Starting phenix.real_space_refine on Fri Jul 3 12:29:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5g_35194/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.cif" model { file = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5g_35194/07_2026/8i5g_35194.cif" } 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-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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: 122 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: 4.45, per 1000 atoms: 0.33 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: 1.22 Conformation dependent library (CDL) restraints added in 910.4 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: 0.52 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: 2.34 Time building geometry restraints manager: 1.56 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: 7567 27.84 - 55.69: 453 55.69 - 83.53: 52 83.53 - 111.37: 4 111.37 - 139.21: 4 Dihedral angle restraints: 8080 sinusoidal: 3473 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 8077 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 16.757 139.213 5071 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/Z covalent geometry : bond 0.00602 / 0.30 (13687) covalent geometry : angle 0.75947 / 0.37 (18507) SS BOND : bond 0.00208 / 0.14 ( 11) SS BOND : angle 0.84376 / 0.51 ( 22) hydrogen bonds : bond 0.13823 / 8.83 ( 809) hydrogen bonds : angle 5.75357 / 4.07 ( 2286) link_BETA1-4 : bond 0.00775 / 0.44 ( 3) link_BETA1-4 : angle 3.05022 / 1.52 ( 9) link_NAG-ASN : bond 0.00792 / 0.66 ( 8) link_NAG-ASN : angle 4.14026 / 2.96 ( 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 : 0.503 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: 0.5230 time to fit residues: 113.5858 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 : 0.501 ------------------------------------------------------------------------------- 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... 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 = 0.4131 r_free = 0.4131 target = 0.186714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119134 restraints weight = 28974.598| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.16 r_work: 0.3093 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13709 Z= 0.121 Angle : 0.544 11.267 18562 Z= 0.275 Chirality : 0.042 0.444 2103 Planarity : 0.004 0.057 2205 Dihedral : 11.597 131.060 2085 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.77 % Allowed : 16.35 % 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: 1.81 (0.22), residues: 1555 helix: 2.08 (0.17), residues: 921 sheet: 0.16 (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 0.021 0.001 TYR A 367 PHE 0.019 0.001 PHE A1583 TRP 0.020 0.001 TRP A 151 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13687) covalent geometry : angle 0.51841 / 0.27 (18507) SS BOND : bond 0.00304 / 0.21 ( 11) SS BOND : angle 0.84672 / 0.53 ( 22) hydrogen bonds : bond 0.04317 / 2.87 ( 809) hydrogen bonds : angle 4.52605 / 3.22 ( 2286) link_BETA1-4 : bond 0.01392 / 0.78 ( 3) link_BETA1-4 : angle 3.35983 / 1.61 ( 9) link_NAG-ASN : bond 0.00762 / 0.63 ( 8) link_NAG-ASN : angle 4.12589 / 2.90 ( 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 231 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 170 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 121 LYS cc_start: 0.8011 (tttp) cc_final: 0.7524 (tptp) REVERT: A 215 THR cc_start: 0.8330 (m) cc_final: 0.8062 (t) REVERT: A 218 VAL cc_start: 0.8922 (t) cc_final: 0.8716 (p) REVERT: A 297 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: A 371 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9031 (mp) REVERT: A 763 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8416 (mtp) REVERT: A 1711 LYS cc_start: 0.8389 (mtmp) cc_final: 0.8088 (mttp) outliers start: 39 outliers final: 16 residues processed: 220 average time/residue: 0.5302 time to fit residues: 129.1586 Evaluate side-chains 204 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 19 SER 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: 4.9990 chunk 148 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A1256 ASN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.182732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114438 restraints weight = 30513.447| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.25 r_work: 0.2998 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13709 Z= 0.224 Angle : 0.628 10.252 18562 Z= 0.316 Chirality : 0.046 0.525 2103 Planarity : 0.005 0.051 2205 Dihedral : 11.382 107.323 2076 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.98 % Allowed : 15.28 % Favored : 80.74 % 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: 1.64 (0.21), residues: 1555 helix: 1.95 (0.17), residues: 908 sheet: -0.00 (0.42), residues: 142 loop : -0.11 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 835 TYR 0.034 0.002 TYR A 367 PHE 0.021 0.002 PHE A1740 TRP 0.011 0.002 TRP A 151 HIS 0.013 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (13687) covalent geometry : angle 0.60350 / 0.31 (18507) SS BOND : bond 0.00494 / 0.36 ( 11) SS BOND : angle 1.17499 / 0.76 ( 22) hydrogen bonds : bond 0.05023 / 3.28 ( 809) hydrogen bonds : angle 4.56820 / 3.26 ( 2286) link_BETA1-4 : bond 0.00705 / 0.39 ( 3) link_BETA1-4 : angle 3.39034 / 1.69 ( 9) link_NAG-ASN : bond 0.00714 / 0.60 ( 8) link_NAG-ASN : angle 4.32898 / 2.75 ( 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 240 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8215 (mm-30) REVERT: B 170 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 121 LYS cc_start: 0.8050 (tttp) cc_final: 0.7581 (tptp) REVERT: A 220 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7943 (mtp85) REVERT: A 297 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: A 323 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7723 (mp-120) REVERT: A 798 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6425 (ppp) REVERT: A 1308 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7753 (ttm110) REVERT: A 1315 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 1711 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8107 (mttp) outliers start: 56 outliers final: 27 residues processed: 219 average time/residue: 0.5486 time to fit residues: 133.0222 Evaluate side-chains 213 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL 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 30 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 166 GLU 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 752 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 798 MET 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 1362 SER Chi-restraints excluded: chain A residue 1410 ILE 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 1727 GLU Chi-restraints excluded: chain A residue 1756 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 956 ASN A1502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.182308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106734 restraints weight = 35192.525| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.61 r_work: 0.2960 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13709 Z= 0.152 Angle : 0.554 9.065 18562 Z= 0.280 Chirality : 0.044 0.654 2103 Planarity : 0.004 0.050 2205 Dihedral : 10.949 93.871 2076 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.06 % Allowed : 16.77 % Favored : 80.17 % 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: 1.78 (0.21), residues: 1555 helix: 2.06 (0.17), residues: 909 sheet: 0.08 (0.41), residues: 142 loop : -0.04 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 835 TYR 0.025 0.001 TYR A 367 PHE 0.019 0.002 PHE A 391 TRP 0.011 0.001 TRP A 151 HIS 0.009 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13687) covalent geometry : angle 0.53674 / 0.28 (18507) SS BOND : bond 0.00366 / 0.25 ( 11) SS BOND : angle 0.97594 / 0.61 ( 22) hydrogen bonds : bond 0.04321 / 2.88 ( 809) hydrogen bonds : angle 4.36152 / 3.10 ( 2286) link_BETA1-4 : bond 0.00482 / 0.27 ( 3) link_BETA1-4 : angle 3.12241 / 1.43 ( 9) link_NAG-ASN : bond 0.00536 / 0.45 ( 8) link_NAG-ASN : angle 3.28887 / 1.97 ( 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 233 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 121 LYS cc_start: 0.8049 (tttp) cc_final: 0.7803 (mmmm) REVERT: A 220 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: A 297 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 323 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7599 (mp-120) REVERT: A 763 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (mtp) REVERT: A 798 MET cc_start: 0.6589 (ptm) cc_final: 0.6346 (ppp) REVERT: A 1308 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7817 (ttm110) REVERT: A 1711 LYS cc_start: 0.8430 (mtmp) cc_final: 0.8107 (mttp) outliers start: 43 outliers final: 25 residues processed: 218 average time/residue: 0.5376 time to fit residues: 129.3814 Evaluate side-chains 213 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 166 GLU Chi-restraints excluded: chain A residue 215 THR 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 752 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 771 GLU 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 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 1756 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4077 r_free = 0.4077 target = 0.181789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106238 restraints weight = 36926.184| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.66 r_work: 0.2936 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13709 Z= 0.173 Angle : 0.570 9.899 18562 Z= 0.288 Chirality : 0.046 0.812 2103 Planarity : 0.004 0.049 2205 Dihedral : 10.908 91.747 2076 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.34 % Allowed : 17.06 % Favored : 79.60 % 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: 1.73 (0.21), residues: 1555 helix: 2.01 (0.17), residues: 909 sheet: 0.07 (0.41), residues: 142 loop : -0.04 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 835 TYR 0.028 0.002 TYR A 367 PHE 0.022 0.002 PHE A 391 TRP 0.010 0.001 TRP A1700 HIS 0.009 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (13687) covalent geometry : angle 0.55053 / 0.28 (18507) SS BOND : bond 0.00424 / 0.31 ( 11) SS BOND : angle 1.06939 / 0.66 ( 22) hydrogen bonds : bond 0.04469 / 2.97 ( 809) hydrogen bonds : angle 4.36511 / 3.10 ( 2286) link_BETA1-4 : bond 0.00541 / 0.30 ( 3) link_BETA1-4 : angle 3.17866 / 1.49 ( 9) link_NAG-ASN : bond 0.01226 / 1.04 ( 8) link_NAG-ASN : angle 3.55919 / 2.11 ( 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 237 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 45 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7797 (ttp-170) REVERT: B 170 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 121 LYS cc_start: 0.8024 (tttp) cc_final: 0.7781 (mmmm) REVERT: A 131 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 220 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7829 (mtp85) REVERT: A 297 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 323 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7630 (mp-120) REVERT: A 752 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 763 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8655 (mtp) REVERT: A 798 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6310 (ppp) REVERT: A 1308 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7769 (ttm110) REVERT: A 1711 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8078 (mttp) outliers start: 47 outliers final: 27 residues processed: 216 average time/residue: 0.5136 time to fit residues: 122.1848 Evaluate side-chains 221 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG 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 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 166 GLU Chi-restraints excluded: chain A residue 215 THR 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 752 ILE 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 786 ILE 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 1456 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 Chi-restraints excluded: chain A residue 1711 LYS 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: 0.6980 chunk 4 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1256 ASN A1450 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 = 0.4095 r_free = 0.4095 target = 0.183611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108802 restraints weight = 33142.513| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.56 r_work: 0.2985 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 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 = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1526 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= 0.111 Angle : 0.512 8.510 18562 Z= 0.260 Chirality : 0.040 0.307 2103 Planarity : 0.004 0.049 2205 Dihedral : 10.397 87.399 2076 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.63 % Allowed : 17.70 % 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: 1.96 (0.22), residues: 1555 helix: 2.18 (0.17), residues: 909 sheet: 0.21 (0.42), residues: 142 loop : 0.05 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 835 TYR 0.020 0.001 TYR A 367 PHE 0.022 0.001 PHE A 391 TRP 0.011 0.001 TRP A1700 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13687) covalent geometry : angle 0.49523 / 0.26 (18507) SS BOND : bond 0.00295 / 0.21 ( 11) SS BOND : angle 0.87178 / 0.52 ( 22) hydrogen bonds : bond 0.03878 / 2.61 ( 809) hydrogen bonds : angle 4.19765 / 2.98 ( 2286) link_BETA1-4 : bond 0.00534 / 0.30 ( 3) link_BETA1-4 : angle 2.89134 / 1.27 ( 9) link_NAG-ASN : bond 0.00674 / 0.56 ( 8) link_NAG-ASN : angle 3.11524 / 1.99 ( 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 219 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7685 (ttp-170) REVERT: A 121 LYS cc_start: 0.8045 (tttp) cc_final: 0.7602 (tptp) REVERT: A 131 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7722 (tp) REVERT: A 166 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7947 (pp20) REVERT: A 323 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7563 (mp-120) REVERT: A 752 ILE cc_start: 0.8509 (mm) cc_final: 0.8290 (mp) REVERT: A 763 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8646 (mtp) REVERT: A 798 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5650 (pmt) REVERT: A 1711 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8102 (mttp) outliers start: 37 outliers final: 19 residues processed: 204 average time/residue: 0.5099 time to fit residues: 115.0998 Evaluate side-chains 203 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG 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 166 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 407 GLU 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 798 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1354 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 140 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A1256 ASN A1502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109692 restraints weight = 47495.751| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.39 r_work: 0.2849 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13709 Z= 0.241 Angle : 0.618 9.965 18562 Z= 0.314 Chirality : 0.046 0.308 2103 Planarity : 0.004 0.049 2205 Dihedral : 11.067 88.821 2076 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.06 % Allowed : 17.63 % 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: 1.66 (0.21), residues: 1555 helix: 1.94 (0.17), residues: 902 sheet: 0.08 (0.42), residues: 142 loop : -0.03 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 835 TYR 0.033 0.002 TYR A 367 PHE 0.024 0.002 PHE A 391 TRP 0.009 0.002 TRP A1260 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (13687) covalent geometry : angle 0.59958 / 0.31 (18507) SS BOND : bond 0.00515 / 0.38 ( 11) SS BOND : angle 1.16789 / 0.76 ( 22) hydrogen bonds : bond 0.04892 / 3.21 ( 809) hydrogen bonds : angle 4.42929 / 3.15 ( 2286) link_BETA1-4 : bond 0.00596 / 0.33 ( 3) link_BETA1-4 : angle 3.44702 / 1.66 ( 9) link_NAG-ASN : bond 0.00848 / 0.71 ( 8) link_NAG-ASN : angle 3.58235 / 2.12 ( 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 226 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8284 (mm-30) REVERT: B 45 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7793 (ttp-170) REVERT: B 118 ASP cc_start: 0.8506 (m-30) cc_final: 0.8147 (m-30) REVERT: B 170 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 131 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7792 (tp) REVERT: A 234 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 323 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7699 (mp-120) REVERT: A 752 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 763 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8601 (mtp) REVERT: A 798 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5760 (pmt) REVERT: A 1251 LYS cc_start: 0.5436 (pmtt) cc_final: 0.5081 (pmtt) REVERT: A 1308 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7807 (ttm110) REVERT: A 1711 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8148 (mtmt) REVERT: A 1761 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6324 (mp0) outliers start: 43 outliers final: 26 residues processed: 209 average time/residue: 0.5065 time to fit residues: 117.4173 Evaluate side-chains 216 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG 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 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 166 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 VAL 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 1362 SER Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1448 THR 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 Chi-restraints excluded: chain A residue 1761 GLU 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: 0.9990 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4080 r_free = 0.4080 target = 0.181913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106647 restraints weight = 35208.505| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.62 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13709 Z= 0.148 Angle : 0.545 8.540 18562 Z= 0.278 Chirality : 0.042 0.306 2103 Planarity : 0.004 0.049 2205 Dihedral : 10.686 86.212 2076 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.84 % Allowed : 17.63 % 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: 1.78 (0.21), residues: 1555 helix: 2.03 (0.17), residues: 909 sheet: 0.21 (0.43), residues: 137 loop : -0.01 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 835 TYR 0.025 0.001 TYR A 367 PHE 0.022 0.002 PHE A 391 TRP 0.011 0.001 TRP A1700 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13687) covalent geometry : angle 0.52793 / 0.27 (18507) SS BOND : bond 0.00357 / 0.25 ( 11) SS BOND : angle 0.95024 / 0.59 ( 22) hydrogen bonds : bond 0.04209 / 2.79 ( 809) hydrogen bonds : angle 4.27476 / 3.04 ( 2286) link_BETA1-4 : bond 0.00626 / 0.35 ( 3) link_BETA1-4 : angle 3.12995 / 1.42 ( 9) link_NAG-ASN : bond 0.00721 / 0.60 ( 8) link_NAG-ASN : angle 3.15620 / 1.93 ( 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 224 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7695 (ttp-170) REVERT: B 170 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 131 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 220 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8063 (mtp85) REVERT: A 323 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7630 (mp-120) REVERT: A 752 ILE cc_start: 0.8508 (mm) cc_final: 0.8288 (mp) REVERT: A 763 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8644 (mtp) REVERT: A 781 LEU cc_start: 0.8430 (tp) cc_final: 0.8227 (mt) REVERT: A 798 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5749 (pmt) REVERT: A 1308 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7898 (ttm110) REVERT: A 1711 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8179 (mtmt) outliers start: 40 outliers final: 25 residues processed: 210 average time/residue: 0.5354 time to fit residues: 123.8502 Evaluate side-chains 214 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 137 SER 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 220 ARG Chi-restraints excluded: chain A residue 242 VAL 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 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 1362 SER Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1448 THR 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: 2.9990 chunk 134 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4073 r_free = 0.4073 target = 0.181327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105680 restraints weight = 37700.689| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.69 r_work: 0.2934 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13709 Z= 0.167 Angle : 0.561 8.470 18562 Z= 0.286 Chirality : 0.043 0.309 2103 Planarity : 0.004 0.050 2205 Dihedral : 10.744 83.975 2076 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.06 % Allowed : 17.70 % 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: 1.77 (0.21), residues: 1555 helix: 2.02 (0.17), residues: 903 sheet: 0.15 (0.42), residues: 137 loop : 0.01 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 835 TYR 0.028 0.001 TYR A 367 PHE 0.024 0.002 PHE A 391 TRP 0.011 0.001 TRP A1260 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13687) covalent geometry : angle 0.54429 / 0.28 (18507) SS