Starting phenix.real_space_refine on Wed Mar 4 06:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj8_25919/03_2026/7tj8_25919_neut.cif" } resolution = 3.2 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= -0.008 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 C 7087 2.51 5 N 1598 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8805 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 1045} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 382 Unusual residues: {'CLR': 1, 'NAG': 2, 'PEV': 3, 'PLM': 6, 'POV': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 1, 'PLM:plan-1': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 2.54, per 1000 atoms: 0.24 Number of scatterers: 10551 At special positions: 0 Unit cell: (129.897, 110.37, 115.464, 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 88 16.00 P 4 15.00 O 1774 8.00 N 1598 7.00 C 7087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2412 " - " ASN A 309 " " NAG A2414 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 515.7 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 69.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.657A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 137 removed outlier: 4.054A pdb=" N GLN A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.919A pdb=" N GLU A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.906A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.609A pdb=" N MET A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.941A pdb=" N ILE A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 382 removed outlier: 4.205A pdb=" N PHE A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.906A pdb=" N GLU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.749A pdb=" N ASN A 518 " --> pdb=" O CYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 556 removed outlier: 4.583A pdb=" N LEU A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.620A pdb=" N VAL A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 4.866A pdb=" N MET A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 609 removed outlier: 3.773A pdb=" N PHE A 598 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 656 removed outlier: 3.631A pdb=" N SER A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 4.168A pdb=" N ILE A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 687 Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.176A pdb=" N THR A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 733 Proline residue: A 707 - end of helix removed outlier: 3.656A pdb=" N SER A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 Processing helix chain 'A' and resid 933 through 950 Processing helix chain 'A' and resid 951 through 954 Processing helix chain 'A' and resid 955 through 960 removed outlier: 4.412A pdb=" N ASP A 959 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 990 removed outlier: 3.547A pdb=" N LYS A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 998 removed outlier: 3.517A pdb=" N TYR A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.528A pdb=" N LEU A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 7.106A pdb=" N GLU A1022 " --> pdb=" O THR A1019 " (cutoff:3.500A) Proline residue: A1025 - end of helix removed outlier: 3.605A pdb=" N LYS A1030 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1041 removed outlier: 4.100A pdb=" N LEU A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1056 removed outlier: 3.694A pdb=" N LYS A1045 " --> pdb=" O PHE A1041 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.639A pdb=" N LEU A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1064 " --> pdb=" O ASN A1060 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1079 " --> pdb=" O MET A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.516A pdb=" N CYS A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1140 removed outlier: 3.610A pdb=" N LEU A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1154 removed outlier: 3.577A pdb=" N ILE A1147 " --> pdb=" O GLY A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1169 through 1180 removed outlier: 3.937A pdb=" N PHE A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.548A pdb=" N SER A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A1191 " --> pdb=" O MET