Starting phenix.real_space_refine on Wed Jul 30 21:20:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlh_36397/07_2025/8jlh_36397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlh_36397/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlh_36397/07_2025/8jlh_36397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlh_36397/07_2025/8jlh_36397.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlh_36397/07_2025/8jlh_36397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlh_36397/07_2025/8jlh_36397.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.00, per 1000 atoms: 0.63 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.91 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: 5.30 Time building geometry restraints manager: 3.97 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: 2.820 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP A 333 HIS 0.003 0.001 HIS A 367 PHE 0.012 0.001 PHE A 497 TYR 0.025 0.001 TYR A 169 ARG 0.007 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 6) link_NAG-ASN : angle 5.68294 ( 18) link_BETA1-4 : bond 0.00889 ( 2) link_BETA1-4 : angle 1.01471 ( 6) hydrogen bonds : bond 0.12915 ( 587) hydrogen bonds : angle 6.13264 ( 1689) link_BETA1-6 : bond 0.00496 ( 2) link_BETA1-6 : angle 1.36029 ( 6) covalent geometry : bond 0.00363 (12897) covalent geometry : angle 0.63491 (17434) *********************** 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 : 1.351 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: 1.3969 time to fit residues: 272.2582 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 : 1.452 ------------------------------------------------------------------------------- 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 130 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 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 C 568 ASN D 913 GLN D 960 ASN D1003 GLN D1021 ASN D1106 GLN D1177 ASN D1199 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.226806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163196 restraints weight = 12858.961| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.52 r_work: 0.3300 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12907 Z= 0.137 Angle : 0.570 11.234 17464 Z= 0.300 Chirality : 0.045 0.320 1916 Planarity : 0.003 0.059 2203 Dihedral : 6.063 73.059 1931 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.73 % Allowed : 16.18 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1532 helix: 2.00 (0.24), residues: 438 sheet: 0.30 (0.28), residues: 336 loop : -1.07 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS A 378 PHE 0.014 0.001 PHE D1072 TYR 0.019 0.001 TYR A 169 ARG 0.006 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 6) link_NAG-ASN : angle 5.30299 ( 18) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 0.70993 ( 6) hydrogen bonds : bond 0.04196 ( 587) hydrogen bonds : angle 4.99108 ( 1689) link_BETA1-6 : bond 0.00535 ( 2) link_BETA1-6 : angle 1.40797 ( 6) covalent geometry : bond 0.00311 (12897) covalent geometry : angle 0.54364 (17434) *********************** 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 215 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.5169 (tpp) cc_final: 0.4692 (tpt) REVERT: A 366 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7081 (ttmt) REVERT: A 444 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5296 (ttt180) REVERT: A 515 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: A 568 ASN cc_start: 0.8048 (t0) cc_final: 0.7731 (t0) REVERT: A 712 LYS cc_start: 0.7587 (mtpm) cc_final: 0.7052 (ttpp) REVERT: B 1086 ASP cc_start: 0.8020 (t70) cc_final: 0.7314 (t0) REVERT: D 906 TYR cc_start: 0.6259 (m-80) cc_final: 0.5543 (m-10) REVERT: D 961 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: D 1054 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5248 (tmm) REVERT: D 1055 PHE cc_start: 0.8004 (m-10) cc_final: 0.7716 (m-10) REVERT: D 1237 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6234 (mtm) outliers start: 51 outliers final: 19 residues processed: 196 average time/residue: 1.6037 time to fit residues: 347.7841 Evaluate side-chains 172 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 608 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 741 LEU 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 1073 ASN 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 C residue 542 SER 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 1237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 144 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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 B1115 ASN B1268 ASN C 568 ASN D 912 ASN D 960 ASN D1003 GLN D1106 GLN D1177 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.223546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157707 restraints weight = 13064.112| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.22 r_work: 0.3296 