Starting phenix.real_space_refine on Sun May 3 15:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5g_35194/05_2026/8i5g_35194.map" } resolution = 2.7 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= 0.009 sd= 0.083 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: 8 Type Number sf(0) Gaussians P 13 5.49 5 S 99 5.16 5 Cl 2 4.86 5 Na 1 4.78 5 C 8835 2.51 5 N 2048 2.21 5 O 2390 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13389 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 978 Chain: "A" Number of atoms: 10273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1273, 10259 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1273, 10259 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 10491 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: 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: "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 Chain: "A" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 594 Unusual residues: {' NA': 1, '9Z9': 1, 'LPE': 8, 'NAG': 2, 'PCW': 5, 'T70': 1, 'Y01': 2} Classifications: {'undetermined': 20, 'water': 5} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 190 " occ=0.34 ... (26 atoms not shown) pdb=" CH2BTRP A 190 " occ=0.66 Time building chain proxies: 5.19, per 1000 atoms: 0.39 Number of scatterers: 13389 At special positions: 0 Unit cell: (130.615, 141.86, 128.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 99 16.00 P 13 15.00 Na 1 11.00 F 1 9.00 O 2390 8.00 N 2048 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2004 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN B 135 " " NAG E 1 " - " ASN A1352 " " NAG F 1 " - " ASN A1366 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 859.6 milliseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 65.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.605A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.189A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.856A pdb=" N ATRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.893A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.713A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.781A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.844A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 418 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 745 through 761 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 833 through 848 removed outlier: 4.084A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 840 " --> pdb=" O PHE A 837 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 841 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.518A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.377A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.687A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 removed outlier: 3.898A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.722A pdb=" N ASN A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 Processing helix chain 'A' and resid 1215 through 1218 Processing helix chain 'A' and resid 1219 through 1256 removed outlier: 7.252A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A1256 " --> pdb=" O THR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1283 through 1291 removed outlier: 3.858A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1298 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 4.106A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.994A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.966A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1445 removed outlier: 3.754A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1467 removed outlier: 3.538A pdb=" N ASP A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A1467 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1489 removed outlier: 3.545A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.500A pdb=" N ASN A1514 " --> pdb=" O ASP A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1535 removed outlier: 3.779A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A1535 " --> pdb=" O THR A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.219A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 Processing helix chain 'A' and resid 1627 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.099A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1767 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.367A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.376A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.175A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.718A pdb=" N PHE A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA8, first strand: chain 'A' and resid 1357 through 1358 809 hydrogen bonds defined for protein. 