Starting phenix.real_space_refine on Sat Aug 23 14:45:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlh_36397/08_2025/8jlh_36397.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8117 2.51 5 N 2099 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12610 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 918 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.88, per 1000 atoms: 0.23 Number of scatterers: 12610 At special positions: 0 Unit cell: (92.13, 151.89, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2332 8.00 N 2099 7.00 C 8117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 802 " - " ASN A 498 " " NAG A 803 " - " ASN A 548 " " NAG C 900 " - " ASN C 498 " " NAG C 901 " - " ASN C 548 " " NAG E 1 " - " ASN A 573 " " NAG F 1 " - " ASN C 573 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 555.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 31.4% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.618A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 191 - end of helix removed outlier: 4.285A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.599A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.527A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.295A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.717A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.064A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.821A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.566A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.644A pdb=" N PHE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 591 through 619 removed outlier: 4.250A pdb=" N TYR A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.593A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.788A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.800A pdb=" N VAL D 933 " --> pdb=" O ASN D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 958 Processing helix chain 'D' and resid 1080 through 1092 Processing helix chain 'D' and resid 1210 through 1215 removed outlier: 4.225A pdb=" N VAL D1214 " --> pdb=" O ILE D1211 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY D1215 " --> pdb=" O PRO D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 540 through 542 removed outlier: 7.088A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 5.916A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.649A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.649A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE B1069 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 962 through 968 removed outlier: 6.856A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA9, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.920A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.316A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.531A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 16.017A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 16.795A pdb=" N ALA B1259 " --> pdb=" O ALA B1208 " (cutoff:3.500A) removed outlier: 12.520A pdb=" N ALA B1208 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B1261 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B1204 " --> pdb=" O ALA B1263 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N THR B1195 " --> pdb=" O VAL B1180 " (cutoff:3.500A) removed outlier: 15.168A pdb=" N VAL B1180 " --> pdb=" O THR B1195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 485 through 488 removed outlier: 9.277A pdb=" N THR C 500 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 523 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 502 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER C 525 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN C 504 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 527 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS C 506 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 485 through 488 removed outlier: 9.277A pdb=" N THR C 500 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 523 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 502 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER C 525 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN C 504 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 527 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS C 506 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C 546 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.619A pdb=" N PHE C 497 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 536 " --> pdb=" O TYR C 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 887 through 890 removed outlier: 3.532A pdb=" N ASP D 887 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D1074 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 880 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D1072 " --> pdb=" O SER D 880 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL D 882 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N LYS D1070 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 16.743A pdb=" N LYS D 884 " --> pdb=" O MET D1068 " (cutoff:3.500A) removed outlier: 18.366A pdb=" N MET D1068 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 905 " --> pdb=" O LYS D 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 887 through 890 removed outlier: 3.532A pdb=" N