Starting phenix.real_space_refine on Thu Jul 2 22:17:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky7_23070/07_2026/7ky7_23070.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 C 6683 2.51 5 N 1655 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10294 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 884, 7031 Classifications: {'peptide': 884} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 858} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2942 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 141 Unusual residues: {' MG': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10294 At special positions: 0 Unit cell: (148.176, 128.625, 98.784, 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 52 16.00 Mg 1 11.99 O 1903 8.00 N 1655 7.00 C 6683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.52 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 ALPHA1-4 " NAG F 2 " - " MAN F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 256 " " NAG D 1 " - " ASN B 298 " " NAG E 1 " - " ASN B 332 " " NAG F 1 " - " ASN B 240 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 236.3 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 52.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 282 through 299 removed outlier: 4.454A pdb=" N ILE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 621 removed outlier: 3.865A pdb=" N ARG A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.721A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 654 Processing helix chain 'A' and resid 659 through 679 removed outlier: 4.486A pdb=" N TYR A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.623A pdb=" N GLN A 705 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.581A pdb=" N ALA A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 779 removed outlier: 3.785A pdb=" N LYS A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 Processing helix chain 'A' and resid 794 through 803 removed outlier: 4.100A pdb=" N LYS A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 822 Processing helix chain 'A' and resid 843 through 856 removed outlier: 3.973A pdb=" N SER A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 950 removed outlier: 3.717A pdb=" N LEU A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 984 through 994 Processing helix chain 'A' and resid 1013 through 1024 Processing helix chain 'A' and resid 1036 through 1046 Processing helix chain 'A' and resid 1071 through 1087 removed outlier: 3.710A pdb=" N VAL A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 3.562A pdb=" N LYS A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1122 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1149 through 1162 Processing helix chain 'A' and resid 1174 through 1182 removed outlier: 3.708A pdb=" N ALA A1179 " --> pdb=" O SER A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1201 Processing helix chain 'A' and resid 1210 through 1217 removed outlier: 4.126A pdb=" N ARG A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1248 Proline residue: A1232 - end of helix removed outlier: 3.911A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 removed outlier: 4.691A pdb=" N ASN A1252 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A1253 " --> pdb=" O ILE A1250 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A1254 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1271 removed outlier: 4.588A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1284 removed outlier: 3.507A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1304 Processing helix chain 'A' and resid 1309 through 1337 Proline residue: A1331 - end of helix removed outlier: 4.391A pdb=" N LYS A1337 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1373 Processing helix chain 'A' and resid 1380 through 1401 Processing helix chain 'A' and resid 1402 through 1406 removed outlier: 3.516A pdb=" N ASN A1406 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1447 removed outlier: 3.713A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1449 through 1461 Processing helix chain 'A' and resid 1462 through 1465 removed outlier: 4.254A pdb=" N LEU A1465 " --> pdb=" O ASP A1462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1462 through 1465' Processing helix chain 'B' and resid 71 through 99 removed outlier: 3.774A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.698A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.514A pdb=" N ALA B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.608A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 