Starting phenix.real_space_refine on Fri Feb 14 20:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_23070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_23070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_23070.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_23070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky7_23070/02_2025/7ky7_23070.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'GLU: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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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: 6.70, per 1000 atoms: 0.65 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.06 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: 4.33 Time building geometry restraints manager: 3.16 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 - 20.34: 6074 20.34 - 40.68: 501 40.68 - 61.02: 96 61.02 - 81.36: 11 81.36 - 101.71: 15 Dihedral angle restraints: 6697 sinusoidal: 3059 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 6694 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: 0.880 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.004 0.043 10537 Z= 0.257 Angle : 0.705 9.123 14323 Z= 0.354 Chirality : 0.054 0.385 1641 Planarity : 0.003 0.064 1761 Dihedral : 15.463 101.706 4353 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 PHE 0.023 0.001 PHE A1408 TYR 0.017 0.001 TYR B 280 ARG 0.003 0.000 ARG A 928 *********************** 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 : 1.063 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: 0.2459 time to fit residues: 40.9583 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 : 1.639 ------------------------------------------------------------------------------- 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 104 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4148 r_free = 0.4148 target = 0.168342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107546 restraints weight = 13094.664| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.12 r_work: 0.3254 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10537 Z= 0.229 Angle : 0.619 10.255 14323 Z= 0.312 Chirality : 0.044 0.201 1641 Planarity : 0.004 0.067 1761 Dihedral : 9.876 84.727 2019 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.02 % Allowed : 15.98 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.23), residues: 1231 helix: -0.68 (0.21), residues: 587 sheet: -1.96 (0.48), residues: 109 loop : -2.81 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1458 HIS 0.003 0.001 HIS A1336 PHE 0.023 0.001 PHE A1408 TYR 0.019 0.001 TYR A1409 ARG 0.005 0.000 ARG A1436 *********************** 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 110 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.039 Fit side-chains REVERT: A 608 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7325 (mp) REVERT: A 619 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (t80) REVERT: A 647 PHE cc_start: 0.7917 (t80) cc_final: 0.7682 (t80) REVERT: A 1095 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 1108 GLN cc_start: 0.7216 (mp10) cc_final: 0.6931 (mp10) REVERT: A 1129 MET cc_start: 0.9013 (tpp) cc_final: 0.8750 (tpp) REVERT: B 113 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7696 (t0) REVERT: B 136 TYR cc_start: 0.8346 (t80) cc_final: 0.7977 (t80) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.1943 time to fit residues: 31.3010 Evaluate side-chains 94 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 1287 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 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN A1208 GLN B 61 GLN B 155 GLN B 354 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105185 restraints weight = 13392.534| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.15 r_work: 0.3209 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10537 Z= 0.299 Angle : 0.629 12.812 14323 Z= 0.313 Chirality : 0.045 0.213 1641 Planarity : 0.004 0.069 1761 Dihedral : 9.264 73.644 2012 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.94 % Allowed : 17.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.23), residues: 1231 helix: -0.33 (0.21), residues: 580 sheet: -1.63 (0.49), residues: 105 loop : -2.59 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1458 HIS 0.004 0.001 HIS A1336 PHE 0.024 0.002 PHE A1408 TYR 0.021 0.002 TYR A1409 ARG 0.004 0.000 ARG A1436 *********************** 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 111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 1.007 Fit side-chains REVERT: A 593 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 608 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7470 (mp) REVERT: A 647 PHE cc_start: 0.7860 (t80) cc_final: 0.7592 (t80) REVERT: A 654 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: A 1108 GLN cc_start: 0.7200 (mp10) cc_final: 0.6908 (mp10) REVERT: A 1129 MET cc_start: 0.9014 (tpp) cc_final: 0.8765 (tpp) REVERT: A 1445 