2286 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: 2.45 Time building geometry restraints manager: 1.86 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: 2102 1.32 - 1.45: 3676 1.45 - 1.58: 7718 1.58 - 1.70: 30 1.70 - 1.83: 161 Bond restraints: 13687 Sorted by residual: bond pdb=" O07 T70 A2005 " pdb=" S03 T70 A2005 " ideal model delta sigma weight residual 1.449 1.650 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" O08 T70 A2005 " pdb=" S03 T70 A2005 " ideal model delta sigma weight residual 1.449 1.648 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C24 T70 A2005 " pdb=" N12 T70 A2005 " ideal model delta sigma weight residual 1.363 1.450 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C15 T70 A2005 " pdb=" C18 T70 A2005 " ideal model delta sigma weight residual 1.458 1.527 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C17 T70 A2005 " pdb=" O06 T70 A2005 " ideal model delta sigma weight residual 1.339 1.406 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 13682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 18124 2.31 - 4.61: 293 4.61 - 6.92: 72 6.92 - 9.22: 17 9.22 - 11.53: 1 Bond angle restraints: 18507 Sorted by residual: angle pdb=" O07 T70 A2005 " pdb=" S03 T70 A2005 " pdb=" O08 T70 A2005 " ideal model delta sigma weight residual 119.54 108.01 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" N GLY A 998 " pdb=" CA GLY A 998 " pdb=" C GLY A 998 " ideal model delta sigma weight residual 112.50 116.53 -4.03 1.16e+00 7.43e-01 1.21e+01 angle pdb=" C ILE A1318 " pdb=" CA ILE A1318 " pdb=" CB ILE A1318 " ideal model delta sigma weight residual 113.70 110.86 2.84 9.50e-01 1.11e+00 8.92e+00 angle pdb=" C ALA A1317 " pdb=" N ILE A1318 " pdb=" CA ILE A1318 " ideal model delta sigma weight residual 120.43 123.30 -2.87 9.60e-01 1.09e+00 8.91e+00 angle pdb=" CA MET A 108 " pdb=" CB MET A 108 " pdb=" CG MET A 108 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.82e+00 ... (remaining 18502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 8007 27.84 - 55.69: 483 55.69 - 83.53: 60 83.53 - 111.37: 6 111.37 - 139.21: 4 Dihedral angle restraints: 8560 sinusoidal: 3953 harmonic: 4607 Sorted by residual: dihedral pdb=" C33 PCW A2018 " pdb=" C31 PCW A2018 " pdb=" C32 PCW A2018 " pdb=" O2 PCW A2018 " ideal model delta sinusoidal sigma weight residual 191.83 52.62 139.21 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" N PCW A2011 " pdb=" C4 PCW A2011 " pdb=" C5 PCW A2011 " pdb=" O4P PCW A2011 " ideal model delta sinusoidal sigma weight residual 293.34 155.66 137.68 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CB CYS A 897 " pdb=" SG CYS A 897 " pdb=" SG CYS A 903 " pdb=" CB CYS A 903 " ideal model delta sinusoidal sigma weight residual 93.00 126.85 -33.85 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 8557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1986 0.083 - 0.165: 107 0.165 - 0.248: 7 0.248 - 0.330: 1 0.330 - 0.413: 2 Chirality restraints: 2103 Sorted by residual: chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A1375 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG A2001 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A2001 " pdb=" O5 NAG A2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB ILE B 172 " pdb=" CA ILE B 172 " pdb=" CG1 ILE B 172 " pdb=" CG2 ILE B 172 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2100 not shown) Planarity restraints: 2213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG E 2 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2004 " 0.298 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG A2004 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A2004 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG A2004 " -0.425 2.00e-02 2.50e+03 pdb=" O7 NAG A2004 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " 0.246 2.00e-02 2.50e+03 2.05e-01 5.27e+02 pdb=" C7 NAG B 303 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " -0.342 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.009 2.00e-02 2.50e+03 ... (remaining 2210 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 247 2.70 - 3.25: 13112 3.25 - 3.80: 21273 3.80 - 4.35: 28473 4.35 - 4.90: 46693 Nonbonded interactions: 109798 Sorted