BOND : bond 0.00416 / 0.30 ( 11) SS BOND : angle 0.99759 / 0.63 ( 22) hydrogen bonds : bond 0.04362 / 2.87 ( 809) hydrogen bonds : angle 4.29197 / 3.05 ( 2286) link_BETA1-4 : bond 0.00588 / 0.33 ( 3) link_BETA1-4 : angle 3.21746 / 1.50 ( 9) link_NAG-ASN : bond 0.00657 / 0.55 ( 8) link_NAG-ASN : angle 3.21876 / 1.93 ( 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 227 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7781 (ttp-170) REVERT: B 118 ASP cc_start: 0.8560 (m-30) cc_final: 0.8219 (m-30) REVERT: B 170 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 220 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8111 (mtp85) REVERT: A 323 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7644 (mp-120) REVERT: A 752 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 763 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8661 (mtp) REVERT: A 781 LEU cc_start: 0.8444 (tp) cc_final: 0.8221 (mt) REVERT: A 798 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5825 (pmt) REVERT: A 1278 LEU cc_start: 0.7945 (mt) cc_final: 0.7336 (tt) REVERT: A 1308 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7909 (ttm110) REVERT: A 1711 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8177 (mtmt) outliers start: 43 outliers final: 23 residues processed: 215 average time/residue: 0.5519 time to fit residues: 130.8327 Evaluate side-chains 209 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 137 SER 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 220 ARG Chi-restraints excluded: chain A residue 242 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4086 r_free = 0.4086 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108142 restraints weight = 30771.361| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.47 r_work: 0.2982 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1875 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= 0.126 Angle : 0.535 8.573 18562 Z= 0.273 Chirality : 0.041 0.309 2103 Planarity : 0.004 0.049 2205 Dihedral : 10.439 80.496 2076 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 18.69 % Favored : 79.39 % 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: 1.89 (0.21), residues: 1555 helix: 2.13 (0.17), residues: 909 sheet: 0.15 (0.42), residues: 142 loop : 0.03 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 835 TYR 0.022 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/Z covalent geometry : bond 0.00285 / 0.13 (13687) covalent geometry : angle 0.51973 / 0.27 (18507) SS BOND : bond 0.00314 / 0.22 ( 11) SS BOND : angle 0.89444 / 0.55 ( 22) hydrogen bonds : bond 0.03955 / 2.63 ( 809) hydrogen bonds : angle 4.18841 / 2.98 ( 2286) link_BETA1-4 : bond 0.00601 / 0.33 ( 3) link_BETA1-4 : angle 3.00803 / 1.34 ( 9) link_NAG-ASN : bond 0.00657 / 0.55 ( 8) link_NAG-ASN : angle 2.98932 / 1.84 ( 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: 27 poor density : 183 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8528 (mtm-85) REVERT: A 323 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7580 (mp-120) REVERT: A 752 ILE cc_start: 0.8514 (mm) cc_final: 0.8302 (mp) REVERT: A 763 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: A 781 LEU cc_start: 0.8433 (tp) cc_final: 0.8221 (mt) REVERT: A 798 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.5737 (pmt) REVERT: A 1278 LEU cc_start: 0.7911 (mt) cc_final: 0.7337 (tt) REVERT: A 1308 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7761 (mtm-85) REVERT: A 1711 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8163 (mtmt) outliers start: 27 outliers final: 19 residues processed: 201 average time/residue: 0.5459 time to fit residues: 121.3540 Evaluate side-chains 201 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 159 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 242 VAL 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 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 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: 0.9990 chunk 13 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4093 r_free = 0.4093 target = 0.183389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108540 restraints weight = 36927.456| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.65 r_work: 0.2979 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13709 Z= 0.115 Angle : 0.514 8.553 18562 Z= 0.262 Chirality : 0.041 0.312 2103 Planarity : 0.004 0.049 2205 Dihedral : 10.119 74.808 2076 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.78 % Allowed : 19.12 % Favored : 79.10 % 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: 2.00 (0.21), residues: 1555 helix: 2.22 (0.17), residues: 908 sheet: 0.24 (0.42), residues: 142 loop : 0.04 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 835 TYR 0.021 0.001 TYR A 367 PHE 0.023 0.001 PHE A 391 TRP 0.011 0.001 TRP A1700 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13687) covalent geometry : angle 0.49936 / 0.26 (18507) SS BOND : bond 0.00301 / 0.21 ( 11) SS BOND : angle 0.87263 / 0.53 ( 22) hydrogen bonds : bond 0.03756 / 2.50 ( 809) hydrogen bonds : angle 4.09752 / 2.92 ( 2286) link_BETA1-4 : bond 0.00589 / 0.33 ( 3) link_BETA1-4 : angle 2.88037 / 1.31 ( 9) link_NAG-ASN : bond 0.00653 / 0.55 ( 8) link_NAG-ASN : angle 2.90114 / 1.81 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6812.95 seconds wall clock time: 116 minutes 29.36 seconds (6989.36 seconds total)