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7064 (mp) REVERT: B 113 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 292 MET cc_start: 0.8393 (ttm) cc_final: 0.8157 (ttm) REVERT: B 388 MET cc_start: 0.7989 (mmt) cc_final: 0.7629 (mmt) outliers start: 32 outliers final: 14 residues processed: 102 average time/residue: 0.1945 time to fit residues: 30.3138 Evaluate side-chains 96 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 626 SER 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 1122 VAL Chi-restraints excluded: chain A residue 1212 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 97 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 876 GLN A1252 ASN B 61 GLN B 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107070 restraints weight = 13127.087| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.12 r_work: 0.3244 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10537 Z= 0.219 Angle : 0.588 7.971 14323 Z= 0.296 Chirality : 0.043 0.235 1641 Planarity : 0.004 0.069 1761 Dihedral : 8.661 61.231 2010 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.75 % Allowed : 18.37 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1231 helix: -0.10 (0.21), residues: 586 sheet: -1.49 (0.49), residues: 105 loop : -2.52 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 PHE 0.022 0.001 PHE A1408 TYR 0.023 0.001 TYR B 136 ARG 0.004 0.000 ARG A1436 *********************** 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 117 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.133 Fit side-chains REVERT: A 593 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 654 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: A 1108 GLN cc_start: 0.7238 (mp10) cc_final: 0.6939 (mp10) REVERT: A 1129 MET cc_start: 0.8998 (tpp) cc_final: 0.8751 (tpp) REVERT: A 1270 LEU cc_start: 0.8406 (mt) cc_final: 0.8128 (mp) REVERT: A 1445 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 66 ILE cc_start: 0.7973 (mp) cc_final: 0.7718 (mp) REVERT: B 113 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7718 (t0) REVERT: B 292 MET cc_start: 0.8424 (ttm) cc_final: 0.8203 (ttm) REVERT: B 388 MET cc_start: 0.8000 (mmt) cc_final: 0.7585 (mmm) REVERT: B 397 LEU cc_start: 0.7526 (tt) cc_final: 0.6808 (mt) outliers start: 30 outliers final: 17 residues processed: 109 average time/residue: 0.1947 time to fit residues: 32.1906 Evaluate side-chains 96 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 GLU 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 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 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4106 r_free = 0.4106 target = 0.164309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103047 restraints weight = 13225.387| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.12 r_work: 0.3177 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10537 Z= 0.363 Angle : 0.644 8.044 14323 Z= 0.324 Chirality : 0.046 0.182 1641 Planarity : 0.004 0.070 1761 Dihedral : 8.223 58.917 2010 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.53 % Rotamer: Outliers : 3.49 % Allowed : 17.72 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.24), residues: 1231 helix: -0.09 (0.21), residues: 582 sheet: -1.54 (0.49), residues: 105 loop : -2.41 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1458 HIS 0.004 0.001 HIS A1336 PHE 0.027 0.002 PHE A1408 TYR 0.026 0.002 TYR A1409 ARG 0.004 0.000 ARG A1436 *********************** 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 117 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.134 Fit side-chains REVERT: A 593 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: A 608 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 625 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6995 (mtt-85) REVERT: A 653 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7094 (tt) REVERT: A 654 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: A 1108 GLN cc_start: 0.7258 (mp10) cc_final: 0.6962 (mp10) REVERT: A 1129 MET cc_start: 0.9043 (tpp) cc_final: 0.8770 (tpp) REVERT: A 1270 LEU cc_start: 0.8447 (mt) cc_final: 0.8187 (mp) REVERT: A 1299 TYR cc_start: 0.8617 (t80) cc_final: 0.8144 (t80) REVERT: A 1336 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8035 (p-80) REVERT: A 1445 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7254 (mp) REVERT: A 1452 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: B 66 ILE cc_start: 0.7930 (mp) cc_final: 0.7722 (mp) REVERT: B 113 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7696 (t0) REVERT: B 388 MET cc_start: 0.8048 (mmt) cc_final: 0.7644 (mmm) outliers start: 38 outliers final: 22 residues processed: 109 average time/residue: 0.2089 time to fit residues: 34.1672 Evaluate side-chains 105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 681 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 719 GLN 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 1164 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1336 