by model distance: nonbonded pdb=" OH TYR A1482 " pdb=" OE1 GLU A1761 " model vdw 2.150 3.040 nonbonded pdb=" OD2 ASP A 747 " pdb=" ND2 ASN A 987 " model vdw 2.218 3.120 nonbonded pdb=" O SER A 211 " pdb=" OG1 THR A 215 " model vdw 2.268 3.040 nonbonded pdb=" O SER A1288 " pdb=" OG1 THR A1291 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 318 " pdb=" OG SER A 321 " model vdw 2.279 3.040 ... (remaining 109793 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 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.201 13709 Z= 0.300 Angle : 0.776 11.917 18562 Z= 0.371 Chirality : 0.042 0.413 2103 Planarity : 0.011 0.290 2205 Dihedral : 16.710 139.213 5551 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.85 % Allowed : 18.05 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.48 (0.22), residues: 1555 helix: 1.85 (0.17), residues: 931 sheet: 0.36 (0.46), residues: 137 loop : -0.50 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1308 TYR 0.019 0.001 TYR A 367 PHE 0.030 0.001 PHE A1509 TRP 0.025 0.001 TRP A 151 HIS 0.009 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00602 (13687) covalent geometry : angle 0.75947 (18507) SS BOND : bond 0.00208 ( 11) SS BOND : angle 0.84376 ( 22) hydrogen bonds : bond 0.13823 ( 809) hydrogen bonds : angle 5.75357 ( 2286) link_BETA1-4 : bond 0.00775 ( 3) link_BETA1-4 : angle 3.05022 ( 9) link_NAG-ASN : bond 0.00792 ( 8) link_NAG-ASN : angle 4.14026 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8186 (m-10) cc_final: 0.7943 (m-80) REVERT: A 233 THR cc_start: 0.8793 (p) cc_final: 0.8534 (t) REVERT: A 243 LYS cc_start: 0.7460 (mptt) cc_final: 0.7237 (mttp) REVERT: A 1251 LYS cc_start: 0.5114 (pmtt) cc_final: 0.4570 (pmmt) REVERT: A 1711 LYS cc_start: 0.8257 (mtmp) cc_final: 0.7894 (mttp) outliers start: 12 outliers final: 8 residues processed: 196 average time/residue: 0.5360 time to fit residues: 115.7871 Evaluate side-chains 179 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 overall best weight: 0.7288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 941 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.186805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119516 restraints weight = 28983.079| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.17 r_work: 0.3088 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13709 Z= 0.119 Angle : 0.552 12.418 18562 Z= 0.276 Chirality : 0.041 0.317 2103 Planarity : 0.004 0.058 2205 Dihedral : 12.313 153.247 2565 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.91 % Allowed : 16.20 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.80 (0.22), residues: 1555 helix: 2.07 (0.17), residues: 921 sheet: 0.15 (0.42), residues: 142 loop : -0.12 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 835 TYR 0.022 0.001 TYR A 367 PHE 0.019 0.001 PHE A1583 TRP 0.021 0.001 TRP A 151 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00255 (13687) covalent geometry : angle 0.52196 (18507) SS BOND : bond 0.00303 ( 11) SS BOND : angle 0.84808 ( 22) hydrogen bonds : bond 0.04328 ( 809) hydrogen bonds : angle 4.51684 ( 2286) link_BETA1-4 : bond 0.01090 ( 3) link_BETA1-4 : angle 3.63975 ( 9) link_NAG-ASN : bond 0.00803 ( 8) link_NAG-ASN : angle 4.50533 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7979 (pt) REVERT: B 170 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 121 LYS cc_start: 0.8017 (tttp) cc_final: 0.7539 (tptp) REVERT: A 215 THR cc_start: 0.8325 (m) cc_final: 0.8067 (t) REVERT: A 218 VAL cc_start: 0.8928 (t) cc_final: 0.8724 (p) REVERT: A 297 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: A 371 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9031 (mp) REVERT: A 763 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: A 1711 LYS cc_start: 0.8402 (mtmp) cc_final: 0.8103 (mttp) outliers start: 41 outliers final: 16 residues processed: 222 average time/residue: 0.5430 time to fit residues: 132.5607 Evaluate side-chains 206 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 ASN A 941 GLN A1256 ASN A1450 ASN A1514 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109782 restraints weight = 30033.272| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.44 r_work: 0.3003 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13709 Z= 0.121 Angle : 0.530 11.360 18562 Z= 0.266 Chirality : 0.041 0.380 2103 Planarity : 0.004 0.050 2205 Dihedral : 11.720 168.850 2556 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.91 % Allowed : 