288 through 292 removed outlier: 4.323A pdb=" N LYS B 291 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.637A pdb=" N ASN B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 398 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.676A pdb=" N LEU B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 3.698A pdb=" N ILE A1114 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A1113 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A1143 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 709 " --> pdb=" O TRP A1029 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A1031 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER A 711 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR A 708 " --> pdb=" O LEU A1169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 732 through 735 removed outlier: 5.723A pdb=" N VAL A 721 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG A1009 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A1004 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 954 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA4, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AA5, first strand: chain 'A' and resid 1188 through 1190 Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129 removed outlier: 6.566A pdb=" N VAL B 173 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 329 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 175 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 120 removed outlier: 6.024A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1314 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: 1.10 Time building geometry restraints manager: 0.86 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: 3203 1.34 - 1.46: 2294 1.46 - 1.58: 4965 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 10537 Sorted by residual: bond pdb=" C1 MAN F 3 " pdb=" C2 MAN F 3 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.71e+00 bond pdb=" C1 MAN F 3 " pdb=" O5 MAN F 3 " ideal model delta sigma weight residual 1.399 1.433 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N ASP A1462 " pdb=" CA ASP A1462 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.17e-02 7.31e+03 2.34e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 10532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 13944 1.82 - 3.65: 293 3.65 - 5.47: 51 5.47 - 7.30: 28 7.30 - 9.12: 7 Bond angle restraints: 14323 Sorted by residual: angle pdb=" N LEU A1164 " pdb=" CA LEU A1164 " pdb=" C LEU A1164 " ideal model delta sigma weight residual 110.91 102.95 7.96 1.17e+00 7.31e-01 4.62e+01 angle pdb=" N ASP B 56 " pdb=" CA ASP B 56 " pdb=" CB ASP B 56 " ideal model delta sigma weight residual 114.10 110.08 4.02 1.00e+00 1.00e+00 1.62e+01 angle pdb=" C GLU B 55 " pdb=" N ASP B 56 " pdb=" CA ASP B 56 " ideal model delta sigma weight residual 126.86 121.69 5.17 1.57e+00 4.06e-01 1.09e+01 angle pdb=" C PHE A1408 " pdb=" N TYR A1409 " pdb=" CA TYR A1409 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" OG1 THR A 991 " pdb=" CB THR A 991 " pdb=" CG2 THR A 991 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 ... (remaining 14318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5428 17.98 - 35.95: 537 35.95 - 53.93: 124 53.93 - 71.90: 14 71.90 - 89.88: 12 Dihedral angle restraints: 6115 sinusoidal: 2477 harmonic: 3638 Sorted by residual: dihedral pdb=" CA ASP A1349 " pdb=" C ASP A1349 " pdb=" N HIS A1350 " pdb=" CA HIS A1350 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A1250 " pdb=" C ILE A1250 " pdb=" N TYR A1251 " pdb=" CA TYR A1251 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 6112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1473 0.077 - 0.154: 144 0.154 - 0.231: 10 0.231 - 0.308: 7 0.308 - 0.385: 7 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C14 CLR A2005 " pdb=" C13 CLR A2005 " pdb=" C15 CLR A2005 " pdb=" C8 CLR A2005 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR B 501 " pdb=" C13 CLR B 501 " pdb=" C15 CLR B 501 " pdb=" C8 CLR B 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C14 CLR B 502 " pdb=" C13 CLR B 502 " pdb=" C15 CLR B 502 " pdb=" C8 CLR B 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1638 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1461 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C GLY A1461 " -0.067 2.00e-02 2.50e+03 pdb=" O GLY A1461 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A1462 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PHE B 398 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE B 