ASP D 887 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D1074 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 880 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D1072 " --> pdb=" O SER D 880 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL D 882 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N LYS D1070 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 16.743A pdb=" N LYS D 884 " --> pdb=" O MET D1068 " (cutoff:3.500A) removed outlier: 18.366A pdb=" N MET D1068 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE D1069 " --> pdb=" O LYS D 948 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS D 948 " --> pdb=" O ILE D1069 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR D1071 " --> pdb=" O TRP D 946 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP D 946 " --> pdb=" O TYR D1071 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP D1037 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D1031 " --> pdb=" O LEU D1035 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU D1035 " --> pdb=" O ILE D1031 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 897 through 900 removed outlier: 7.933A pdb=" N MET D1054 " --> pdb=" O CYS D 967 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS D 967 " --> pdb=" O MET D1054 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS D1056 " --> pdb=" O ILE D 965 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE D 965 " --> pdb=" O LYS D1056 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR D 963 " --> pdb=" O LEU D 978 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 978 " --> pdb=" O THR D 963 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP D 974 " --> pdb=" O CYS D 967 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1112 through 1115 Processing sheet with id=AB9, first strand: chain 'D' and resid 1122 through 1125 Processing sheet with id=AC1, first strand: chain 'D' and resid 1159 through 1164 removed outlier: 4.062A pdb=" N LYS D1159 " --> pdb=" O VAL D1185 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS D1226 " --> pdb=" O LYS D1234 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS D1234 " --> pdb=" O LYS D1226 " (cutoff:3.500A) removed outlier: 27.430A pdb=" N ASN D1233 " --> pdb=" O LEU D1254 " (cutoff:3.500A) removed outlier: 23.467A pdb=" N LEU D1254 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 16.107A pdb=" N CYS D1235 " --> pdb=" O PHE D1252 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N PHE D1252 " --> pdb=" O CYS D1235 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET D1237 " --> pdb=" O ILE D1250 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D1263 " --> pdb=" O LYS D1204 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D1204 " --> pdb=" O ALA D1263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1159 through 1164 removed outlier: 4.062A pdb=" N LYS D1159 " --> pdb=" O VAL D1185 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D1182 " --> pdb=" O LEU D1193 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1689 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: 2.76 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3624 1.33 - 1.46: 2901 1.46 - 1.58: 6273 1.58 - 1.70: 0 1.70 - 1.83: 99 Bond restraints: 12897 Sorted by residual: bond pdb=" C5 UKX A 801 " pdb=" N2 UKX A 801 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 UKX A 801 " pdb=" N1 UKX A 801 " ideal model delta sigma weight residual 1.353 1.391 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CA ILE D1211 " pdb=" CB ILE D1211 " ideal model delta sigma weight residual 1.534 1.545 -0.011 6.80e-03 2.16e+04 2.45e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 12892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 17339 2.87 - 5.75: 82 5.75 - 8.62: 10 8.62 - 11.49: 1 11.49 - 14.37: 2 Bond angle restraints: 17434 Sorted by residual: angle pdb=" CB MET B 937 " pdb=" CG MET B 937 " pdb=" SD MET B 937 " ideal model delta sigma weight residual 112.70 127.07 -14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" N VAL D1202 " pdb=" CA VAL D1202 " pdb=" C VAL D1202 " ideal model delta sigma weight residual 111.81 108.12 3.69 8.60e-01 1.35e+00 1.84e+01 angle pdb=" CB MET A 206 " pdb=" CG MET A 206 " pdb=" SD MET A 206 " ideal model delta sigma weight residual 112.70 125.25 -12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CA GLN D 992 " pdb=" CB GLN D 992 " pdb=" CG GLN D 992 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLN A 430 " pdb=" CB GLN A 430 " pdb=" CG GLN A 430 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 ... (remaining 17429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6820 17.97 - 35.93: 666 35.93 - 53.90: 176 53.90 - 71.86: 37 71.86 - 89.83: 9 Dihedral angle restraints: 7708 sinusoidal: 3223 harmonic: 4485 Sorted by residual: dihedral pdb=" CA PHE C 497 " pdb=" C PHE C 497 " pdb=" N ASN C 498 " pdb=" CA ASN C 498 " ideal model delta harmonic sigma weight residual 180.00 147.21 32.79 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 149.30 30.70 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL B1144 " pdb=" C VAL B1144 " pdb=" N THR B1145 " pdb=" CA THR B1145 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1554 0.055 - 0.109: 315 0.109 - 0.164: 43 0.164 - 0.218: 1 0.218 - 