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12907 Z= 0.187 Angle : 0.600 11.706 17464 Z= 0.312 Chirality : 0.046 0.345 1916 Planarity : 0.003 0.052 2203 Dihedral : 5.568 48.156 1914 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.54 % Allowed : 16.11 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1532 helix: 1.93 (0.24), residues: 440 sheet: 0.20 (0.29), residues: 336 loop : -1.25 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.003 0.001 HIS A 494 PHE 0.018 0.002 PHE B1100 TYR 0.016 0.002 TYR A 306 ARG 0.006 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 6) link_NAG-ASN : angle 5.55189 ( 18) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 0.92924 ( 6) hydrogen bonds : bond 0.04446 ( 587) hydrogen bonds : angle 4.94135 ( 1689) link_BETA1-6 : bond 0.00550 ( 2) link_BETA1-6 : angle 1.45083 ( 6) covalent geometry : bond 0.00446 (12897) covalent geometry : angle 0.57239 (17434) *********************** 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 217 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.5415 (tpp) cc_final: 0.4895 (tpt) REVERT: A 366 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6914 (ttmt) REVERT: A 444 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5391 (ttt-90) REVERT: A 515 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8608 (mttm) REVERT: A 568 ASN cc_start: 0.8331 (t0) cc_final: 0.8028 (t0) REVERT: A 712 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6969 (ttpp) REVERT: B 1086 ASP cc_start: 0.8039 (t70) cc_final: 0.7294 (t70) REVERT: B 1121 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8509 (mtmm) REVERT: B 1187 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8263 (mppt) REVERT: B 1219 GLN cc_start: 0.7927 (pt0) cc_final: 0.7487 (pt0) REVERT: D 906 TYR cc_start: 0.6367 (m-80) cc_final: 0.5461 (m-10) REVERT: D 961 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: D 1054 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5666 (tmm) REVERT: D 1058 ASP cc_start: 0.7421 (t70) cc_final: 0.7078 (p0) REVERT: D 1203 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5261 (mm-30) outliers start: 62 outliers final: 31 residues processed: 196 average time/residue: 1.3693 time to fit residues: 292.7429 Evaluate side-chains 181 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 586 ASP 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 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 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 B residue 1254 LEU Chi-restraints excluded: chain B residue 1280 CYS 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 1037 ASP 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 1294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B1091 GLN B1199 GLN C 568 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D1177 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.226731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159722 restraints weight = 12862.165| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.05 r_work: 0.3355 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12907 Z= 0.124 Angle : 0.551 10.449 17464 Z= 0.288 Chirality : 0.044 0.300 1916 Planarity : 0.003 0.052 2203 Dihedral : 5.235 46.729 1914 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.73 % Allowed : 16.84 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1532 helix: 2.12 (0.24), residues: 440 sheet: 0.24 (0.29), residues: 329 loop : -1.09 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 161 PHE 0.010 0.001 PHE A 497 TYR 0.014 0.001 TYR A 169 ARG 0.008 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 6) link_NAG-ASN : angle 5.05797 ( 18) link_BETA1-4 : bond 0.00503 ( 2) link_BETA1-4 : angle 0.85697 ( 6) hydrogen bonds : bond 0.03845 ( 587) hydrogen bonds : angle 4.77109 ( 1689) link_BETA1-6 : bond 0.00458 ( 2) link_BETA1-6 : angle 1.37500 ( 6) covalent geometry : bond 0.00278 (12897) covalent geometry : angle 0.52613 (17434) *********************** 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 208 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.7185 (mmt) cc_final: 0.6880 (mmt) REVERT: A 324 MET cc_start: 0.5379 (tpp) cc_final: 0.4864 (tpt) REVERT: A 345 VAL cc_start: 0.8169 (t) cc_final: 0.7952 (p) REVERT: A 444 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.5250 (ttt-90) REVERT: A 515 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8538 (mttm) REVERT: A 583 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6927 (m) REVERT: A 712 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7040 (ttpp) REVERT: B 1086 ASP cc_start: 0.8015 (t70) cc_final: 0.7380 (t70) REVERT: B 1187 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8208 (mppt) REVERT: C 560 ASP cc_start: 0.8697 (p0) cc_final: 0.8466 (p0) REVERT: D 911 LYS cc_start: 0.7643 (mttp) cc_final: 0.7279 (mptp) REVERT: D 961 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: D 1054 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5677 (tpt) REVERT: D 1058 ASP cc_start: 0.7386 (t70) cc_final: 0.7014 (p0) REVERT: D 1081 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6728 (tm-30) REVERT: D 1085 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7708 (mtpm) REVERT: D 1192 ARG cc_start: 0.6862 (mmm160) cc_final: 0.6242 (mmm160) REVERT: D 1237 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.6150 (mtm) outliers start: 51 outliers final: 25 residues processed: 190 average time/residue: 1.2505 time to fit residues: 259.3734 Evaluate side-chains 183 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1073 ASN 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 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 1037 ASP Chi-restraints excluded: chain D residue 1054 MET Chi-restraints excluded: chain D residue 1085 LYS Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1237 MET Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS A 568 ASN B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN C 568 ASN D1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.223360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152645 restraints weight = 12973.376| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.23 r_work: 0.3488 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12907 Z= 0.165 Angle : 0.573 10.168 17464 Z= 0.298 Chirality : 0.045 0.298 1916 Planarity : 0.003 0.049 2203 Dihedral : 5.216 47.061 1914 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.76 % Allowed : 16.69 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1532 helix: 2.07 (0.24), residues: 440 sheet: 0.23 (0.30), residues: 306 loop : -1.08 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1266 HIS 0.009 0.001 HIS A 367 PHE 0.014 0.001 PHE B1100 TYR 0.015 0.001 TYR B1149 ARG 0.008 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 6) link_NAG-ASN : angle 5.11964 ( 18) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 0.89707 ( 6) hydrogen bonds : bond 0.04139 ( 587) hydrogen bonds : angle 4.80076 ( 1689) link_BETA1-6 : bond 0.00531 ( 2) link_BETA1-6 : angle 1.48065 ( 6) covalent geometry : bond 0.00390 (12897) covalent geometry : angle 0.54851 (17434) *********************** 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 218 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 345 VAL cc_start: 0.8248 (t) cc_final: 0.8028 (p) REVERT: A 444 ARG cc_start: 0.5677 (OUTLIER) cc_final: 0.5384 (ttt-90) REVERT: A 515 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8589 (mttm) REVERT: A 519 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8850 (pp) REVERT: A 568 ASN cc_start: 0.8131 (t0) cc_final: 0.7788 (t0) REVERT: A 583 CYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7028 (m) REVERT: A 634 MET cc_start: 0.6489 (mtt) cc_final: 0.6077 (mtp) REVERT: A 695 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 712 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7131 (ttpp) REVERT: B 1064 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6529 (mtp85) REVERT: B 1086 ASP cc_start: 0.8037 (t70) cc_final: 0.7335 (t70) REVERT: B 1187 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8243 (mppt) REVERT: B 1219 GLN cc_start: 0.7956 (pt0) cc_final: 0.7510 (pt0) REVERT: C 560 ASP cc_start: 0.8666 (p0) cc_final: 0.8430 (p0) REVERT: D 911 LYS cc_start: 0.7539 (mttp) cc_final: 0.7186 (mptp) REVERT: D 961 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: D 1054 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5766 (tpt) REVERT: D 1058 ASP cc_start: 0.7310 (t70) cc_final: 0.7049 (p0) REVERT: D 1081 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6679 (tm-30) REVERT: D 1085 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7677 (mtpm) REVERT: D 1143 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8333 (p) REVERT: D 1236 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.6075 (ptpp) REVERT: D 1237 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6318 (mtm) outliers start: 65 outliers final: 32 residues processed: 200 average time/residue: 1.2213 time to fit residues: 266.8964 Evaluate side-chains 195 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 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 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 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 923 THR 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 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1193 LEU 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 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 1037 ASP Chi-restraints excluded: chain D residue 1054 MET 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 1236 LYS Chi-restraints excluded: chain D residue 1237 MET Chi-restraints excluded: chain D residue 1270 GLN Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 B1091 GLN C 568 ASN D1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.222833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152612 