HIS 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 377 VAL 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 67 optimal weight: 0.0870 chunk 99 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1252 ASN B 155 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.170461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109524 restraints weight = 13156.514| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.08 r_work: 0.3266 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10537 Z= 0.148 Angle : 0.566 8.466 14323 Z= 0.289 Chirality : 0.042 0.185 1641 Planarity : 0.004 0.072 1761 Dihedral : 7.726 59.807 2010 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.21 % Allowed : 18.82 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1231 helix: 0.19 (0.22), residues: 586 sheet: -1.28 (0.49), residues: 105 loop : -2.41 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1458 HIS 0.005 0.001 HIS A 942 PHE 0.018 0.001 PHE A1408 TYR 0.021 0.001 TYR A1332 ARG 0.003 0.000 ARG A1436 *********************** 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 117 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 1.077 Fit side-chains REVERT: A 619 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8465 (t80) REVERT: A 625 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6829 (mtt-85) REVERT: A 653 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7076 (tt) REVERT: A 654 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: A 799 ASP cc_start: 0.3795 (OUTLIER) cc_final: 0.3205 (p0) REVERT: A 1108 GLN cc_start: 0.7223 (mp10) cc_final: 0.6905 (mp10) REVERT: A 1129 MET cc_start: 0.9016 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1270 LEU cc_start: 0.8312 (mt) cc_final: 0.8064 (mp) REVERT: A 1289 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (p0) REVERT: A 1299 TYR cc_start: 0.8600 (t80) cc_final: 0.8144 (t80) REVERT: A 1336 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.7861 (p-80) REVERT: A 1445 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7265 (mp) REVERT: A 1446 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7863 (m-10) REVERT: A 1452 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: B 66 ILE cc_start: 0.7952 (mp) cc_final: 0.7737 (mp) REVERT: B 113 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 238 MET cc_start: 0.8922 (ttt) cc_final: 0.8297 (ttt) REVERT: B 292 MET cc_start: 0.8306 (ttm) cc_final: 0.8096 (ttm) REVERT: B 388 MET cc_start: 0.8059 (mmt) cc_final: 0.7575 (mmm) REVERT: B 397 LEU cc_start: 0.7671 (tt) cc_final: 0.6988 (mt) outliers start: 35 outliers final: 16 residues processed: 112 average time/residue: 0.2086 time to fit residues: 35.2547 Evaluate side-chains 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 719 GLN 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 1336 HIS 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 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 36 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109742 restraints weight = 13255.470| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.51 r_work: 0.3204 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.199 Angle : 0.562 7.689 14323 Z= 0.287 Chirality : 0.042 0.178 1641 Planarity : 0.004 0.066 1761 Dihedral : 7.500 58.183 2010 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.75 % Allowed : 20.20 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1231 helix: 0.26 (0.22), residues: 588 sheet: -1.18 (0.49), residues: 105 loop : -2.31 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1458 HIS 0.002 0.001 HIS A 942 PHE 0.022 0.001 PHE A1408 TYR 0.029 0.001 TYR B 136 ARG 0.003 0.000 ARG A1436 *********************** 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 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 1.224 Fit side-chains REVERT: A 593 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 619 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8467 (t80) REVERT: A 625 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6812 (mtt-85) REVERT: A 653 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6950 (tt) REVERT: A 654 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: A 1108 GLN cc_start: 0.7252 (mp10) cc_final: 0.6940 (mp10) REVERT: A 1129 MET cc_start: 0.9048 (tpp) cc_final: 0.8791 (tpp) REVERT: A 1299 TYR cc_start: 0.8628 (t80) cc_final: 0.8136 (t80) REVERT: A 1317 MET cc_start: 0.8345 (mtm) cc_final: 0.8124 (mtm) REVERT: A 1445 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 1452 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 113 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7739 (t0) REVERT: B 238 MET cc_start: 0.9020 (ttt) cc_final: 0.8351 (ttt) REVERT: B 292 MET cc_start: 0.8403 (ttm) cc_final: 0.8166 (ttm) REVERT: B 348 TRP cc_start: 0.9508 (OUTLIER) cc_final: 0.8694 (t60) REVERT: B 388 MET cc_start: 0.8027 (mmt) cc_final: 0.7541 (mmm) REVERT: B 397 LEU cc_start: 0.7671 (tt) cc_final: 0.6987 (mt) outliers