16.20 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.88 (0.21), residues: 1555 helix: 2.14 (0.17), residues: 920 sheet: 0.14 (0.41), residues: 142 loop : -0.07 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 835 TYR 0.024 0.001 TYR A 367 PHE 0.021 0.001 PHE A 391 TRP 0.012 0.001 TRP A 151 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00270 (13687) covalent geometry : angle 0.50318 (18507) SS BOND : bond 0.00324 ( 11) SS BOND : angle 0.85904 ( 22) hydrogen bonds : bond 0.04063 ( 809) hydrogen bonds : angle 4.30581 ( 2286) link_BETA1-4 : bond 0.00595 ( 3) link_BETA1-4 : angle 3.23749 ( 9) link_NAG-ASN : bond 0.00835 ( 8) link_NAG-ASN : angle 4.21662 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 121 LYS cc_start: 0.8040 (tttp) cc_final: 0.7552 (tptp) REVERT: A 131 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 215 THR cc_start: 0.8448 (m) cc_final: 0.8243 (t) REVERT: A 220 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7679 (mtp85) REVERT: A 297 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: A 371 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9103 (mp) REVERT: A 1251 LYS cc_start: 0.5177 (pmtt) cc_final: 0.4921 (pmtt) REVERT: A 1315 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 1711 LYS cc_start: 0.8381 (mtmp) cc_final: 0.8074 (mttp) outliers start: 41 outliers final: 18 residues processed: 212 average time/residue: 0.5637 time to fit residues: 131.4081 Evaluate side-chains 205 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1450 ASN A1502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104252 restraints weight = 36240.467| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.63 r_work: 0.2905 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13709 Z= 0.252 Angle : 0.648 11.678 18562 Z= 0.325 Chirality : 0.046 0.301 2103 Planarity : 0.005 0.050 2205 Dihedral : 12.261 178.562 2556 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.62 % Allowed : 15.78 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.50 (0.21), residues: 1555 helix: 1.82 (0.17), residues: 920 sheet: 0.07 (0.41), residues: 142 loop : -0.22 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 835 TYR 0.035 0.002 TYR A 367 PHE 0.023 0.003 PHE A 391 TRP 0.011 0.002 TRP A1193 HIS 0.014 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00607 (13687) covalent geometry : angle 0.61950 (18507) SS BOND : bond 0.00561 ( 11) SS BOND : angle 1.26731 ( 22) hydrogen bonds : bond 0.05092 ( 809) hydrogen bonds : angle 4.53045 ( 2286) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 3.81776 ( 9) link_NAG-ASN : bond 0.00684 ( 8) link_NAG-ASN : angle 4.69857 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 45 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7921 (ttp-170) REVERT: B 118 ASP cc_start: 0.8551 (m-30) cc_final: 0.8208 (m-30) REVERT: B 170 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 121 LYS cc_start: 0.8019 (tttp) cc_final: 0.7791 (mmmm) REVERT: A 131 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7813 (tp) REVERT: A 220 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7932 (mtp85) REVERT: A 297 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 323 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7797 (mp-120) REVERT: A 742 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.5086 (ptp) REVERT: A 763 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (mtp) REVERT: A 1251 LYS cc_start: 0.5542 (pmtt) cc_final: 0.5029 (pmtt) REVERT: A 1308 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7793 (ttm110) REVERT: A 1711 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8176 (mtmt) outliers start: 51 outliers final: 25 residues processed: 219 average time/residue: 0.5571 time to fit residues: 133.8990 Evaluate side-chains 215 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN A1450 ASN A1502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.183797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108771 restraints weight = 37039.262| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.67 r_work: 0.2988 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13709 Z= 0.112 Angle : 0.522 9.875 18562 Z= 0.262 Chirality : 0.041 0.300 2103 Planarity : 0.004 0.049 2205 Dihedral : 11.445 175.774 2556 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.49 % Allowed : 17.48 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.91 (0.21), residues: 1555 helix: 2.17 (0.17), residues: 908 sheet: 0.13 (0.41), residues: 142 loop : 0.01 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 835 TYR 0.019 0.001 TYR A 367 PHE 0.020 0.001 PHE A 391 TRP 0.011 0.001 TRP A 151 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00244 (13687) covalent geometry : angle 0.49557 (18507) SS BOND : bond 0.00309 ( 11) SS BOND : angle 0.93697 ( 22) hydrogen bonds : bond 0.03888 ( 809) hydrogen bonds : angle 4.22121 ( 2286) link_BETA1-4 : bond 0.00624 ( 3) link_BETA1-4 : angle 3.17118 ( 9) link_NAG-ASN : bond 0.00677 ( 8) link_NAG-ASN : angle 4.07967 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8031 (tttp) cc_final: 0.7529 (tptp) REVERT: A 131 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7733 (tp) REVERT: A 323 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7562 (mp-120) REVERT: A 752 ILE cc_start: 0.8465 (mm) cc_final: 0.8253 (mp) REVERT: A 763 MET cc_start: 0.8888 (mtp) cc_final: 0.8669 (mtp) REVERT: A 798 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6309 (ppp) REVERT: A 1251 LYS cc_start: 0.5433 (pmtt) cc_final: 0.4874 (pmtt) REVERT: A 1308 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8368 (mtmp) cc_final: 0.8041 (mttp) outliers start: 35 outliers final: 17 residues processed: 208 average time/residue: 0.5738 time to fit residues: 130.6718 Evaluate side-chains 198 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.181840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109216 restraints weight = 33347.163| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.22 r_work: 0.2922 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13709 Z= 0.163 Angle : 0.563 9.291 18562 Z= 0.284 Chirality : 0.042 0.309 2103 Planarity : 0.004 0.049 2205 Dihedral : 11.504 175.138 2556 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.70 % Allowed : 17.48 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.88 (0.21), residues: 1555 helix: 2.09 (0.17), residues: 910 sheet: 0.24 (0.42), residues: 137 loop : 0.05 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 835 TYR 0.028 0.001 TYR A 367 PHE 0.023 0.002 PHE A 391 TRP 0.009 0.001 TRP A1700 HIS 0.009 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00384 (13687) covalent geometry : angle 0.53729 (18507) SS BOND : bond 0.00424 ( 11) SS BOND : angle 0.98969 ( 22) hydrogen bonds : bond 0.04280 ( 809) hydrogen bonds : angle 4.27580 ( 2286) link_BETA1-4 : bond 0.00668 ( 3) link_BETA1-4 : angle 3.40730 ( 9) link_NAG-ASN : bond 0.00656 ( 8) link_NAG-ASN : angle 4.17348 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8224 (mm-30) REVERT: B 118 ASP cc_start: 0.8503 (m-30) cc_final: 0.8151 (m-30) REVERT: B 170 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 121 LYS cc_start: 0.8031 (tttp) cc_final: 0.7609 (tptp) REVERT: A 131 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 323 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7625 (mp-120) REVERT: A 752 ILE cc_start: 0.8530 (mm) cc_final: 0.8324 (mp) REVERT: A 763 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: A 1251 LYS cc_start: 0.5381 (pmtt) cc_final: 0.4829 (pmtt) REVERT: A 1308 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8069 (mttp) outliers start: 38 outliers final: 24 residues processed: 203 average time/residue: 0.5410 time to fit residues: 120.7488 Evaluate side-chains 207 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 140 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1502 ASN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.182984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113816 restraints weight = 47659.890| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.59 r_work: 0.2906 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13709 Z= 0.130 Angle : 0.528 8.542 18562 Z= 0.266 Chirality : 0.041 0.304 2103 Planarity : 0.004 0.049 2205 Dihedral : 11.165 173.007 2556 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.70 % Allowed : 17.56 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.97 (0.21), residues: 1555 helix: 2.18 (0.17), residues: 909 sheet: 0.31 (0.42), residues: 137 loop : 0.06 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 835 TYR 0.023 0.001 TYR A 367 PHE 0.022 0.001 PHE A 391 TRP 0.010 0.001 TRP A1700 HIS 0.007 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00300 (13687) covalent geometry : angle 0.50365 (18507) SS BOND : bond 0.00337 ( 11) SS BOND : angle 0.89443 ( 22) hydrogen bonds : bond 0.03954 ( 809) hydrogen bonds : angle 4.17581 ( 2286) link_BETA1-4 : bond 0.00622 ( 3) link_BETA1-4 : angle 3.19269 ( 9) link_NAG-ASN : bond 0.00631 ( 8) link_NAG-ASN : angle 3.90299 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 121 LYS cc_start: 0.8014 (tttp) cc_final: 0.7594 (tptp) REVERT: A 131 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 323 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7537 (mp-120) REVERT: A 752 ILE cc_start: 0.8504 (mm) cc_final: 0.8289 (mp) REVERT: A 763 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8579 (mtp) REVERT: A 798 MET cc_start: 0.6519 (ptm) cc_final: 0.5400 (ppp) REVERT: A 1251 LYS cc_start: 0.5530 (pmtt) cc_final: 0.4815 (pmmt) REVERT: A 1278 LEU cc_start: 0.7941 (mt) cc_final: 0.7365 (tt) REVERT: A 1308 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8105 (mttp) outliers start: 38 outliers final: 23 residues processed: 209 average time/residue: 0.5560 time to fit residues: 127.7234 Evaluate side-chains 204 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A1256 ASN A1502 ASN A1514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108866 restraints weight = 35420.414| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.32 r_work: 0.2907 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13709 Z= 0.162 Angle : 0.564 9.040 18562 Z= 0.285 Chirality : 0.042 0.309 2103 Planarity : 0.004 0.049 2205 Dihedral : 11.259 172.759 2556 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.06 % Allowed : 18.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.85 (0.21), residues: 1555 helix: 2.07 (0.17), residues: 910 sheet: 0.24 (0.43), residues: 137 loop : 0.03 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 835 TYR 0.028 0.001 TYR A 367 PHE 0.023 0.002 PHE A 391 TRP 0.010 0.001 TRP A1408 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00382 (13687) covalent geometry : angle 0.54116 (18507) SS BOND : bond 0.00405 ( 11) SS BOND : angle 0.99375 ( 22) hydrogen bonds : bond 0.04265 ( 809) hydrogen bonds : angle 4.24146 ( 2286) link_BETA1-4 : bond 0.00635 ( 3) link_BETA1-4 : angle 3.36512 ( 9) link_NAG-ASN : bond 0.00639 ( 8) link_NAG-ASN : angle 3.88863 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 118 ASP cc_start: 0.8479 (m-30) cc_final: 0.8130 (m-30) REVERT: A 121 LYS cc_start: 0.8018 (tttp) cc_final: 0.7606 (tptp) REVERT: A 297 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: A 323 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7621 (mp-120) REVERT: A 752 ILE cc_start: 0.8535 (mm) cc_final: 0.8327 (mp) REVERT: A 763 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: A 798 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5302 (ppp) REVERT: A 1251 LYS cc_start: 0.5501 (pmtt) cc_final: 0.4915 (pmtt) REVERT: A 1278 LEU cc_start: 0.7952 (mt) cc_final: 0.7360 (tt) REVERT: A 1308 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8183 (mtmt) outliers start: 29 outliers final: 23 residues processed: 202 average time/residue: 0.5585 time to fit residues: 124.2661 Evaluate side-chains 209 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1502 ASN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105749 restraints weight = 37712.198| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.93 r_work: 0.2904 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13709 Z= 0.202 Angle : 0.589 9.767 18562 Z= 0.298 Chirality : 0.044 0.305 2103 Planarity : 0.004 0.050 2205 Dihedral : 11.496 172.711 2556 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.56 % Allowed : 18.12 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.72 (0.21), residues: 1555 helix: 1.99 (0.17), residues: 903 sheet: 0.12 (0.42), residues: 142 loop : -0.04 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 835 TYR 0.030 0.002 TYR A 367 PHE 0.023 0.002 PHE A 391 TRP 0.013 0.002 TRP A1260 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00481 (13687) covalent geometry : angle 0.56622 (18507) SS BOND : bond 0.00479 ( 11) SS BOND : angle 1.09150 ( 22) hydrogen bonds : bond 0.04563 ( 809) hydrogen bonds : angle 4.33928 ( 2286) link_BETA1-4 : bond 0.00587 ( 3) link_BETA1-4 : angle 3.56478 ( 9) link_NAG-ASN : bond 0.00668 ( 8) link_NAG-ASN : angle 3.91758 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 118 ASP cc_start: 0.8459 (m-30) cc_final: 0.8115 (m-30) REVERT: B 170 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 121 LYS cc_start: 0.7977 (tttp) cc_final: 0.7754 (mmmm) REVERT: A 297 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 323 