restraints weight = 13084.411| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.24 r_work: 0.3296 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12907 Z= 0.170 Angle : 0.584 11.321 17464 Z= 0.303 Chirality : 0.045 0.293 1916 Planarity : 0.003 0.049 2203 Dihedral : 5.225 49.244 1912 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.42 % Allowed : 16.76 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1532 helix: 2.03 (0.24), residues: 440 sheet: 0.19 (0.30), residues: 306 loop : -1.05 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1266 HIS 0.009 0.001 HIS A 367 PHE 0.014 0.001 PHE B1100 TYR 0.015 0.001 TYR B1149 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 6) link_NAG-ASN : angle 5.11544 ( 18) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 0.91156 ( 6) hydrogen bonds : bond 0.04197 ( 587) hydrogen bonds : angle 4.82374 ( 1689) link_BETA1-6 : bond 0.00504 ( 2) link_BETA1-6 : angle 1.50916 ( 6) covalent geometry : bond 0.00406 (12897) covalent geometry : angle 0.56043 (17434) *********************** 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 224 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 345 VAL cc_start: 0.8152 (t) cc_final: 0.7923 (p) REVERT: A 444 ARG cc_start: 0.5622 (OUTLIER) cc_final: 0.5294 (ttt-90) REVERT: A 515 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8569 (mttm) REVERT: A 519 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 568 ASN cc_start: 0.8276 (t0) cc_final: 0.7935 (t0) REVERT: A 583 CYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6974 (m) REVERT: A 695 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 712 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7019 (ttpp) REVERT: B 1064 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6527 (mtp85) REVERT: B 1085 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6913 (mptt) REVERT: B 1086 ASP cc_start: 0.8060 (t70) cc_final: 0.7376 (t0) REVERT: B 1187 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8202 (mppt) REVERT: B 1219 GLN cc_start: 0.7964 (pt0) cc_final: 0.7447 (pt0) REVERT: C 513 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8905 (m-40) REVERT: C 560 ASP cc_start: 0.8704 (p0) cc_final: 0.8446 (p0) REVERT: D 911 LYS cc_start: 0.7645 (mttp) cc_final: 0.7297 (mptp) REVERT: D 961 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: D 1054 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5804 (tpt) REVERT: D 1064 ARG cc_start: 0.6863 (mtm180) cc_final: 0.6586 (mpp80) REVERT: D 1081 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6757 (tm-30) REVERT: D 1085 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7660 (mtpm) REVERT: D 1143 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8305 (p) REVERT: D 1236 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5925 (ptpp) outliers start: 74 outliers final: 34 residues processed: 206 average time/residue: 1.2748 time to fit residues: 287.3669 Evaluate side-chains 198 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 923 THR 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 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 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 513 ASN 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 1037 ASP Chi-restraints excluded: chain D residue 1054 MET 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 1236 LYS Chi-restraints excluded: chain D residue 1270 GLN Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN B 960 ASN B1003 GLN B1046 ASN B1091 GLN C 568 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.223538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163304 restraints weight = 12938.637| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.67 r_work: 0.3259 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1550 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= 0.132 Angle : 0.561 11.831 17464 Z= 0.290 Chirality : 0.044 0.313 1916 Planarity : 0.003 0.048 2203 Dihedral : 5.088 48.985 1912 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.47 % Allowed : 17.72 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1532 helix: 2.07 (0.24), residues: 441 sheet: 0.21 (0.30), residues: 313 loop : -0.96 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1266 HIS 0.008 0.001 HIS A 367 PHE 0.010 0.001 PHE A 497 TYR 0.013 0.001 TYR B 962 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 6) link_NAG-ASN : angle 4.88816 ( 18) link_BETA1-4 : bond 0.00509 ( 2) link_BETA1-4 : angle 0.86690 ( 6) hydrogen bonds : bond 0.03888 ( 587) hydrogen bonds : angle 4.76352 ( 1689) link_BETA1-6 : bond 0.00493 ( 2) link_BETA1-6 : angle 1.47007 ( 6) covalent geometry : bond 0.00304 (12897) covalent geometry : angle 0.53785 (17434) *********************** 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 213 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: A 345 VAL cc_start: 0.8184 (t) cc_final: 