start: 30 outliers final: 17 residues processed: 103 average time/residue: 0.2098 time to fit residues: 32.6544 Evaluate side-chains 99 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 719 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 0.0170 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4149 r_free = 0.4149 target = 0.169172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111515 restraints weight = 13150.240| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.45 r_work: 0.3241 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.164 Angle : 0.549 7.495 14323 Z= 0.284 Chirality : 0.042 0.183 1641 Planarity : 0.004 0.070 1761 Dihedral : 7.212 58.570 2010 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.12 % Allowed : 19.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1231 helix: 0.35 (0.22), residues: 589 sheet: -1.30 (0.46), residues: 113 loop : -2.31 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1458 HIS 0.002 0.000 HIS A1336 PHE 0.020 0.001 PHE A1408 TYR 0.031 0.001 TYR B 136 ARG 0.003 0.000 ARG A1436 *********************** 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 111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 1.065 Fit side-chains REVERT: A 593 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: A 619 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8445 (t80) REVERT: A 625 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6824 (mtt-85) REVERT: A 653 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6977 (tt) REVERT: A 654 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: A 799 ASP cc_start: 0.3987 (OUTLIER) cc_final: 0.3401 (p0) REVERT: A 952 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.6903 (mmm160) REVERT: A 1108 GLN cc_start: 0.7226 (mp10) cc_final: 0.6897 (mp10) REVERT: A 1127 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 1129 MET cc_start: 0.9034 (tpp) cc_final: 0.8788 (tpp) REVERT: A 1289 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8327 (p0) REVERT: A 1299 TYR cc_start: 0.8635 (t80) cc_final: 0.8171 (t80) REVERT: A 1445 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7294 (mp) REVERT: A 1452 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 113 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7563 (t0) REVERT: B 238 MET cc_start: 0.8931 (ttt) cc_final: 0.8257 (ttt) REVERT: B 292 MET cc_start: 0.8398 (ttm) cc_final: 0.8174 (ttm) REVERT: B 342 LEU cc_start: 0.8547 (tp) cc_final: 0.8237 (tp) REVERT: B 348 TRP cc_start: 0.9471 (OUTLIER) cc_final: 0.8579 (t60) REVERT: B 397 LEU cc_start: 0.7702 (tt) cc_final: 0.6973 (mt) outliers start: 34 outliers final: 16 residues processed: 107 average time/residue: 0.2256 time to fit residues: 35.6217 Evaluate side-chains 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 719 GLN 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 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 216 CYS 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 115 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.167446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107627 restraints weight = 13197.599| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.09 r_work: 0.3243 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10537 Z= 0.208 Angle : 0.563 7.289 14323 Z= 0.289 Chirality : 0.042 0.176 1641 Planarity : 0.004 0.065 1761 Dihedral : 7.108 56.004 2010 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.03 % Allowed : 20.29 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1231 helix: 0.35 (0.22), residues: 592 sheet: -1.05 (0.48), residues: 105 loop : -2.22 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1458 HIS 0.003 0.001 HIS A 942 PHE 0.022 0.001 PHE A1408 TYR 0.031 0.001 TYR B 136 ARG 0.003 0.000 ARG A1436 *********************** 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 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.321 Fit side-chains REVERT: A 593 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: A 619 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (t80) REVERT: A 625 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6890 (mtt-85) REVERT: A 653 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7007 (tt) REVERT: A 654 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: A 799 ASP cc_start: 0.3873 (OUTLIER) cc_final: 0.3275 (p0) REVERT: A 952 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7010 (mmm160) REVERT: A 1108 GLN cc_start: 0.7237 (mp10) cc_final: 0.6906 (mp10) REVERT: A 1127 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 1129 MET cc_start: 0.9024 (tpp) cc_final: 0.8774 (tpp) REVERT: A 1289 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8371 (p0) REVERT: A 1299 TYR cc_start: 0.8636 (t80) cc_final: 0.8200 (t80) REVERT: A 1336 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.7908 (p-80) REVERT: A 1445 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 1446 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: A 1452 