398 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY B 399 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 623 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 624 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 624 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 624 " 0.036 5.00e-02 4.00e+02 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 27 2.34 - 2.98: 5457 2.98 - 3.62: 15428 3.62 - 4.26: 24834 4.26 - 4.90: 40726 Nonbonded interactions: 86472 Sorted by model distance: nonbonded pdb=" OG1 THR A 714 " pdb="MG MG A2001 " model vdw 1.705 2.170 nonbonded pdb=" O ASP A1173 " pdb="MG MG A2001 " model vdw 1.938 2.170 nonbonded pdb=" O GLY A1013 " pdb=" OG SER A1017 " model vdw 2.208 3.040 nonbonded pdb=" O PHE A1272 " pdb=" OG SER A1388 " model vdw 2.220 3.040 nonbonded pdb=" O LEU A1136 " pdb=" ND2 ASN A1139 " model vdw 2.228 3.120 ... (remaining 86467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.006 0.488 10548 Z= 0.303 Angle : 0.729 17.260 14354 Z= 0.364 Chirality : 0.054 0.385 1641 Planarity : 0.003 0.064 1761 Dihedral : 15.082 89.879 3771 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 1.01 % Allowed : 13.22 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.21), residues: 1231 helix: -1.61 (0.19), residues: 559 sheet: -2.24 (0.45), residues: 114 loop : -3.17 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 928 TYR 0.017 0.001 TYR B 280 PHE 0.023 0.001 PHE A1408 TRP 0.019 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (10537) covalent geometry : angle 0.70453 / 0.35 (14323) SS BOND : bond 0.34473 / 19.15 ( 2) SS BOND : angle 10.50037 / 6.17 ( 4) hydrogen bonds : bond 0.15438 / 9.72 ( 465) hydrogen bonds : angle 6.97003 / 4.77 ( 1314) link_ALPHA1-4 : bond 0.01160 / 0.73 ( 1) link_ALPHA1-4 : angle 1.14786 / 0.54 ( 3) link_BETA1-4 : bond 0.00551 / 0.33 ( 4) link_BETA1-4 : angle 1.53795 / 0.80 ( 12) link_NAG-ASN : bond 0.00194 / 0.11 ( 4) link_NAG-ASN : angle 1.85926 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.313 Fit side-chains REVERT: A 647 PHE cc_start: 0.7965 (t80) cc_final: 0.7726 (t80) REVERT: A 894 MET cc_start: -0.0872 (pmm) cc_final: -0.2393 (tmm) REVERT: A 1095 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 1108 GLN cc_start: 0.7037 (mp10) cc_final: 0.6756 (mp10) REVERT: A 1129 MET cc_start: 0.8895 (tpp) cc_final: 0.8658 (tpp) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.0828 time to fit residues: 13.9887 Evaluate side-chains 86 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 810 LYS Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN A 719 GLN A 888 ASN A1047 ASN A1051 ASN A1182 GLN A1219 HIS A1269 ASN A1323 GLN A1374 GLN B 61 GLN B 97 ASN B 131 HIS B 155 GLN B 186 HIS B 366 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107667 restraints weight = 13104.138| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.13 r_work: 0.3249 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10548 Z= 0.158 Angle : 0.615 9.575 14354 Z= 0.310 Chirality : 0.043 0.177 1641 Planarity : 0.004 0.067 1761 Dihedral : 6.173 55.578 1437 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.93 % Allowed : 15.89 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.23), residues: 1231 helix: -0.73 (0.21), residues: 589 sheet: -1.96 (0.48), residues: 109 loop : -2.87 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1436 TYR 0.019 0.001 TYR A1409 PHE 0.023 0.001 PHE A1408 TRP 0.021 0.001 TRP A1458 HIS 0.003 0.001 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10537) covalent geometry : angle 0.61216 / 0.31 (14323) SS BOND : bond 0.00665 / 0.37 ( 2) SS BOND : angle 0.95991 / 0.57 ( 4) hydrogen bonds : bond 0.04893 / 3.20 ( 465) hydrogen bonds : angle 5.24741 / 3.57 ( 1314) link_ALPHA1-4 : bond 0.01265 / 0.79 ( 1) link_ALPHA1-4 : angle 1.39721 / 0.69 ( 3) link_BETA1-4 : bond 0.00620 / 0.35 ( 4) link_BETA1-4 : angle 1.26405 / 0.67 ( 12) link_NAG-ASN : bond 0.00123 / 0.08 ( 4) link_NAG-ASN : angle 1.75275 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.306 Fit side-chains REVERT: A 608 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 619 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8465 (t80) REVERT: A 647 PHE cc_start: 0.7926 (t80) cc_final: 0.7693 (t80) REVERT: A 1095 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 1108 GLN cc_start: 0.7212 (mp10) cc_final: 0.6929 (mp10) REVERT: A 1129 MET cc_start: 0.9003 (tpp) cc_final: 0.8749 (tpp) REVERT: B 113 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7692 (t0) REVERT: B 136 TYR cc_start: 0.8334 (t80) cc_final: 0.7938 (t80) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 0.0661 time to fit residues: 10.7583 Evaluate side-chains 93 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107336 restraints weight = 13306.775| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.12 r_work: 0.3251 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10548 Z= 0.157 Angle : 0.590 8.965 14354 Z= 0.296 Chirality : 0.043 0.181 1641 Planarity : 0.004 0.067 1761 Dihedral : 5.813 48.737 1430 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.39 % Allowed : 17.63 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.24), residues: 1231 helix: -0.28 (0.21), residues: 587 sheet: -1.68 (0.49), residues: 108 loop : -2.62 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1436 TYR 0.019 0.001 TYR A1409 PHE 0.023 0.001 PHE A1408 TRP 0.020 0.001 TRP A1458 HIS 0.003 0.001 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10537) covalent geometry : angle 0.58665 / 0.30 (14323) SS BOND : bond 0.00284 / 0.18 ( 2) SS BOND : angle 0.75829 / 0.41 ( 4) hydrogen bonds : bond 0.04418 / 2.89 ( 465) hydrogen bonds : angle 4.98678 / 3.38 ( 1314) link_ALPHA1-4 : bond 0.01158 / 0.72 ( 1) link_ALPHA1-4 : angle 1.22370 / 0.62 ( 3) link_BETA1-4 : bond 0.00524 / 0.31 ( 4) link_BETA1-4 : angle 1.28018 / 0.65 ( 12) link_NAG-ASN : bond 0.00228 / 0.14 ( 4) link_NAG-ASN : angle 1.83790 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.382 Fit side-chains REVERT: A 593 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: A 608 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7412 (mp) REVERT: A 647 PHE cc_start: 0.7887 (t80) cc_final: 0.7622 (t80) REVERT: A 654 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 1108 GLN cc_start: 0.7249 (mp10) cc_final: 0.6970 (mp10) REVERT: A 1129 MET cc_start: 0.9015 (tpp) cc_final: 0.8769 (tpp) REVERT: A 1270 LEU cc_start: 0.8539 (mt) cc_final: 0.8264 (mp) REVERT: A 1445 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7033 (mp) REVERT: B 113 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7700 (t0) REVERT: B 136 TYR cc_start: 0.8306 (t80) cc_final: 0.7963 (t80) REVERT: B 292 MET cc_start: 0.8419 (ttm) cc_final: 0.8199 (ttm) REVERT: B 397 LEU cc_start: 0.7484 (tt) cc_final: 0.6753 (mt) outliers start: 26 outliers final: 13 residues processed: 99 average time/residue: 0.0673 time to fit residues: 10.3748 Evaluate side-chains 94 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 46 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN A1139 ASN A1252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108928 restraints weight = 13224.065| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.17 r_work: 0.3266 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10548 Z= 0.122 Angle : 0.565 7.867 14354 Z= 0.286 Chirality : 0.042 0.184 1641 Planarity : 0.004 0.065 1761 Dihedral : 5.667 50.265 1428 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.94 % Allowed : 17.63 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.24), residues: 1231 helix: -0.07 (0.22), residues: 587 sheet: -1.47 (0.49), residues: 107 loop : -2.52 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1436 TYR 0.019 0.001 TYR A1332 PHE 0.021 0.001 PHE A1408 TRP 0.019 0.001 TRP A1458 HIS 0.002 0.000 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10537) covalent geometry : angle 0.56226 / 0.29 (14323) SS BOND : bond 0.00232 / 0.14 ( 2) SS BOND : angle 0.50244 / 0.26 ( 4) hydrogen bonds : bond 0.04085 / 2.68 ( 465) hydrogen bonds : angle 4.82956 / 3.27 ( 1314) link_ALPHA1-4 : bond 0.01121 / 0.70 ( 1) link_ALPHA1-4 : angle 1.35947 / 0.70 ( 3) link_BETA1-4 : bond 0.00511 / 0.30 ( 4) link_BETA1-4 : angle 1.20211 / 0.63 ( 12) link_NAG-ASN : bond 0.00146 / 0.09 ( 4) link_NAG-ASN : angle 1.69761 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.240 Fit side-chains REVERT: A 593 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 654 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 1108 GLN cc_start: 0.7236 (mp10) cc_final: 0.6944 (mp10) REVERT: A 1129 MET cc_start: 0.9023 (tpp) cc_final: 0.8769 (tpp) REVERT: A 1270 LEU cc_start: 0.8491 (mt) cc_final: 0.8226 (mp) REVERT: A 1299 TYR cc_start: 0.8494 (t80) cc_final: 0.8041 (t80) REVERT: A 1445 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 61 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8686 (mt0) REVERT: B 113 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 136 TYR cc_start: 0.8319 (t80) cc_final: 0.7967 (t80) REVERT: B 292 MET cc_start: 0.8430 (ttm) cc_final: 0.8211 (ttm) REVERT: B 388 MET cc_start: 0.8050 (mmt) cc_final: 0.7653 (mmm) REVERT: B 397 LEU cc_start: 0.7518 (tt) cc_final: 0.6806 (mt) outliers start: 32 outliers final: 18 residues processed: 106 average time/residue: 0.0663 time to fit residues: 10.9203 Evaluate side-chains 96 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 32 optimal weight: 0.0070 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.170006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109636 restraints weight = 13166.983| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3275 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.120 Angle : 0.548 6.605 14354 Z= 0.280 Chirality : 0.041 0.182 1641 Planarity : 0.004 0.064 1761 Dihedral : 5.575 52.537 1428 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.57 % Allowed : 18.27 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.24), residues: 1231 helix: 0.14 (0.22), residues: 587 sheet: -1.34 (0.49), residues: 107 loop : -2.38 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.018 0.001 TYR B 280 PHE 0.022 0.001 PHE A 647 TRP 0.018 0.001 TRP B 348 HIS 0.002 0.000 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10537) covalent geometry : angle 0.54546 / 0.28 (14323) SS BOND : bond 0.00206 / 0.12 ( 2) SS BOND : angle 0.46284 / 0.24 ( 4) hydrogen bonds : bond 0.03933 / 2.59 ( 465) hydrogen bonds : angle 4.67630 / 3.15 ( 1314) link_ALPHA1-4 : bond 0.00983 / 0.61 ( 1) link_ALPHA1-4 : angle 1.25883 / 0.66 ( 3) link_BETA1-4 : bond 0.00496 / 0.29 ( 4) link_BETA1-4 : angle 1.20853 / 0.64 ( 12) link_NAG-ASN : bond 0.00113 / 0.07 ( 4) link_NAG-ASN : angle 1.57762 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.251 Fit side-chains REVERT: A 593 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: A 619 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 653 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7080 (tt) REVERT: A 654 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 1108 GLN cc_start: 0.7213 (mp10) cc_final: 0.6903 (mp10) REVERT: A 1129 MET cc_start: 0.9010 (tpp) cc_final: 0.8767 (tpp) REVERT: A 1270 LEU cc_start: 0.8323 (mt) cc_final: 0.8056 (mp) REVERT: A 1299 TYR cc_start: 0.8531 (t80) cc_final: 0.8189 (t80) REVERT: A 1445 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7095 (mp) REVERT: A 1452 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: B 61 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8632 (mt0) REVERT: B 113 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7534 (t0) REVERT: B 136 TYR cc_start: 0.8293 (t80) cc_final: 0.7980 (t80) REVERT: B 292 MET cc_start: 0.8360 (ttm) cc_final: 0.8138 (ttm) REVERT: B 342 LEU cc_start: 0.8551 (tp) cc_final: 0.8181 (tp) REVERT: B 388 MET cc_start: 0.8032 (mmt) cc_final: 0.7650 (mmm) REVERT: B 397 LEU cc_start: 0.7565 (tt) cc_final: 0.6862 (mt) outliers start: 28 outliers final: 15 residues processed: 111 average time/residue: 0.0649 time to fit residues: 11.1109 Evaluate side-chains 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1251 TYR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 0.0270 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.168832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107892 restraints weight = 13318.561| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.15 r_work: 0.3240 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.138 Angle : 0.555 6.589 14354 Z= 0.284 Chirality : 0.042 0.181 1641 Planarity : 0.004 0.064 1761 Dihedral : 5.567 54.452 1428 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.31 % Allowed : 18.18 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.24), residues: 1231 helix: 0.26 (0.22), residues: 589 sheet: -1.30 (0.48), residues: 107 loop : -2.33 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.018 0.001 TYR B 280 PHE 0.022 0.001 PHE A1408 TRP 0.012 0.001 TRP A1458 HIS 0.006 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10537) covalent geometry : angle 0.55164 / 0.28 (14323) SS BOND : bond 0.00304 / 0.18 ( 2) SS BOND : angle 0.56375 / 0.28 ( 4) hydrogen bonds : bond 0.03902 / 2.54 ( 465) hydrogen bonds : angle 4.61118 / 3.10 ( 1314) link_ALPHA1-4 : bond 0.01032 / 0.64 ( 1) link_ALPHA1-4 : angle 1.18881 / 0.61 ( 3) link_BETA1-4 : bond 0.00486 / 0.28 ( 4) link_BETA1-4 : angle 1.26982 / 0.67 ( 12) link_NAG-ASN : bond 0.00197 / 0.12 ( 4) link_NAG-ASN : angle 1.62586 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.254 Fit side-chains REVERT: A 593 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 619 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8523 (t80) REVERT: A 625 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6800 (mtt-85) REVERT: A 653 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7048 (tt) REVERT: A 654 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A 1108 GLN cc_start: 0.7258 (mp10) cc_final: 0.6946 (mp10) REVERT: A 1129 MET cc_start: 0.9022 (tpp) cc_final: 0.8776 (tpp) REVERT: A 1270 LEU cc_start: 0.8331 (mt) cc_final: 0.8042 (mp) REVERT: A 1289 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 1299 TYR cc_start: 0.8569 (t80) cc_final: 0.8149 (t80) REVERT: A 1445 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7128 (mp) REVERT: A 1452 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: B 61 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8669 (mt0) REVERT: B 113 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 136 TYR cc_start: 0.8324 (t80) cc_final: 0.7988 (t80) REVERT: B 292 MET cc_start: 0.8396 (ttm) cc_final: 0.8164 (ttm) REVERT: B 388 MET cc_start: 0.8029 (mmt) cc_final: 0.7551 (mmm) REVERT: B 397 LEU cc_start: 0.7683 (tt) cc_final: 0.7000 (mt) outliers start: 36 outliers final: 19 residues processed: 112 average time/residue: 0.0728 time to fit residues: 12.3963 Evaluate side-chains 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1251 TYR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 807 HIS B 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104410 restraints weight = 13179.218| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10548 Z= 0.204 Angle : 0.602 7.671 14354 Z= 0.306 Chirality : 0.044 0.175 1641 Planarity : 0.004 0.065 1761 Dihedral : 5.800 55.936 1428 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.31 % Allowed : 19.19 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1231 helix: 0.18 (0.21), residues: 588 sheet: -1.18 (0.49), residues: 105 loop : -2.25 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.022 0.002 TYR A1409 PHE 0.027 0.002 PHE A1408 TRP 0.016 0.001 TRP A1458 HIS 0.003 0.001 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (10537) covalent geometry : angle 0.59860 / 0.30 (14323) SS BOND : bond 0.00557 / 0.34 ( 2) SS BOND : angle 0.99438 / 0.46 ( 4) hydrogen bonds : bond 0.04233 / 2.73 ( 465) hydrogen bonds : angle 4.72401 / 3.18 ( 1314) link_ALPHA1-4 : bond 0.01222 / 0.76 ( 1) link_ALPHA1-4 : angle 1.12274 / 0.55 ( 3) link_BETA1-4 : bond 0.00532 / 0.31 ( 4) link_BETA1-4 : angle 1.39240 / 0.72 ( 12) link_NAG-ASN : bond 0.00405 / 0.25 ( 4) link_NAG-ASN : angle 1.91567 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.327 Fit side-chains REVERT: A 593 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: A 608 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7461 (mp) REVERT: A 625 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6987 (mtt-85) REVERT: A 653 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7081 (tt) REVERT: A 654 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: A 706 ILE cc_start: 0.9038 (mm) cc_final: 0.8472 (mm) REVERT: A 799 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.3322 (p0) REVERT: A 1108 GLN cc_start: 0.7296 (mp10) cc_final: 0.6990 (mp10) REVERT: A 1129 MET cc_start: 0.9021 (tpp) cc_final: 0.8765 (tpp) REVERT: A 1270 LEU cc_start: 0.8364 (mt) cc_final: 0.8084 (mp) REVERT: A 1299 TYR cc_start: 0.8623 (t80) cc_final: 0.8171 (t80) REVERT: A 1445 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7266 (mp) REVERT: A 1452 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 113 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 292 MET cc_start: 0.8413 (ttm) cc_final: 0.8181 (ttm) REVERT: B 348 TRP cc_start: 0.9494 (OUTLIER) cc_final: 0.8697 (t60) REVERT: B 388 MET cc_start: 0.8025 (mmt) cc_final: 0.7639 (mmm) outliers start: 36 outliers final: 20 residues processed: 112 average time/residue: 0.0736 time to fit residues: 12.6204 Evaluate side-chains 105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 120 optimal weight: 0.0980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.168902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108140 restraints weight = 13086.145| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.13 r_work: 0.3246 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.122 Angle : 0.568 8.461 14354 Z= 0.293 Chirality : 0.042 0.182 1641 Planarity : 0.004 0.068 1761 Dihedral : 5.620 58.052 1428 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.85 % Allowed : 20.20 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1231 helix: 0.31 (0.21), residues: 588 sheet: -1.03 (0.48), residues: 