A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1222 removed outlier: 3.880A pdb=" N GLN A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 3.733A pdb=" N THR A1249 " --> pdb=" O PHE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1270 removed outlier: 3.513A pdb=" N ILE A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A1270 " --> pdb=" O ILE A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1302 removed outlier: 3.607A pdb=" N ALA A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A1286 " --> pdb=" O ALA A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1330 removed outlier: 3.521A pdb=" N PHE A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 3.919A pdb=" N LEU A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 7.268A pdb=" N LEU A1359 " --> pdb=" O MET A1356 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A1360 " --> pdb=" O LEU A1357 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A1362 " --> pdb=" O LEU A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1402 removed outlier: 3.770A pdb=" N HIS A1367 " --> pdb=" O PRO A1363 " (cutoff:3.500A) Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1419 through 1432 Processing helix chain 'A' and resid 1436 through 1444 removed outlier: 3.753A pdb=" N ALA A1442 " --> pdb=" O GLY A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1449 removed outlier: 3.785A pdb=" N TRP A1448 " --> pdb=" O ASN A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1502 removed outlier: 3.693A pdb=" N PHE A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A1494 " --> pdb=" O MET A1490 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1497 " --> pdb=" O VAL A1493 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 186 removed outlier: 5.295A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.704A pdb=" N ALA B 35 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 119 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.696A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1590 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: 1.51 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1618 1.32 - 1.45: 2939 1.45 - 1.57: 5925 1.57 - 1.69: 172 1.69 - 1.82: 151 Bond restraints: 10805 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.642 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.752 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C31 POV A2402 " pdb=" O31 POV A2402 " ideal model delta sigma weight residual 1.327 1.507 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C31 POV A2408 " pdb=" O31 POV A2408 " ideal model delta sigma weight residual 1.327 1.506 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C21 POV A2402 " pdb=" O21 POV A2402 " ideal model delta sigma weight residual 1.330 1.505 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 10800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 14372 3.74 - 7.48: 141 7.48 - 11.22: 28 11.22 - 14.95: 4 14.95 - 18.69: 7 Bond angle restraints: 14552 Sorted by residual: angle pdb=" N PHE B 72 " pdb=" CA PHE B 72 " pdb=" C PHE B 72 " ideal model delta sigma weight residual 111.37 130.06 -18.69 1.64e+00 3.72e-01 1.30e+02 angle pdb=" C PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta sigma weight residual 111.56 96.54 15.02 1.65e+00 3.67e-01 8.28e+01 angle pdb=" N TYR B 64 " pdb=" CA TYR B 64 " pdb=" C TYR B 64 " ideal model delta sigma weight residual 111.33 121.18 -9.85 1.21e+00 6.83e-01 6.63e+01 angle pdb=" C PHE B 63 " pdb=" N TYR B 64 " pdb=" CA TYR B 64 " ideal model delta sigma weight residual 120.38 129.17 -8.79 1.37e+00 5.33e-01 4.12e+01 angle pdb=" O VAL B 84 " pdb=" C VAL B 84 " pdb=" N GLU B 85 " ideal model delta sigma weight residual 122.06 115.75 6.31 1.14e+00 7.69e-01 3.07e+01 ... (remaining 14547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6248 34.29 - 68.58: 231 68.58 - 102.87: 28 102.87 - 137.16: 4 137.16 - 171.45: 2 Dihedral angle restraints: 6513 sinusoidal: 2878 harmonic: 3635 Sorted by residual: dihedral pdb=" C PRO B 66 " pdb=" N PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta harmonic sigma weight residual -120.70 -101.90 -18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N ILE A 582 " pdb=" CA ILE A 582 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA MET B 177 " pdb=" C MET B 