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 113 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7637 (t0) REVERT: B 238 MET cc_start: 0.9009 (ttt) cc_final: 0.8397 (ttt) REVERT: B 292 MET cc_start: 0.8354 (ttm) cc_final: 0.8123 (ttm) REVERT: B 348 TRP cc_start: 0.9497 (OUTLIER) cc_final: 0.8641 (t60) REVERT: B 397 LEU cc_start: 0.7725 (tt) cc_final: 0.6994 (mt) REVERT: B 402 LYS cc_start: 0.8026 (tttm) cc_final: 0.7568 (mmtm) outliers start: 33 outliers final: 18 residues processed: 105 average time/residue: 0.2205 time to fit residues: 34.3239 Evaluate side-chains 103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 716 THR Chi-restraints excluded: chain A residue 719 GLN 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 1252 ASN Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1336 HIS 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 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 76 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** 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 = 0.4144 r_free = 0.4144 target = 0.168498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108955 restraints weight = 13251.744| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.10 r_work: 0.3257 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.169 Angle : 0.567 7.490 14323 Z= 0.294 Chirality : 0.042 0.185 1641 Planarity : 0.004 0.070 1761 Dihedral : 6.879 55.973 2007 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.12 % Allowed : 20.20 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1231 helix: 0.35 (0.22), residues: 592 sheet: -1.20 (0.46), residues: 113 loop : -2.22 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1458 HIS 0.003 0.001 HIS A 942 PHE 0.021 0.001 PHE A1408 TYR 0.030 0.001 TYR B 136 ARG 0.003 0.000 ARG A1436 ********************** 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 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 1.179 Fit side-chains REVERT: A 593 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: A 619 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8475 (t80) REVERT: A 625 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6889 (mtt-85) REVERT: A 653 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7028 (tt) REVERT: A 654 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 799 ASP cc_start: 0.4000 (OUTLIER) cc_final: 0.3347 (p0) REVERT: A 952 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7001 (mmm160) REVERT: A 1108 GLN cc_start: 0.7227 (mp10) cc_final: 0.6889 (mp10) REVERT: A 1127 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 1129 MET cc_start: 0.9020 (tpp) cc_final: 0.8774 (tpp) REVERT: A 1289 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8346 (p0) REVERT: A 1299 TYR cc_start: 0.8641 (t80) cc_final: 0.8232 (t80) REVERT: A 1336 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.7902 (p-80) REVERT: A 1445 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7382 (mp) REVERT: A 1446 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: A 1452 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: B 113 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 238 MET cc_start: 0.8962 (ttt) cc_final: 0.8327 (ttt) REVERT: B 292 MET cc_start: 0.8353 (ttm) cc_final: 0.8136 (ttm) REVERT: B 342 LEU cc_start: 0.8534 (tp) cc_final: 0.8230 (tp) REVERT: B 348 TRP cc_start: 0.9471 (OUTLIER) cc_final: 0.8598 (t60) REVERT: B 388 MET cc_start: 0.8101 (mmt) cc_final: 0.7824 (mmm) REVERT: B 397 LEU cc_start: 0.7710 (tt) cc_final: 0.6989 (mt) REVERT: B 402 LYS cc_start: 0.8008 (tttm) cc_final: 0.7561 (mmtm) outliers start: 34 outliers final: 19 residues processed: 103 average time/residue: 0.2167 time to fit residues: 32.8330 Evaluate side-chains 104 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 716 THR Chi-restraints excluded: chain A residue 719 GLN 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 1336 HIS 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 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 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4139 r_free = 0.4139 target = 0.168076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111451 restraints weight = 13123.985| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.42 r_work: 0.3230 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.189 Angle : 0.565 8.325 14323 Z= 0.291 Chirality : 0.042 0.185 1641 Planarity : 0.004 0.066 1761 Dihedral : 6.823 55.844 2007 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.21 % Allowed : 20.29 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.24), residues: 1231 helix: 0.37 (0.22), residues: 592 sheet: -1.18 (0.46), residues: 113 loop : -2.16 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1458 HIS 0.002 0.001 HIS B 186 PHE 0.021 0.001 PHE A1408 TYR 0.028 0.001 TYR B 136 ARG 0.003 0.000 ARG A1436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6746.10 seconds wall clock time: 119 minutes 59.83 seconds (7199.83 seconds total)