0.7956 (p) REVERT: A 444 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.4976 (ttt-90) REVERT: A 515 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8522 (mttm) REVERT: A 519 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 568 ASN cc_start: 0.8184 (t0) cc_final: 0.7829 (t0) REVERT: A 583 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6980 (m) REVERT: A 675 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7015 (pt0) REVERT: A 695 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7661 (tp) REVERT: A 712 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7095 (ttpp) REVERT: B 1046 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6904 (t0) REVERT: B 1064 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6503 (mtp85) REVERT: B 1085 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7064 (mptt) REVERT: B 1086 ASP cc_start: 0.7966 (t70) cc_final: 0.7312 (t0) REVERT: B 1187 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8225 (mppt) REVERT: B 1219 GLN cc_start: 0.7916 (pt0) cc_final: 0.7418 (pt0) REVERT: C 483 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7721 (mtm-85) REVERT: D 961 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: D 1054 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5945 (tpt) REVERT: D 1058 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 1064 ARG cc_start: 0.6775 (mtm180) cc_final: 0.6551 (mpp80) REVERT: D 1081 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6727 (tm-30) REVERT: D 1085 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7647 (mtpm) REVERT: D 1143 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8653 (t) outliers start: 61 outliers final: 30 residues processed: 195 average time/residue: 1.2020 time to fit residues: 256.6891 Evaluate side-chains 196 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 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 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 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 1037 ASP 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 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 1270 GLN Chi-restraints excluded: chain D residue 1294 SER 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 17 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.222591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157308 restraints weight = 13027.701| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.34 r_work: 0.3291 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1590 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= 0.146 Angle : 0.582 12.188 17464 Z= 0.299 Chirality : 0.045 0.327 1916 Planarity : 0.003 0.047 2203 Dihedral : 5.063 49.397 1911 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.54 % Allowed : 17.79 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1532 helix: 2.05 (0.24), residues: 441 sheet: 0.09 (0.30), residues: 304 loop : -0.89 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1266 HIS 0.010 0.001 HIS B1048 PHE 0.011 0.001 PHE A 497 TYR 0.014 0.001 TYR B1149 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 6) link_NAG-ASN : angle 4.80424 ( 18) link_BETA1-4 : bond 0.00394 ( 2) link_BETA1-4 : angle 0.93618 ( 6) hydrogen bonds : bond 0.03949 ( 587) hydrogen bonds : angle 4.76693 ( 1689) link_BETA1-6 : bond 0.00493 ( 2) link_BETA1-6 : angle 1.50017 ( 6) covalent geometry : bond 0.00342 (12897) covalent geometry : angle 0.56121 (17434) *********************** 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 213 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: A 310 MET cc_start: 0.7275 (mmt) cc_final: 0.6978 (mtt) REVERT: A 345 VAL cc_start: 0.8210 (t) cc_final: 0.7968 (p) REVERT: A 444 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5155 (ttt-90) REVERT: A 515 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: A 519 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 568 ASN cc_start: 0.8376 (t0) cc_final: 0.8034 (t0) REVERT: A 583 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7023 (m) REVERT: A 634 MET cc_start: 0.6545 (mtt) cc_final: 0.6120 (mtp) REVERT: A 675 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7249 (pt0) REVERT: A 695 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (tp) REVERT: A 712 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7188 (ttpp) REVERT: B 1064 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6516 (mtp85) REVERT: B 1085 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7077 (mptt) REVERT: B 1086 ASP cc_start: 0.7986 (t70) cc_final: 0.7311 (t0) REVERT: B 1187 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8234 (mppt) REVERT: B 1219 GLN cc_start: 0.7889 (pt0) cc_final: 0.7373 (pt0) REVERT: C 483 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7700 (mtm-85) REVERT: C 513 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8935 (m-40) REVERT: C 560 ASP cc_start: 0.8703 (p0) cc_final: 0.8501 (p0) REVERT: D 911 