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7651 (mp-120) REVERT: A 752 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 763 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8521 (mtp) REVERT: A 798 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.5321 (ppp) REVERT: A 835 ARG cc_start: 0.8012 (mtm110) cc_final: 0.7790 (mtm110) REVERT: A 1251 LYS cc_start: 0.5684 (pmtt) cc_final: 0.4999 (pmtt) REVERT: A 1278 LEU cc_start: 0.7944 (mt) cc_final: 0.7356 (tt) REVERT: A 1308 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7739 (ttm110) REVERT: A 1711 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (mtmt) outliers start: 36 outliers final: 23 residues processed: 206 average time/residue: 0.5584 time to fit residues: 126.6562 Evaluate side-chains 210 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN A1256 ASN A1459 ASN A1502 ASN A1514 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109153 restraints weight = 30808.214| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.48 r_work: 0.2993 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13709 Z= 0.109 Angle : 0.520 8.634 18562 Z= 0.263 Chirality : 0.040 0.309 2103 Planarity : 0.004 0.050 2205 Dihedral : 10.940 171.468 2556 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.85 % Allowed : 18.48 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.95 (0.22), residues: 1555 helix: 2.19 (0.17), residues: 910 sheet: 0.29 (0.42), residues: 142 loop : -0.01 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 835 TYR 0.020 0.001 TYR A 367 PHE 0.022 0.001 PHE A 391 TRP 0.012 0.001 TRP A1700 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00240 (13687) covalent geometry : angle 0.49941 (18507) SS BOND : bond 0.00320 ( 11) SS BOND : angle 0.99327 ( 22) hydrogen bonds : bond 0.03758 ( 809) hydrogen bonds : angle 4.12618 ( 2286) link_BETA1-4 : bond 0.00660 ( 3) link_BETA1-4 : angle 3.18086 ( 9) link_NAG-ASN : bond 0.00616 ( 8) link_NAG-ASN : angle 3.45156 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 162 MET cc_start: 0.7890 (mmm) cc_final: 0.7515 (mmp) REVERT: B 170 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 121 LYS cc_start: 0.7983 (tttp) cc_final: 0.7742 (mmmm) REVERT: A 131 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 297 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: A 323 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7546 (mp-120) REVERT: A 752 ILE cc_start: 0.8508 (mm) cc_final: 0.8288 (mp) REVERT: A 761 MET cc_start: 0.8837 (mtp) cc_final: 0.8610 (mtm) REVERT: A 763 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (mtp) REVERT: A 798 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5280 (ppp) REVERT: A 835 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7765 (mtm110) REVERT: A 1251 LYS cc_start: 0.5512 (pmtt) cc_final: 0.4873 (pmtt) REVERT: A 1278 LEU cc_start: 0.7887 (mt) cc_final: 0.7309 (tt) REVERT: A 1308 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8160 (mtmt) outliers start: 26 outliers final: 17 residues processed: 199 average time/residue: 0.5279 time to fit residues: 116.0842 Evaluate side-chains 203 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1711 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1459 ASN A1502 ASN A1514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105366 restraints weight = 36899.185| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.65 r_work: 0.2921 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13709 Z= 0.201 Angle : 0.586 9.413 18562 Z= 0.296 Chirality : 0.044 0.308 2103 Planarity : 0.004 0.050 2205 Dihedral : 11.305 172.693 2556 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.85 % Allowed : 18.91 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.81 (0.21), residues: 1555 helix: 2.06 (0.17), residues: 903 sheet: 0.22 (0.42), residues: 142 loop : -0.00 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 835 TYR 0.029 0.002 TYR A 367 PHE 0.025 0.002 PHE A 391 TRP 0.012 0.002 TRP A1260 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00483 (13687) covalent geometry : angle 0.56433 (18507) SS BOND : bond 0.00477 ( 11) SS BOND : angle 1.14021 ( 22) hydrogen bonds : bond 0.04490 ( 809) hydrogen bonds : angle 4.28199 ( 2286) link_BETA1-4 : bond 0.00635 ( 3) link_BETA1-4 : angle 3.52613 ( 9) link_NAG-ASN : bond 0.00661 ( 8) link_NAG-ASN : angle 3.73460 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.46 seconds wall clock time: 116 minutes 21.62 seconds (6981.62 seconds total)