0.273: 3 Chirality restraints: 1916 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C6 UKX A 801 " pdb=" C5 UKX A 801 " pdb=" C7 UKX A 801 " pdb=" N1 UKX A 801 " both_signs ideal model delta sigma weight residual False 2.45 2.67 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 548 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1913 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 487 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO C 488 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 488 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 488 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 992 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C GLN D 992 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN D 992 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN D 993 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1213 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASP B1213 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B1213 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1214 " -0.011 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 395 2.71 - 3.26: 12213 3.26 - 3.80: 20202 3.80 - 4.35: 26699 4.35 - 4.90: 45152 Nonbonded interactions: 104661 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR D 943 " pdb=" O ASN D1073 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.225 3.120 nonbonded pdb=" O PHE A 546 " pdb=" OG SER A 569 " model vdw 2.228 3.040 nonbonded pdb=" O GLY D1132 " pdb=" OG SER D1207 " model vdw 2.232 3.040 ... (remaining 104656 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 'B' selection = chain 'D' } ncs_group { reference = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12907 Z= 0.171 Angle : 0.661 14.367 17464 Z= 0.358 Chirality : 0.045 0.273 1916 Planarity : 0.004 0.065 2203 Dihedral : 15.498 89.830 4842 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.39 % Allowed : 18.23 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: 0.04 (0.21), residues: 1532 helix: 1.71 (0.24), residues: 432 sheet: 0.24 (0.28), residues: 332 loop : -1.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 737 TYR 0.025 0.001 TYR A 169 PHE 0.012 0.001 PHE A 497 TRP 0.014 0.001 TRP A 333 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00363 (12897) covalent geometry : angle 0.63491 (17434) hydrogen bonds : bond 0.12915 ( 587) hydrogen bonds : angle 6.13264 ( 1689) link_BETA1-4 : bond 0.00889 ( 2) link_BETA1-4 : angle 1.01471 ( 6) link_BETA1-6 : bond 0.00496 ( 2) link_BETA1-6 : angle 1.36029 ( 6) link_NAG-ASN : bond 0.00484 ( 6) link_NAG-ASN : angle 5.68294 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 324 MET cc_start: 0.5335 (tpp) cc_final: 0.5046 (tpt) REVERT: A 712 LYS cc_start: 0.6670 (mtpm) cc_final: 0.6114 (ttpp) REVERT: B 1086 ASP cc_start: 0.7278 (t0) cc_final: 0.6995 (t70) REVERT: D 1203 GLU cc_start: 0.4058 (mm-30) cc_final: 0.3774 (mm-30) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 0.6475 time to fit residues: 125.9538 Evaluate side-chains 165 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 434 ASN A 568 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN B1046 ASN B1091 GLN B1176 ASN B1270 GLN C 568 ASN D 913 GLN D 960 ASN D1003 GLN D1106 GLN D1177 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.223774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156583 restraints weight = 12892.835| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.33 r_work: 0.3280 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12907 Z= 0.201 Angle : 0.623 11.674 17464 Z= 0.326 Chirality : 0.047 0.352 1916 Planarity : 0.004 0.058 2203 Dihedral : 6.265 73.823 1931 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.61 % Allowed : 15.67 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.00 (0.21), residues: 1532 helix: 1.81 (0.24), residues: 439 sheet: 0.24 (0.28), residues: 350 loop : -1.27 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 737 TYR 0.017 0.002 TYR A 169 PHE 0.020 0.002 PHE B1100 TRP 0.014 0.002 TRP A 333 HIS 0.003 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00477 (12897) covalent geometry : angle 0.59466 (17434) hydrogen bonds : bond 0.04721 ( 587) hydrogen bonds : angle 5.11241 ( 1689) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 0.85509 ( 6) link_BETA1-6 : bond 0.00517 ( 2) link_BETA1-6 : angle 1.64407 ( 6) link_NAG-ASN : bond 0.00713 ( 6) link_NAG-ASN : angle 5.77171 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: A 324 MET cc_start: 0.5361 (tpp) cc_final: 0.4835 (tpt) REVERT: A 366 LYS cc_start: 0.7226 (ttpt) cc_final: 0.7022 (ttmt) REVERT: A 444 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5311 (ttt-90) REVERT: A 515 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: A 568 ASN cc_start: 0.8319 (t0) cc_final: 0.8038 (t0) REVERT: A 712 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6973 (ttpp) REVERT: B 925 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 1086 ASP cc_start: 0.8053 (t70) cc_final: 0.7278 (t0) REVERT: B 1187 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8216 (mppt) REVERT: D 906 TYR cc_start: 0.6311 (m-80) cc_final: 0.5448 (m-10) REVERT: D 960 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7518 (t0) REVERT: D 961 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: D 1054 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5617 (tmm) outliers start: 63 outliers final: 25 residues processed: 207 average time/residue: 0.6164 time to fit residues: 139.4004 Evaluate side-chains 183 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 960 ASN Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1188 ASN Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN B1093 ASN B1199 GLN B1268 ASN C 568 ASN D 912 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D1021 ASN D1106 GLN D1177 ASN D1199 GLN D1270 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.222381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151076 restraints weight = 13075.384| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.20 r_work: 0.3292 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12907 Z= 0.213 Angle : 0.627 11.490 17464 Z= 0.326 Chirality : 0.047 0.349 1916 Planarity : 0.004 0.054 2203 Dihedral : 5.797 50.537 1916 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.69 % Allowed : 16.40 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.02 (0.21), residues: 1532 helix: 1.82 (0.24), residues: 440 sheet: 0.21 (0.30), residues: 306 loop : -1.21 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 737 TYR 0.017 0.002 TYR D 962 PHE 0.019 0.002 PHE B1100 TRP 0.014 0.002 TRP A 333 HIS 0.003 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00512 (12897) covalent geometry : angle 0.59790 (17434) hydrogen bonds : bond 0.04673 ( 587) hydrogen bonds : angle 5.03741 ( 1689) link_BETA1-4 : bond 0.00363 ( 2) link_BETA1-4 : angle 0.99310 ( 6) link_BETA1-6 : bond 0.00463 ( 2) link_BETA1-6 : angle 1.51202 ( 6) link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 5.81972 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 VAL cc_start: 0.8187 (t) cc_final: 0.7965 (p) REVERT: A 444 ARG cc_start: 0.5643 (OUTLIER) cc_final: 0.5320 (ttt-90) REVERT: A 515 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8615 (mttm) REVERT: A 568 ASN cc_start: 0.8289 (t0) cc_final: 0.8074 (t160) REVERT: A 583 CYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6976 (m) REVERT: A 712 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6968 (ttpp) REVERT: B 1064 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6589 (mtp85) REVERT: B 1086 ASP cc_start: 0.8039 (t70) cc_final: 0.7277 (t70) REVERT: B 1121 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8436 (mtmm) REVERT: B 1187 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8232 (mppt) REVERT: B 1219 GLN cc_start: 0.7887 (pt0) cc_final: 0.7381 (pt0) REVERT: D 1054 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5698 (tmm) REVERT: D 1203 GLU cc_start: 0.5349 (mm-30) cc_final: 0.5125 (mm-30) outliers start: 64 outliers final: 38 residues processed: 196 average time/residue: 0.6239 time to fit residues: 133.3229 Evaluate side-chains 188 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1280 CYS Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1177 ASN Chi-restraints excluded: chain D residue 1188 ASN Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B 960 ASN B1003 GLN B1046 ASN B1091 GLN B1115 ASN C 568 ASN D 960 ASN D1003 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.223691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153364 restraints weight = 13001.117| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.25 r_work: 0.3292 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12907 Z= 0.182 Angle : 0.599 11.039 17464 Z= 0.312 Chirality : 0.046 0.324 1916 Planarity : 0.003 0.053 2203 Dihedral : 5.605 50.679 1916 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.27 % Allowed : 16.98 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.03 (0.21), residues: 1532 helix: 1.87 (0.24), residues: 442 sheet: 0.19 (0.30), residues: 306 loop : -1.17 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 737 TYR 0.015 0.001 TYR B1149 PHE 0.014 0.002 PHE A 497 TRP 0.013 0.001 TRP A 333 HIS 0.003 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00432 (12897) covalent geometry : angle 0.57027 (17434) hydrogen bonds : bond 0.04414 ( 587) hydrogen bonds : angle 4.95866 ( 1689) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 0.91566 ( 6) link_BETA1-6 : bond 0.00436 ( 2) link_BETA1-6 : angle 1.56984 ( 6) link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 5.61839 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 152 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: A 345 VAL cc_start: 0.8132 (t) cc_final: 0.7906 (p) REVERT: A 366 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6967 (ttmt) REVERT: A 444 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.4907 (ttt-90) REVERT: A 515 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8621 (mttm) REVERT: A 519 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 568 ASN cc_start: 0.8302 (t0) cc_final: 0.8049 (t160) REVERT: A 583 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6944 (m) REVERT: A 695 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7681 (tp) REVERT: A 712 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6914 (ttpp) REVERT: B 1064 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6553 (mtp85) REVERT: B 1086 ASP cc_start: 0.8077 (t70) cc_final: 0.7357 (t70) REVERT: B 1187 LYS cc_start: 0.8648 (mmpt) cc_final: 0.8204 (mppt) REVERT: B 1219 GLN cc_start: 0.7954 (pt0) cc_final: 0.7392 (pt0) REVERT: C 560 ASP cc_start: 0.8724 (p0) cc_final: 0.8419 (p0) REVERT: D 911 LYS cc_start: 0.7622 (mttp) cc_final: 0.7264 (mptp) REVERT: D 1054 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5677 (tpt) REVERT: D 1203 GLU cc_start: 0.5274 (mm-30) cc_final: 0.5023 (mm-30) REVERT: D 1236 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5831 (ptpp) outliers start: 72 outliers final: 39 residues processed: 202 average time/residue: 0.5926 time to fit residues: 130.8714 Evaluate side-chains 196 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1188 ASN Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Chi-restraints excluded: chain D residue 1294 SER Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 138 optimal weight: 0.0370 chunk 136 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN B1046 ASN B1091 GLN C 568 ASN D 960 ASN D1003 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.222474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151703 restraints weight = 13071.114| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.22 r_work: 0.3398 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12907 Z= 0.140 Angle : 0.569 10.565 17464 Z= 0.295 Chirality : 0.045 0.302 1916 Planarity : 0.003 0.052 2203 Dihedral : 5.369 50.159 1916 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.61 % Allowed : 17.86 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1532 helix: 2.00 (0.24), residues: 442 sheet: 0.19 (0.30), residues: 313 loop : -1.09 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 737 TYR 0.014 0.001 TYR B 962 PHE 0.011 0.001 PHE A 497 TRP 0.012 0.001 TRP A 333 HIS 0.009 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00323 (12897) covalent geometry : angle 0.54271 (17434) hydrogen bonds : bond 0.04024 ( 587) hydrogen bonds : angle 4.83391 ( 1689) link_BETA1-4 : bond 0.00497 ( 2) link_BETA1-4 : angle 0.87156 ( 6) link_BETA1-6 : bond 0.00528 ( 2) link_BETA1-6 : angle 1.49526 ( 6) link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 5.22850 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: A 345 VAL cc_start: 0.8188 (t) cc_final: 0.7958 (p) REVERT: A 444 ARG cc_start: 0.5559 (OUTLIER) cc_final: 0.5110 (ttt-90) REVERT: A 515 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8571 (mttm) REVERT: A 568 ASN cc_start: 0.8203 (t0) cc_final: 0.7978 (t160) REVERT: A 583 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6969 (m) REVERT: A 634 MET cc_start: 0.6366 (mtt) cc_final: 0.5953 (mtp) REVERT: A 695 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7705 (tp) REVERT: A 712 LYS cc_start: 0.7685 (mtpm) cc_final: 0.7027 (ttpp) REVERT: B 1064 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6464 (mtp85) REVERT: B 1085 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6980 (mptt) REVERT: B 1086 ASP cc_start: 0.8026 (t70) cc_final: 0.7319 (t70) REVERT: B 1187 LYS cc_start: 0.8650 (mmpt) cc_final: 0.8212 (mppt) REVERT: B 1219 GLN cc_start: 0.7948 (pt0) cc_final: 0.7513 (pt0) REVERT: C 560 ASP cc_start: 0.8666 (p0) cc_final: 0.8366 (p0) REVERT: D 911 LYS cc_start: 0.7718 (mttp) cc_final: 0.7387 (mptp) REVERT: D 961 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: D 1054 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5713 (tpt) REVERT: D 1058 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6736 (p0) REVERT: D 1064 ARG cc_start: 0.6848 (mtm180) cc_final: 0.6585 (mpp80) REVERT: D 1081 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6738 (tm-30) REVERT: D 1085 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7711 (mtpm) outliers start: 63 outliers final: 29 residues processed: 203 average time/residue: 0.6449 time to fit residues: 142.5145 Evaluate side-chains 192 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN B1046 ASN B1091 GLN C 568 ASN D 912 ASN D 960 ASN D1003 GLN D1177 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.223727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152573 restraints weight = 12966.467| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.20 r_work: 0.3323 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12907 Z= 0.140 Angle : 0.568 10.155 17464 Z= 0.294 Chirality : 0.045 0.319 1916 Planarity : 0.003 0.049 2203 Dihedral : 5.269 50.069 1916 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.61 % Allowed : 18.01 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1532 helix: 2.06 (0.24), residues: 441 sheet: 0.20 (0.30), residues: 313 loop : -1.04 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 737 TYR 0.013 0.001 TYR B 962 PHE 0.011 0.001 PHE D1072 TRP 0.011 0.001 TRP A 333 HIS 0.008 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00324 (12897) covalent geometry : angle 0.54427 (17434) hydrogen bonds : bond 0.03977 ( 587) hydrogen bonds : angle 4.80089 ( 1689) link_BETA1-4 : bond 0.00604 ( 2) link_BETA1-4 : angle 0.92873 ( 6) link_BETA1-6 : bond 0.00575 ( 2) link_BETA1-6 : angle 1.53205 ( 6) link_NAG-ASN : bond 0.00519 ( 6) link_NAG-ASN : angle 5.04398 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 165 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: A 288 LYS cc_start: 0.7440 (mttm) cc_final: 0.7225 (mtmt) REVERT: A 310 MET cc_start: 0.7144 (mmt) cc_final: 