177 " pdb=" N ILE B 178 " pdb=" CA ILE B 178 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1595 0.119 - 0.239: 36 0.239 - 0.358: 4 0.358 - 0.478: 2 0.478 - 0.597: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG A2414 " pdb=" ND2 ASN A1103 " pdb=" C2 NAG A2414 " pdb=" O5 NAG A2414 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.94 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 1638 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A2403 " 0.235 2.00e-02 2.50e+03 2.35e-01 5.51e+02 pdb=" C29 POV A2403 " -0.236 2.00e-02 2.50e+03 pdb="C210 POV A2403 " -0.233 2.00e-02 2.50e+03 pdb="C211 POV A2403 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1331 " -0.109 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO A1332 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO A1332 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1332 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 84 " -0.032 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C VAL B 84 " 0.104 2.00e-02 2.50e+03 pdb=" O VAL B 84 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU B 85 " -0.034 2.00e-02 2.50e+03 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 69 2.61 - 3.19: 9475 3.19 - 3.76: 14138 3.76 - 4.33: 20285 4.33 - 4.90: 33619 Nonbonded interactions: 77586 Sorted by model distance: nonbonded pdb=" O ASN B 95 " pdb=" OD1 ASN B 95 " model vdw 2.042 3.040 nonbonded pdb=" ND2 ASN B 95 " pdb=" C1 NAG B 302 " model vdw 2.086 3.550 nonbonded pdb=" ND2 ASN B 109 " pdb=" C1 NAG B 303 " model vdw 2.173 3.550 nonbonded pdb=" O ILE A1016 " pdb=" OG1 THR A1019 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR B 138 " pdb=" O7 NAG B 301 " model vdw 2.292 3.040 ... (remaining 77581 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.990 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.730 Find NCS groups from input model: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.015 0.309 10810 Z= 0.738 Angle : 1.059 18.692 14565 Z= 0.528 Chirality : 0.057 0.597 1641 Planarity : 0.010 0.235 1736 Dihedral : 17.586 171.453 4155 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.95 % Favored : 93.39 % Rotamer: Outliers : 0.80 % Allowed : 7.83 % Favored : 91.37 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.21), residues: 1226 helix: -1.82 (0.15), residues: 746 sheet: -2.10 (0.56), residues: 69 loop : -1.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.003 ARG B 44 TYR 0.028 0.003 TYR A 354 PHE 0.026 0.002 PHE B 63 TRP 0.022 0.002 TRP A 610 HIS 0.012 0.002 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.01453 (10805) covalent geometry : angle 1.03209 (14552) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.87942 ( 4) hydrogen bonds : bond 0.15567 ( 572) hydrogen bonds : angle 6.09185 ( 1590) link_NAG-ASN : bond 0.10248 ( 3) link_NAG-ASN : angle 9.58213 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 229 time to evaluate : 0.402 Fit side-chains REVERT: A 538 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (m-40) REVERT: A 661 ASP cc_start: 0.8171 (t70) cc_final: 0.7836 (t0) REVERT: A 1256 ILE cc_start: 0.8828 (mm) cc_final: 0.8529 (mt) REVERT: A 1361 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7814 (mmpt) REVERT: A 1496 MET cc_start: 0.8201 (mmm) cc_final: 0.7902 (mmm) REVERT: A 1497 GLU cc_start: 0.8114 (tp30) cc_final: 0.7894 (tp30) outliers start: 9 outliers final: 4 residues processed: 233 average time/residue: 0.0877 time to fit residues: 30.2467 Evaluate side-chains 192 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117804 restraints weight = 16235.055| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.34 r_work: 0.3209 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10810 Z= 0.146 Angle : 0.686 13.958 14565 Z= 0.346 Chirality : 0.045 0.352 1641 Planarity : 0.007 0.150 1736 Dihedral : 15.301 178.854 1784 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 10.50 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1226 helix: 0.28 (0.19), residues: 755 sheet: -1.63 (0.60), residues: 69 loop : -1.26 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 144 TYR 0.014 0.001 TYR A 354 PHE 0.023 0.001 PHE A 246 TRP 0.023 0.001 TRP A 610 HIS 0.010 0.001 HIS A1199 Details of bonding type rmsd covalent geometry : bond 0.00284 (10805) covalent geometry : angle 0.66780 (14552) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.26321 ( 4) hydrogen bonds : bond 0.05581 ( 572) hydrogen bonds : angle 4.39627 ( 1590) link_NAG-ASN : bond 0.01278 ( 3) link_NAG-ASN : angle 6.31900 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6343 (t80) REVERT: A 538 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: A 560 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.5713 (m90) REVERT: A 655 GLU cc_start: 0.8278 (tp30) cc_final: 0.7863 (tt0) REVERT: A 658 CYS cc_start: 0.9109 (m) cc_final: 0.8792 (m) REVERT: A 661 ASP cc_start: 0.8510 (t70) cc_final: 0.8147 (t70) REVERT: A 1218 TYR cc_start: 0.8269 (t80) cc_final: 0.8045 (t80) REVERT: A 1324 PHE cc_start: 0.8592 (m-80) cc_final: 0.8391 (m-80) REVERT: A 1361 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7697 (mmtt) REVERT: A 1496 MET cc_start: 0.8721 (mmm) cc_final: 0.8518 (mmm) REVERT: A 1497 GLU cc_start: 0.8607 (tp30) cc_final: 0.8324 (tp30) outliers start: 25 outliers final: 7 residues processed: 219 average time/residue: 0.0772 time to fit residues: 25.2247 Evaluate side-chains 191 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A1264 GLN A1275 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109719 restraints weight = 16448.025| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.40 r_work: 0.3104 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10810 Z= 0.187 Angle : 0.687 13.340 14565 Z= 0.345 Chirality : 0.045 0.326 1641 Planarity : 0.006 0.136 1736 Dihedral : 14.247 176.750 1776 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 2.14 % Allowed : 12.37 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.24), residues: 1226 helix: 0.74 (0.19), residues: 757 sheet: -1.56 (0.62), residues: 69 loop : -1.32 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 132 TYR 0.017 0.001 TYR A1475 PHE 0.024 0.002 PHE A 246 TRP 0.020 0.001 TRP B 94 HIS 0.009 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00434 (10805) covalent geometry : angle 0.67055 (14552) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.53654 ( 4) hydrogen bonds : bond 0.06310 ( 572) hydrogen bonds : angle 4.28377 ( 1590) link_NAG-ASN : bond 0.01026 ( 3) link_NAG-ASN : angle 5.91166 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.395 Fit side-chains REVERT: A 135 MET cc_start: 0.8249 (ttp) cc_final: 0.7993 (ptm) REVERT: A 148 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 178 ASP cc_start: 0.8110 (t0) cc_final: 0.7884 (t0) REVERT: A 538 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (m-40) REVERT: A 560 HIS cc_start: 0.6154 (OUTLIER) cc_final: 0.5845 (m90) REVERT: A 658 CYS cc_start: 0.9221 (m) cc_final: 0.8883 (m) REVERT: A 661 ASP cc_start: 0.8633 (t70) cc_final: 0.8372 (t70) REVERT: A 1110 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7805 (pp) REVERT: A 1356 MET cc_start: 0.8056 (mtp) cc_final: 0.7782 (ttm) REVERT: A 1361 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7626 (mmtt) REVERT: A 1496 MET cc_start: 0.8687 (mmm) cc_final: 0.8404 (mmm) outliers start: 24 outliers final: 11 residues processed: 216 average time/residue: 0.0772 time to fit residues: 25.1650 Evaluate side-chains 210 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 81 HIS B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113892 restraints weight = 16347.079| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3214 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10810 Z= 0.156 Angle : 0.635 12.979 14565 Z= 0.317 Chirality : 0.044 0.306 1641 Planarity : 0.005 0.098 1736 Dihedral : 13.737 178.417 1776 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 2.58 % Allowed : 14.23 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1226 helix: 1.07 (0.19), residues: 756 sheet: -1.64 (0.62), residues: 69 loop : -1.36 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 132 TYR 0.017 0.001 TYR A1475 PHE 0.023 0.001 PHE A 246 TRP 0.015 0.001 TRP B 94 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00347 (10805) covalent geometry : angle 0.61901 (14552) SS BOND : bond 0.00488 ( 2) SS BOND : angle 1.51295 ( 4) hydrogen bonds : bond 0.05647 ( 572) hydrogen bonds : angle 4.01786 ( 1590) link_NAG-ASN : bond 0.01006 ( 3) link_NAG-ASN : angle 5.70584 