.747 11.451 16602 Z= 0.370 Chirality : 0.045 0.200 1921 Planarity : 0.004 0.050 2019 Dihedral : 5.500 55.752 1894 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.26 % Allowed : 19.44 % 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: 0.85 (0.23), residues: 1435 helix: 1.54 (0.18), residues: 832 sheet: 0.44 (0.55), residues: 99 loop : -1.06 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B1185 HIS 0.008 0.001 HIS B1727 PHE 0.021 0.002 PHE B 148 TYR 0.041 0.002 TYR B1580 ARG 0.004 0.001 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 7) link_NAG-ASN : angle 2.52654 ( 21) link_BETA1-4 : bond 0.00489 ( 10) link_BETA1-4 : angle 2.36768 ( 30) hydrogen bonds : bond 0.03887 ( 734) hydrogen bonds : angle 4.37672 ( 2088) SS BOND : bond 0.00417 ( 10) SS BOND : angle 2.65274 ( 20) covalent geometry : bond 0.00590 (12200) covalent geometry : angle 0.73037 (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: 29 poor density : 155 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8577 (t80) cc_final: 0.8227 (t80) REVERT: D 184 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8328 (mttt) REVERT: B 139 MET cc_start: 0.6645 (tpp) cc_final: 0.5705 (ttm) REVERT: B 848 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 858 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: B 1206 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7315 (t80) REVERT: B 1265 CYS cc_start: 0.8584 (m) cc_final: 0.8211 (m) REVERT: B 1286 TYR cc_start: 0.6966 (m-80) cc_final: 0.6413 (m-80) REVERT: B 1301 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 1304 LEU cc_start: 0.8939 (mt) cc_final: 0.8726 (mt) REVERT: B 1437 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8617 (t0) REVERT: C 66 ASN cc_start: 0.5555 (OUTLIER) cc_final: 0.5329 (m-40) REVERT: C 79 MET cc_start: 0.7299 (pmm) cc_final: 0.6529 (tmm) REVERT: C 82 GLN cc_start: 0.8464 (mt0) cc_final: 0.8039 (mm110) outliers start: 29 outliers final: 22 residues processed: 170 average time/residue: 0.2179 time to fit residues: 56.2188 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 190 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 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP 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 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1646 MET Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 ASN 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: 0.7980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 58 optimal weight: 20.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.142504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103187 restraints weight = 23367.124| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.55 r_work: 0.3462 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12227 Z= 0.120 Angle : 0.651 9.670 16602 Z= 0.318 Chirality : 0.041 0.196 1921 Planarity : 0.004 0.050 2019 Dihedral : 5.128 53.615 1894 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.80 % Allowed : 20.53 % Favored : 77.67 % 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: 1.09 (0.23), residues: 1435 helix: 1.71 (0.18), residues: 838 sheet: 0.49 (0.55), residues: 99 loop : -0.94 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1415 HIS 0.003 0.001 HIS D 122 PHE 0.022 0.001 PHE B1616 TYR 0.040 0.002 TYR B1580 ARG 0.005 0.000 ARG C 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 7) link_NAG-ASN : angle 2.14638 ( 21) link_BETA1-4 : bond 0.00509 ( 10) link_BETA1-4 : angle 2.09569 ( 30) hydrogen bonds : bond 0.03461 ( 734) hydrogen bonds : angle 4.19162 ( 2088) SS BOND : bond 0.00403 ( 10) SS BOND : angle 2.21673 ( 20) covalent geometry : bond 0.00262 (12200) covalent geometry : angle 0.63758 (16531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6782.15 seconds wall clock time: 117 minutes 8.06 seconds (7028.06 seconds total)