105 loop : -2.25 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.029 0.001 TYR B 136 PHE 0.020 0.001 PHE A1408 TRP 0.012 0.001 TRP A1458 HIS 0.002 0.000 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10537) covalent geometry : angle 0.56512 / 0.29 (14323) SS BOND : bond 0.00267 / 0.16 ( 2) SS BOND : angle 0.46517 / 0.23 ( 4) hydrogen bonds : bond 0.03888 / 2.54 ( 465) hydrogen bonds : angle 4.62208 / 3.11 ( 1314) link_ALPHA1-4 : bond 0.00987 / 0.62 ( 1) link_ALPHA1-4 : angle 1.30658 / 0.68 ( 3) link_BETA1-4 : bond 0.00484 / 0.28 ( 4) link_BETA1-4 : angle 1.20712 / 0.65 ( 12) link_NAG-ASN : bond 0.00104 / 0.06 ( 4) link_NAG-ASN : angle 1.55897 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.501 Fit side-chains REVERT: A 593 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 619 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (t80) REVERT: A 625 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6811 (mtt-85) REVERT: A 653 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7027 (tt) REVERT: A 654 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: A 706 ILE cc_start: 0.8972 (mm) cc_final: 0.8345 (mm) REVERT: A 799 ASP cc_start: 0.4005 (OUTLIER) cc_final: 0.3416 (p0) REVERT: A 1108 GLN cc_start: 0.7248 (mp10) cc_final: 0.6915 (mp10) REVERT: A 1129 MET cc_start: 0.9016 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1289 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8325 (p0) REVERT: A 1299 TYR cc_start: 0.8569 (t80) cc_final: 0.8108 (t80) REVERT: A 1445 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 1452 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 113 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 292 MET cc_start: 0.8359 (ttm) cc_final: 0.8130 (ttm) REVERT: B 348 TRP cc_start: 0.9446 (OUTLIER) cc_final: 0.8704 (t60) REVERT: B 376 ILE cc_start: 0.8783 (mt) cc_final: 0.8492 (mt) REVERT: B 388 MET cc_start: 0.8044 (mmt) cc_final: 0.7561 (mmm) REVERT: B 397 LEU cc_start: 0.7654 (tt) cc_final: 0.7000 (mt) outliers start: 31 outliers final: 16 residues processed: 104 average time/residue: 0.0735 time to fit residues: 11.5734 Evaluate side-chains 98 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.167662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107008 restraints weight = 13153.742| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10548 Z= 0.157 Angle : 0.581 8.406 14354 Z= 0.298 Chirality : 0.042 0.180 1641 Planarity : 0.004 0.065 1761 Dihedral : 5.670 58.450 1428 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.03 % Allowed : 20.02 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.24), residues: 1231 helix: 0.31 (0.21), residues: 591 sheet: -1.04 (0.48), residues: 105 loop : -2.24 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.026 0.001 TYR B 136 PHE 0.023 0.002 PHE A1234 TRP 0.013 0.001 TRP A1458 HIS 0.002 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10537) covalent geometry : angle 0.57795 / 0.30 (14323) SS BOND : bond 0.00387 / 0.23 ( 2) SS BOND : angle 0.69191 / 0.32 ( 4) hydrogen bonds : bond 0.03975 / 2.57 ( 465) hydrogen bonds : angle 4.62745 / 3.10 ( 1314) link_ALPHA1-4 : bond 0.01111 / 0.69 ( 1) link_ALPHA1-4 : angle 1.21235 / 0.61 ( 3) link_BETA1-4 : bond 0.00486 / 0.28 ( 4) link_BETA1-4 : angle 1.29075 / 0.68 ( 12) link_NAG-ASN : bond 0.00246 / 0.15 ( 4) link_NAG-ASN : angle 1.67737 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.367 Fit side-chains REVERT: A 593 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 619 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8474 (t80) REVERT: A 625 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6913 (mtt-85) REVERT: A 653 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 654 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 706 ILE cc_start: 0.9011 (mm) cc_final: 0.8447 (mm) REVERT: A 799 ASP cc_start: 0.3980 (OUTLIER) cc_final: 0.3398 (p0) REVERT: A 952 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.6972 (mmm160) REVERT: A 1108 GLN cc_start: 0.7274 (mp10) cc_final: 0.6956 (mp10) REVERT: A 1129 MET cc_start: 0.9019 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1289 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8371 (p0) REVERT: A 1299 TYR cc_start: 0.8595 (t80) cc_final: 0.8209 (t80) REVERT: A 1445 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 1452 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: B 113 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7736 (t0) REVERT: B 292 MET cc_start: 0.8361 (ttm) cc_final: 0.8133 (ttm) REVERT: B 348 TRP