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.386 Fit side-chains REVERT: A 135 MET cc_start: 0.8253 (ttp) cc_final: 0.8007 (ptm) REVERT: A 148 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 178 ASP cc_start: 0.8114 (t0) cc_final: 0.7899 (t0) REVERT: A 510 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6583 (t80) REVERT: A 538 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: A 560 HIS cc_start: 0.6277 (OUTLIER) cc_final: 0.6023 (m90) REVERT: A 658 CYS cc_start: 0.9138 (m) cc_final: 0.8844 (m) REVERT: A 1356 MET cc_start: 0.8031 (mtp) cc_final: 0.7813 (ttm) REVERT: A 1361 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7656 (mmtt) REVERT: B 37 GLN cc_start: 0.8614 (tt0) cc_final: 0.8410 (tt0) outliers start: 29 outliers final: 14 residues processed: 211 average time/residue: 0.0759 time to fit residues: 24.2167 Evaluate side-chains 206 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1414 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 659 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116973 restraints weight = 16136.970| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.34 r_work: 0.3205 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10810 Z= 0.118 Angle : 0.586 12.390 14565 Z= 0.289 Chirality : 0.042 0.299 1641 Planarity : 0.004 0.095 1736 Dihedral : 12.862 177.534 1776 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.22 % Allowed : 14.86 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1226 helix: 1.46 (0.20), residues: 747 sheet: -1.20 (0.64), residues: 69 loop : -1.28 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 132 TYR 0.017 0.001 TYR A1475 PHE 0.021 0.001 PHE A 246 TRP 0.018 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00243 (10805) covalent geometry : angle 0.56885 (14552) SS BOND : bond 0.00415 ( 2) SS BOND : angle 1.46145 ( 4) hydrogen bonds : bond 0.04709 ( 572) hydrogen bonds : angle 3.73599 ( 1590) link_NAG-ASN : bond 0.01051 ( 3) link_NAG-ASN : angle 5.69616 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.321 Fit side-chains REVERT: A 135 MET cc_start: 0.8311 (ttp) cc_final: 0.8033 (ptm) REVERT: A 148 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 510 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6293 (t80) REVERT: A 538 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: A 658 CYS cc_start: 0.9241 (m) cc_final: 0.8978 (m) REVERT: A 661 ASP cc_start: 0.8507 (t70) cc_final: 0.8282 (t70) REVERT: A 1361 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7551 (mmtt) REVERT: B 50 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8364 (mtmt) outliers start: 25 outliers final: 13 residues processed: 215 average time/residue: 0.0862 time to fit residues: 27.4050 Evaluate side-chains 203 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1414 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.0070 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119521 restraints weight = 16233.712| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.35 r_work: 0.3232 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 10810 Z= 0.112 Angle : 0.577 11.950 14565 Z= 0.284 Chirality : 0.042 0.360 1641 Planarity : 0.004 0.093 1736 Dihedral : 12.179 170.997 1776 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.87 % Allowed : 16.01 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1226 helix: 1.72 (0.20), residues: 747 sheet: -1.17 (0.62), residues: 71 loop : -1.26 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.014 0.001 TYR A1475 PHE 0.021 0.001 PHE A 246 TRP 0.015 0.001 TRP B 94 HIS 0.002 0.000 HIS A1199 Details of bonding type rmsd covalent geometry : bond 0.00227 (10805) covalent geometry : angle 0.55499 (14552) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.29311 ( 4) hydrogen bonds : bond 0.04176 ( 572) hydrogen bonds : angle 3.57666 ( 1590) link_NAG-ASN : bond 0.01091 ( 3) link_NAG-ASN : angle 6.26421 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.366 Fit side-chains REVERT: A 135 MET cc_start: 0.8291 (ttp) cc_final: 0.8020 (ptm) REVERT: A 148 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 510 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6103 (t80) REVERT: A 538 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8104 (m-40) REVERT: A 658 CYS cc_start: 