LYS cc_start: 0.7672 (mttp) cc_final: 0.7307 (mptp) REVERT: D 961 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: D 1054 MET cc_start: 0.6144 (mmt) cc_final: 0.5896 (tpt) REVERT: D 1058 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6850 (p0) REVERT: D 1064 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6668 (mpp80) REVERT: D 1081 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6780 (tm-30) REVERT: D 1085 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7671 (mtpm) REVERT: D 1143 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8674 (t) outliers start: 62 outliers final: 33 residues processed: 198 average time/residue: 1.2266 time to fit residues: 265.3249 Evaluate side-chains 197 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 369 GLU 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 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 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 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 1064 ARG Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1209 LEU 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 513 ASN 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 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 1270 GLN Chi-restraints excluded: chain D residue 1294 SER 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 132 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 135 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 ASN B1003 GLN B1091 GLN D 912 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.225376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156974 restraints weight = 12999.569| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.06 r_work: 0.3542 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1686 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= 0.119 Angle : 0.573 13.566 17464 Z= 0.292 Chirality : 0.045 0.355 1916 Planarity : 0.003 0.047 2203 Dihedral : 4.942 48.309 1911 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 19.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1532 helix: 2.13 (0.24), residues: 441 sheet: 0.13 (0.28), residues: 341 loop : -0.94 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1266 HIS 0.002 0.000 HIS A 161 PHE 0.012 0.001 PHE D1117 TYR 0.014 0.001 TYR B 962 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 6) link_NAG-ASN : angle 4.56253 ( 18) link_BETA1-4 : bond 0.00556 ( 2) link_BETA1-4 : angle 0.86904 ( 6) hydrogen bonds : bond 0.03692 ( 587) hydrogen bonds : angle 4.70746 ( 1689) link_BETA1-6 : bond 0.00521 ( 2) link_BETA1-6 : angle 1.44600 ( 6) covalent geometry : bond 0.00269 (12897) covalent geometry : angle 0.55380 (17434) *********************** 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 197 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 VAL cc_start: 0.8218 (t) cc_final: 0.7979 (p) REVERT: A 366 LYS cc_start: 0.7186 (ttmt) cc_final: 0.6948 (ttpt) REVERT: A 444 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.5118 (ttt-90) REVERT: A 515 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8533 (mttm) REVERT: A 519 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8702 (pp) REVERT: A 583 CYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7028 (m) REVERT: A 675 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7066 (pt0) REVERT: A 712 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7228 (ttpp) REVERT: B 1003 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: B 1064 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6339 (mtp85) REVERT: B 1085 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7070 (mptt) REVERT: B 1086 ASP cc_start: 0.7949 (t70) cc_final: 0.7308 (t0) REVERT: B 1187 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8226 (mppt) REVERT: B 1219 GLN cc_start: 0.7811 (pt0) cc_final: 0.7309 (pt0) REVERT: D 911 LYS cc_start: 0.7491 (mttp) cc_final: 0.7231 (mptp) REVERT: D 961 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: D 1055 PHE cc_start: 0.7731 (m-10) cc_final: 0.7467 (m-10) REVERT: D 1058 ASP cc_start: 0.7109 (t70) cc_final: 0.6842 (p0) REVERT: D 1081 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6761 (tm-30) REVERT: D 1085 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7666 (mtpm) REVERT: D 1143 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8650 (t) outliers start: 48 outliers final: 26 residues processed: 184 average time/residue: 1.3362 time to fit residues: 267.6812 Evaluate side-chains 181 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 369 GLU 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 519 LEU 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 1209 LEU 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 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 1270 GLN Chi-restraints excluded: chain D residue 1294 SER 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 126 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 