cc_start: 0.9500 (OUTLIER) cc_final: 0.8750 (t60) REVERT: B 397 LEU cc_start: 0.7621 (tt) cc_final: 0.6924 (mt) outliers start: 33 outliers final: 19 residues processed: 103 average time/residue: 0.0757 time to fit residues: 11.8769 Evaluate side-chains 104 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 114 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108824 restraints weight = 13064.060| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.12 r_work: 0.3258 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.122 Angle : 0.566 8.594 14354 Z= 0.293 Chirality : 0.042 0.186 1641 Planarity : 0.004 0.068 1761 Dihedral : 5.598 59.663 1428 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.12 % Allowed : 19.93 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1231 helix: 0.36 (0.21), residues: 591 sheet: -0.97 (0.48), residues: 105 loop : -2.26 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.028 0.001 TYR B 136 PHE 0.021 0.001 PHE A1408 TRP 0.012 0.001 TRP A1458 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10537) covalent geometry : angle 0.56328 / 0.29 (14323) SS BOND : bond 0.00243 / 0.15 ( 2) SS BOND : angle 0.43303 / 0.21 ( 4) hydrogen bonds : bond 0.03827 / 2.50 ( 465) hydrogen bonds : angle 4.59539 / 3.07 ( 1314) link_ALPHA1-4 : bond 0.00986 / 0.62 ( 1) link_ALPHA1-4 : angle 1.32467 / 0.69 ( 3) link_BETA1-4 : bond 0.00466 / 0.27 ( 4) link_BETA1-4 : angle 1.20179 / 0.65 ( 12) link_NAG-ASN : bond 0.00101 / 0.06 ( 4) link_NAG-ASN : angle 1.50680 / 0.84 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.369 Fit side-chains REVERT: A 593 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 619 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8468 (t80) REVERT: A 625 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: A 653 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7048 (tt) REVERT: A 654 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: A 706 ILE cc_start: 0.8991 (mm) cc_final: 0.8382 (mm) REVERT: A 799 ASP cc_start: 0.4022 (OUTLIER) cc_final: 0.3375 (p0) REVERT: A 952 ARG cc_start: 0.7907 (mmt-90) cc_final: 0.6952 (mmm160) REVERT: A 1108 GLN cc_start: 0.7242 (mp10) cc_final: 0.6909 (mp10) REVERT: A 1129 MET cc_start: 0.9028 (tpp) cc_final: 0.8790 (tpp) REVERT: A 1289 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8302 (p0) REVERT: A 1299 TYR cc_start: 0.8593 (t80) cc_final: 0.8177 (t80) REVERT: A 1445 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7331 (mp) REVERT: A 1446 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: A 1452 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 113 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7802 (t0) REVERT: B 292 MET cc_start: 0.8373 (ttm) cc_final: 0.8143 (ttm) REVERT: B 342 LEU cc_start: 0.8529 (tp) cc_final: 0.8201 (tp) REVERT: B 348 TRP cc_start: 0.9459 (OUTLIER) cc_final: 0.8696 (t60) REVERT: B 397 LEU cc_start: 0.7676 (tt) cc_final: 0.6997 (mt) REVERT: B 402 LYS cc_start: 0.8053 (tttm) cc_final: 0.7610 (mmtm) outliers start: 34 outliers final: 17 residues processed: 106 average time/residue: 0.0801 time to fit residues: 12.9216 Evaluate side-chains 104 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1446 PHE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107259 restraints weight = 13186.661| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.13 r_work: 0.3234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.151 Angle : 0.577 8.330 14354 Z= 0.297 Chirality : 0.042 0.180 1641 Planarity : 0.004 0.064 1761 Dihedral : 5.652 59.770 1428 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.85 % Allowed : 19.93 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1231 helix: 0.37 (0.21), residues: 592 sheet: -0.96 (0.48), residues: 105 loop : -2.18 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1436 TYR 0.027 0.001 TYR B 136 PHE 0.023 0.001 PHE A1408 TRP 0.013 0.001 TRP A1458 HIS 0.003 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10537) covalent geometry : angle 0.57425 / 0.30 (14323) SS BOND : bond 0.00341 / 0.21 ( 2) SS BOND : angle 0.62123 / 0.29 ( 4) hydrogen bonds : bond 0.03915 / 2.53 ( 465) hydrogen bonds : angle 4.61527 / 3.09 ( 1314) link_ALPHA1-4 : bond 0.01071 / 0.67 ( 1) link_ALPHA1-4 : angle 1.20649 / 0.61 ( 3) link_BETA1-4 : bond 0.00467 / 0.27 ( 4) link_BETA1-4 : angle 1.27777 / 0.68 ( 12) link_NAG-ASN : bond 0.00223 / 0.14 ( 4) link_NAG-ASN : angle 1.59915 / 0.88 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.25 seconds wall clock time: 51 minutes 24.34 seconds (3084.34 seconds total)