0.9248 (m) cc_final: 0.8987 (m) REVERT: A 993 LYS cc_start: 0.7574 (tptp) cc_final: 0.7131 (ptmt) REVERT: A 1361 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7370 (mmtt) outliers start: 21 outliers final: 9 residues processed: 205 average time/residue: 0.0922 time to fit residues: 27.4900 Evaluate side-chains 198 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A1195 ASN ** B 95 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 = 0.3665 r_free = 0.3665 target = 0.139301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118817 restraints weight = 16365.558| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.42 r_work: 0.3284 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10810 Z= 0.142 Angle : 0.606 11.771 14565 Z= 0.302 Chirality : 0.043 0.311 1641 Planarity : 0.004 0.092 1736 Dihedral : 12.014 167.363 1776 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 1.87 % Allowed : 16.64 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1226 helix: 1.70 (0.20), residues: 748 sheet: -1.33 (0.61), residues: 69 loop : -1.25 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.016 0.001 TYR A1475 PHE 0.022 0.001 PHE A 246 TRP 0.010 0.001 TRP B 94 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00321 (10805) covalent geometry : angle 0.58920 (14552) SS BOND : bond 0.00466 ( 2) SS BOND : angle 1.48717 ( 4) hydrogen bonds : bond 0.04907 ( 572) hydrogen bonds : angle 3.70102 ( 1590) link_NAG-ASN : bond 0.00990 ( 3) link_NAG-ASN : angle 5.57715 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.399 Fit side-chains REVERT: A 135 MET cc_start: 0.8212 (ttp) cc_final: 0.7958 (ptm) REVERT: A 148 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 510 PHE cc_start: 0.7256 (t80) cc_final: 0.6372 (t80) REVERT: A 538 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: A 658 CYS cc_start: 0.9193 (m) cc_final: 0.8903 (m) REVERT: A 661 ASP cc_start: 0.8308 (t70) cc_final: 0.7980 (t70) REVERT: A 1324 PHE cc_start: 0.8488 (m-80) cc_final: 0.8152 (m-80) outliers start: 21 outliers final: 14 residues processed: 204 average time/residue: 0.0874 time to fit residues: 26.4544 Evaluate side-chains 199 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122170 restraints weight = 16216.753| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.37 r_work: 0.3327 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10810 Z= 0.113 Angle : 0.581 11.611 14565 Z= 0.287 Chirality : 0.041 0.306 1641 Planarity : 0.004 0.088 1736 Dihedral : 11.606 162.471 1776 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.60 % Allowed : 17.17 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1226 helix: 1.87 (0.20), residues: 746 sheet: -1.19 (0.58), residues: 72 loop : -1.33 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.015 0.001 TYR A1475 PHE 0.020 0.001 PHE A 246 TRP 0.011 0.001 TRP B 94 HIS 0.002 0.001 HIS A1199 Details of bonding type rmsd covalent geometry : bond 0.00235 (10805) covalent geometry : angle 0.56501 (14552) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.29357 ( 4) hydrogen bonds : bond 0.04265 ( 572) hydrogen bonds : angle 3.55128 ( 1590) link_NAG-ASN : bond 0.01098 ( 3) link_NAG-ASN : angle 5.42522 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.421 Fit side-chains REVERT: A 135 MET cc_start: 0.8266 (ttp) cc_final: 0.8013 (ptm) REVERT: A 148 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 510 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6152 (t80) REVERT: A 538 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: A 658 CYS cc_start: 0.9287 (m) cc_final: 0.9031 (m) REVERT: A 661 ASP cc_start: 0.8454 (t70) cc_final: 0.8137 (t70) REVERT: A 993 LYS cc_start: 0.7559 (tptp) cc_final: 0.7114 (ptmt) outliers start: 18 outliers final: 12 residues processed: 199 average time/residue: 0.0896 time to fit residues: 26.7284 Evaluate side-chains 199 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117894 restraints weight = 16252.716| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.33 r_work: 0.3275 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10810 Z= 0.158 Angle : 0.624 11.421 14565 Z= 0.312 Chirality : 0.043 0.308 1641 Planarity : 0.004 0.088 1736 Dihedral : 11.703 158.088 1776 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 1.69 % Allowed : 17.53 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1226 helix: 1.80 (0.19), residues: 739 sheet: -1.36 (0.59), residues: 69 loop : -1.30 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.027 0.001 TYR A1218 PHE 0.021 0.001 PHE A 246 TRP 0.013 0.001 TRP B 94 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00362 (10805) covalent geometry : angle 0.60970 (14552) SS BOND : bond 0.00526 ( 2) SS BOND : angle 1.52611 ( 4) hydrogen bonds : bond 0.05315 ( 572) hydrogen bonds : angle 3.77148 ( 1590) link_NAG-ASN : bond 0.01045 ( 3) link_NAG-ASN : angle 5.23443 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8300 (ttp) cc_final: 0.8011 (ptm) REVERT: A 148 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 178 ASP cc_start: 0.8194 (t0) cc_final: 0.7984 (t0) REVERT: A 538 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8267 (m-40) REVERT: A 658 CYS cc_start: 0.9306 (m) cc_final: 0.9053 (m) REVERT: A 661 ASP cc_start: 0.8573 (t70) cc_final: 0.8266 (t70) REVERT: A 1116 MET cc_start: 0.6425 (mtt) cc_final: 0.5957 (mtt) REVERT: A 1239 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.5536 (ptmm) outliers start: 19 outliers final: 13 residues processed: 204 average time/residue: 0.0859 time to fit residues: 26.0127 Evaluate side-chains 205 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122217 restraints weight = 15973.853| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.24 r_work: 0.3256 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10810 Z= 0.121 Angle : 0.588 11.289 14565 Z= 0.293 Chirality : 0.042 0.306 1641 Planarity : 0.004 0.087 1736 Dihedral : 11.384 151.024 1776 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 18.42 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.25), residues: 1226 helix: 1.95 (0.20), residues: 740 sheet: -1.83 (0.56), residues: 75 loop : -1.20 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.023 0.001 TYR A1218 PHE 0.021 0.001 PHE A 246 TRP 0.012 0.001 TRP B 94 HIS 0.003 0.001 HIS A1199 Details of bonding type rmsd covalent geometry : bond 0.00261 (10805) covalent geometry : angle 0.57521 (14552) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.36024 ( 4) hydrogen bonds : bond 0.04618 ( 572) hydrogen bonds : angle 3.61055 ( 1590) link_NAG-ASN : bond 0.01030 ( 3) link_NAG-ASN : angle 4.96357 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.393 Fit side-chains REVERT: A 135 MET cc_start: 0.8247 (ttp) cc_final: 0.7969 (ptm) REVERT: A 148 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 510 PHE cc_start: 0.7143 (t80) cc_final: 0.6287 (t80) REVERT: A 538 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: A 658 CYS cc_start: 0.9323 (m) cc_final: 0.9038 (m) REVERT: A 661 ASP cc_start: 0.8439 (t70) cc_final: 0.8054 (t70) REVERT: A 1239 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5489 (ptmm) REVERT: A 1333 MET cc_start: 0.5514 (mtm) cc_final: 0.4271 (ttp) REVERT: B 55 GLU cc_start: 0.7658 (pt0) cc_final: 0.7313 (tt0) outliers start: 15 outliers final: 12 residues processed: 195 average time/residue: 0.0938 time to fit residues: 26.9295 Evaluate side-chains 200 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123940 restraints weight = 16328.249| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.39 r_work: 0.3390 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 10810 Z= 0.106 Angle : 0.566 11.065 14565 Z= 0.279 Chirality : 0.041 0.306 1641 Planarity : 0.004 0.088 1736 Dihedral : 10.832 135.442 1776 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 1.07 % Allowed : 18.77 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.16 (0.25), residues: 1226 helix: 2.07 (0.20), residues: 748 sheet: -1.58 (0.54), residues: 77 loop : -1.29 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.014 0.001 TYR A1218 PHE 0.024 0.001 PHE B 63 TRP 0.013 0.001 TRP B 94 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00214 (10805) covalent geometry : angle 0.55079 (14552) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.26058 ( 4) hydrogen bonds : bond 0.03782 ( 572) hydrogen bonds : angle 3.41561 ( 1590) link_NAG-ASN : bond 0.01123 ( 3) link_NAG-ASN : angle 5.20947 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.46 seconds wall clock time: 42 minutes 36.29 seconds (2556.29 seconds total)