899 ASN B1003 GLN B1022 ASN B1046 ASN D 912 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D1091 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.222800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151463 restraints weight = 13002.977| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.18 r_work: 0.3310 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12907 Z= 0.184 Angle : 0.629 14.269 17464 Z= 0.321 Chirality : 0.046 0.338 1916 Planarity : 0.003 0.046 2203 Dihedral : 5.146 49.670 1910 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.51 % Allowed : 19.40 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1532 helix: 1.99 (0.24), residues: 441 sheet: 0.10 (0.29), residues: 325 loop : -0.96 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1266 HIS 0.003 0.001 HIS C 494 PHE 0.015 0.002 PHE B1100 TYR 0.017 0.002 TYR B1149 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 6) link_NAG-ASN : angle 4.96346 ( 18) link_BETA1-4 : bond 0.00465 ( 2) link_BETA1-4 : angle 0.91714 ( 6) hydrogen bonds : bond 0.04225 ( 587) hydrogen bonds : angle 4.84303 ( 1689) link_BETA1-6 : bond 0.00417 ( 2) link_BETA1-6 : angle 1.58926 ( 6) covalent geometry : bond 0.00443 (12897) covalent geometry : angle 0.60826 (17434) ********************** 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 192 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 VAL cc_start: 0.8133 (t) cc_final: 0.7889 (p) REVERT: A 366 LYS cc_start: 0.6959 (ttmt) cc_final: 0.6726 (ttpt) REVERT: A 444 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.5082 (ttt-90) REVERT: A 515 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8573 (mttm) REVERT: A 519 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8751 (pp) REVERT: A 568 ASN cc_start: 0.8092 (t0) cc_final: 0.7801 (t0) REVERT: A 583 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6967 (m) REVERT: A 634 MET cc_start: 0.6502 (mtt) cc_final: 0.6065 (mtp) REVERT: A 675 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7178 (pt0) REVERT: A 712 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7093 (ttpp) REVERT: B 1003 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: B 1064 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6471 (mtp85) REVERT: B 1085 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6958 (mptt) REVERT: B 1187 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8172 (mppt) REVERT: B 1219 GLN cc_start: 0.7849 (pt0) cc_final: 0.7291 (pt0) REVERT: C 483 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7685 (mtm-85) REVERT: D 961 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: D 1081 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6838 (tm-30) REVERT: D 1085 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7661 (mtpm) REVERT: D 1143 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8688 (t) outliers start: 48 outliers final: 29 residues processed: 181 average time/residue: 1.3149 time to fit residues: 260.5779 Evaluate side-chains 185 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 369 GLU 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 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 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 712 LYS Chi-restraints excluded: chain B residue 956 ILE 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 1085 LYS Chi-restraints excluded: chain B residue 1209 LEU 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 1156 GLU Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1270 GLN Chi-restraints excluded: chain D residue 1294 SER 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 116 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.223032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153257 restraints weight = 13008.897| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.27 r_work: 0.3301 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12907 Z= 0.169 Angle : 0.624 14.335 17464 Z= 0.319 Chirality : 0.046 0.313 1916 Planarity : 0.003 0.047 2203 Dihedral : 5.174 49.532 1910 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.51 % Allowed : 19.47 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1532 helix: 1.99 (0.24), residues: 441 sheet: 0.08 (0.28), residues: 355 loop : -1.06 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1266 HIS 0.008 0.001 HIS A 367 PHE 0.014 0.001 PHE D1117 TYR 0.015 0.001 TYR A 306 ARG 0.009 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 6) link_NAG-ASN : angle 4.86758 ( 18) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 0.87386 ( 6) hydrogen bonds : bond 0.04136 ( 587) hydrogen bonds : angle 4.84447 ( 1689) link_BETA1-6 : bond 0.00482 ( 2) link_BETA1-6 : angle 1.59898 ( 6) covalent geometry : bond 0.00403 (12897) covalent geometry : angle 0.60394 (17434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12600.97 seconds wall clock time: 222 minutes 49.44 seconds (13369.44 seconds total)