0.6792 (mmt) REVERT: A 324 MET cc_start: 0.5467 (tpp) cc_final: 0.5199 (mpp) REVERT: A 345 VAL cc_start: 0.8112 (t) cc_final: 0.7875 (p) REVERT: A 444 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.5112 (ttt-90) REVERT: A 515 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8550 (mttm) REVERT: A 568 ASN cc_start: 0.8263 (t0) cc_final: 0.8029 (t160) REVERT: A 583 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6938 (m) REVERT: A 695 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7667 (tp) REVERT: A 712 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6991 (ttpp) REVERT: B 1046 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6747 (t0) REVERT: B 1064 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6416 (mtp85) REVERT: B 1085 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6946 (mptt) REVERT: B 1086 ASP cc_start: 0.8046 (t70) cc_final: 0.7364 (t0) REVERT: B 1187 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8195 (mppt) REVERT: B 1219 GLN cc_start: 0.7969 (pt0) cc_final: 0.7471 (pt0) REVERT: C 560 ASP cc_start: 0.8654 (p0) cc_final: 0.8359 (p0) REVERT: D 911 LYS cc_start: 0.7495 (mttp) cc_final: 0.7142 (mptp) REVERT: D 961 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: D 1054 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5827 (tpt) REVERT: D 1058 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6739 (p0) REVERT: D 1064 ARG cc_start: 0.6824 (mtm180) cc_final: 0.6614 (mpp80) REVERT: D 1081 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 1085 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7669 (mtpm) outliers start: 63 outliers final: 31 residues processed: 203 average time/residue: 0.6302 time to fit residues: 139.4830 Evaluate side-chains 199 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1046 ASN Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.0570 chunk 141 optimal weight: 0.1980 chunk 140 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN B1091 GLN C 568 ASN D1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.225238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161723 restraints weight = 12974.503| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.45 r_work: 0.3288 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12907 Z= 0.120 Angle : 0.554 11.603 17464 Z= 0.289 Chirality : 0.044 0.290 1916 Planarity : 0.003 0.048 2203 Dihedral : 5.082 49.811 1914 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.95 % Allowed : 18.81 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1532 helix: 2.14 (0.24), residues: 442 sheet: 0.10 (0.30), residues: 311 loop : -0.86 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 737 TYR 0.013 0.001 TYR A 169 PHE 0.012 0.001 PHE D1055 TRP 0.011 0.001 TRP A 333 HIS 0.008 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00268 (12897) covalent geometry : angle 0.53224 (17434) hydrogen bonds : bond 0.03742 ( 587) hydrogen bonds : angle 4.72637 ( 1689) link_BETA1-4 : bond 0.00625 ( 2) link_BETA1-4 : angle 0.92157 ( 6) link_BETA1-6 : bond 0.00707 ( 2) link_BETA1-6 : angle 1.51114 ( 6) link_NAG-ASN : bond 0.00440 ( 6) link_NAG-ASN : angle 4.78199 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 165 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6200 (mp10) REVERT: A 324 MET cc_start: 0.5275 (tpp) cc_final: 0.5067 (mpp) REVERT: A 345 VAL cc_start: 0.8217 (t) cc_final: 0.7983 (p) REVERT: A 366 LYS cc_start: 0.7151 (ttmt) cc_final: 0.6914 (ttmt) REVERT: A 444 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.5167 (ttt-90) REVERT: A 515 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8502 (mttm) REVERT: A 568 ASN cc_start: 0.8099 (t0) cc_final: 0.7885 (t160) REVERT: A 634 MET cc_start: 0.6424 (mtt) cc_final: 0.6005 (mtp) REVERT: A 675 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7028 (pt0) REVERT: A 712 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7107 (ttpp) REVERT: B 1064 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6428 (mtp85) REVERT: B 1085 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7131 (mptt) REVERT: B 1086 ASP cc_start: 0.7996 (t70) cc_final: 0.7276 (t0) REVERT: B 1187 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8241 (mppt) REVERT: B 1219 GLN cc_start: 0.7926 (pt0) cc_final: 0.7513 (pt0) REVERT: C 560 ASP cc_start: 0.8495 (p0) cc_final: 0.8200 (p0) REVERT: D 961 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: D 1054 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5948 (tpt) REVERT: D 1058 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6784 (p0) REVERT: D 1081 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6742 (tm-30) REVERT: D 1085 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7650 (mtpm) outliers start: 54 outliers final: 29 residues processed: 199 average time/residue: 0.6320 time to fit residues: 137.4638 Evaluate side-chains 195 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN C 568 ASN D1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.225697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156596 restraints weight = 12852.953| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.29 r_work: 0.3334 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12907 Z= 0.114 Angle : 0.553 12.136 17464 Z= 0.286 Chirality : 0.044 0.277 1916 Planarity : 0.003 0.048 2203 Dihedral : 4.969 49.128 1914 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.59 % Allowed : 19.47 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1532 helix: 2.20 (0.24), residues: 441 sheet: 0.09 (0.30), residues: 311 loop : -0.82 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 737 TYR 0.013 0.001 TYR A 169 PHE 0.010 0.001 PHE D1117 TRP 0.010 0.001 TRP A 333 HIS 0.008 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00255 (12897) covalent geometry : angle 0.53249 (17434) hydrogen bonds : bond 0.03636 ( 587) hydrogen bonds : angle 4.67464 ( 1689) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 0.78294 ( 6) link_BETA1-6 : bond 0.00488 ( 2) link_BETA1-6 : angle 1.43647 ( 6) link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 4.55856 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: A 165 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6095 (mp10) REVERT: A 324 MET cc_start: 0.5457 (tpp) cc_final: 0.4885 (mpp) REVERT: A 345 VAL cc_start: 0.8067 (t) cc_final: 0.7837 (p) REVERT: A 366 LYS cc_start: 0.7011 (ttmt) cc_final: 0.6742 (ttmt) REVERT: A 444 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.5005 (ttt-90) REVERT: A 515 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8542 (mttm) REVERT: A 568 ASN cc_start: 0.8281 (t0) cc_final: 0.8065 (t160) REVERT: A 583 CYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6901 (m) REVERT: A 647 SER cc_start: 0.7972 (p) cc_final: 0.7624 (t) REVERT: A 675 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6999 (pt0) REVERT: A 712 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7063 (ttpp) REVERT: B 1003 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: B 1064 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6270 (mtp85) REVERT: B 1085 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6982 (mptt) REVERT: B 1086 ASP cc_start: 0.7971 (t70) cc_final: 0.7305 (t0) REVERT: B 1187 LYS cc_start: 0.8650 (mmpt) cc_final: 0.8208 (mppt) REVERT: B 1219 GLN cc_start: 0.7902 (pt0) cc_final: 0.7484 (pt0) REVERT: C 522 LYS cc_start: 0.8061 (tttt) cc_final: 0.7558 (mttp) REVERT: D 961 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: D 1054 MET cc_start: 0.6127 (mmt) cc_final: 0.5889 (tpt) REVERT: D 1055 PHE cc_start: 0.7576 (m-10) cc_final: 0.7336 (m-10) REVERT: D 1058 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6733 (p0) REVERT: D 1081 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6827 (tm-30) REVERT: D 1085 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7645 (mtpm) outliers start: 49 outliers final: 22 residues processed: 188 average time/residue: 0.6749 time to fit residues: 138.0640 Evaluate side-chains 180 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 24 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN B1022 ASN B1046 ASN B1091 GLN B1233 ASN D1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.220445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149732 restraints weight = 13029.131| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.23 r_work: 0.3269 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12907 Z= 0.247 Angle : 0.658 12.672 17464 Z= 0.340 Chirality : 0.048 0.303 1916 Planarity : 0.004 0.049 2203 Dihedral : 5.356 51.527 1912 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.51 % Allowed : 19.69 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.07 (0.21), residues: 1532 helix: 1.88 (0.24), residues: 441 sheet: -0.00 (0.29), residues: 328 loop : -1.05 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 737 TYR 0.021 0.002 TYR A 306 PHE 0.022 0.002 PHE B1100 TRP 0.010 0.002 TRP A 333 HIS 0.008 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00602 (12897) covalent geometry : angle 0.63704 (17434) hydrogen bonds : bond 0.04657 ( 587) hydrogen bonds : angle 4.92226 ( 1689) link_BETA1-4 : bond 0.00496 ( 2) link_BETA1-4 : angle 1.07388 ( 6) link_BETA1-6 : bond 0.00467 ( 2) link_BETA1-6 : angle 1.72603 ( 6) link_NAG-ASN : bond 0.00670 ( 6) link_NAG-ASN : angle 5.05329 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: A 165 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6207 (mp10) REVERT: A 324 MET cc_start: 0.5639 (tpp) cc_final: 0.5419 (mpp) REVERT: A 345 VAL cc_start: 0.8125 (t) cc_final: 0.7874 (p) REVERT: A 444 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.5146 (ttt-90) REVERT: A 515 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8651 (mttm) REVERT: A 568 ASN cc_start: 0.8324 (t0) cc_final: 0.8080 (t160) REVERT: A 583 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6965 (m) REVERT: A 634 MET cc_start: 0.6416 (mtt) cc_final: 0.5989 (mtp) REVERT: A 647 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7704 (t) REVERT: A 675 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7346 (pt0) REVERT: A 712 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7006 (ttpp) REVERT: B 1003 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: B 1064 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6532 (mtp85) REVERT: B 1074 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7082 (tt) REVERT: B 1084 ILE cc_start: 0.7615 (mm) cc_final: 0.7356 (mt) REVERT: B 1085 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (mptt) REVERT: B 1187 LYS cc_start: 0.8669 (mmpt) cc_final: 0.8227 (mppt) REVERT: B 1219 GLN cc_start: 0.7935 (pt0) cc_final: 0.7483 (pt0) REVERT: D 961 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: D 1054 MET cc_start: 0.6147 (mmt) cc_final: 0.5867 (tpt) REVERT: D 1055 PHE cc_start: 0.7644 (m-10) cc_final: 0.7395 (m-10) REVERT: D 1081 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6844 (tm-30) REVERT: D 1085 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7670 (mtpm) outliers start: 48 outliers final: 26 residues processed: 188 average time/residue: 0.5872 time to fit residues: 121.2700 Evaluate side-chains 187 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1280 CYS Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN C 568 ASN D1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.225222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155085 restraints weight = 13055.020| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.23 r_work: 0.3327 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12907 Z= 0.131 Angle : 0.592 14.356 17464 Z= 0.304 Chirality : 0.045 0.295 1916 Planarity : 0.003 0.049 2203 Dihedral : 5.121 50.200 1912 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.07 % Allowed : 20.42 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1532 helix: 2.04 (0.24), residues: 441 sheet: 0.04 (0.30), residues: 325 loop : -0.93 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 737 TYR 0.015 0.001 TYR B 962 PHE 0.012 0.001 PHE D1117 TRP 0.012 0.001 TRP A 333 HIS 0.002 0.000 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00300 (12897) covalent geometry : angle 0.57255 (17434) hydrogen bonds : bond 0.03902 ( 587) hydrogen bonds : angle 4.77359 ( 1689) link_BETA1-4 : bond 0.00493 ( 2) link_BETA1-4 : angle 0.79415 ( 6) link_BETA1-6 : bond 0.00453 ( 2) link_BETA1-6 : angle 1.54413 ( 6) link_NAG-ASN : bond 0.00456 ( 6) link_NAG-ASN : angle 4.63607 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: A 324 MET cc_start: 0.5564 (tpp) cc_final: 0.5340 (mpp) REVERT: A 345 VAL cc_start: 0.8055 (t) cc_final: 0.7817 (p) REVERT: A 444 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.4918 (ttt-90) REVERT: A 515 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8532 (mttm) REVERT: A 568 ASN cc_start: 0.8291 (t0) cc_final: 0.8063 (t160) REVERT: A 583 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6942 (m) REVERT: A 675 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7106 (pt0) REVERT: A 712 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7043 (ttpp) REVERT: B 906 TYR cc_start: 0.8485 (m-80) cc_final: 0.8220 (m-80) REVERT: B 1003 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: B 1064 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6370 (mtp85) REVERT: B 1074 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6984 (tt) REVERT: B 1085 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6882 (mptt) REVERT: B 1086 ASP cc_start: 0.7938 (t0) cc_final: 0.7245 (t0) REVERT: B 1187 LYS cc_start: 0.8612 (mmpt) cc_final: 0.8171 (mppt) REVERT: B 1219 GLN cc_start: 0.7860 (pt0) cc_final: 0.7362 (pt0) REVERT: C 520 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8202 (mmm160) REVERT: C 522 LYS cc_start: 0.8087 (tttt) cc_final: 0.7638 (mttp) REVERT: D 961 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: D 1055 PHE cc_start: 0.7512 (m-10) cc_final: 0.7294 (m-10) REVERT: D 1081 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6840 (tm-30) REVERT: D 1085 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7658 (mtpm) REVERT: D 1143 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8666 (t) outliers start: 42 outliers final: 22 residues processed: 174 average time/residue: 0.5714 time to fit residues: 108.3575 Evaluate side-chains 174 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1236 LYS Chi-restraints excluded: chain D residue 1295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 132 optimal weight: 0.0970 chunk 77 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B1003 GLN D1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.224772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154146 restraints weight = 13121.975| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.26 r_work: 0.3342 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12907 Z= 0.121 Angle : 0.582 14.423 17464 Z= 0.300 Chirality : 0.045 0.280 1916 Planarity : 0.003 0.047 2203 Dihedral : 5.054 49.745 1912 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.07 % Allowed : 20.20 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.33 (0.21), residues: 1532 helix: 2.11 (0.24), residues: 441 sheet: 0.06 (0.30), residues: 311 loop : -0.83 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 737 TYR 0.013 0.001 TYR B 962 PHE 0.012 0.001 PHE D1117 TRP 0.011 0.001 TRP A 333 HIS 0.001 0.000 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00270 (12897) covalent geometry : angle 0.56386 (17434) hydrogen bonds : bond 0.03729 ( 587) hydrogen bonds : angle 4.74576 ( 1689) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 0.81019 ( 6) link_BETA1-6 : bond 0.00464 ( 2) link_BETA1-6 : angle 1.48458 ( 6) link_NAG-ASN : bond 0.00422 ( 6) link_NAG-ASN : angle 4.44423 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6185.21 seconds wall clock time: 106 minutes 2.52 seconds (6362.52 seconds total)