Starting phenix.real_space_refine on Fri Sep 11 19:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a90_6995/09_2026/6a90_6995.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 Na 1 4.78 5 C 7319 2.51 5 N 1780 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10537 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1275} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} 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 chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' NA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.71, per 1000 atoms: 0.24 Number of scatterers: 11085 At special positions: 0 Unit cell: (133.102, 134.193, 122.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 Na 1 11.00 O 1911 8.00 N 1780 7.00 C 7319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.02 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.05 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.04 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 711.8 milliseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 69.0% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.861A pdb=" N ARG A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.751A pdb=" N THR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.552A pdb=" N ALA A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.939A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.905A pdb=" N TYR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.701A pdb=" N ARG A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.838A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.544A pdb=" N ALA A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.543A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.392A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 removed outlier: 3.866A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N THR A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.689A pdb=" N ASN A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.921A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.884A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 435 removed outlier: 3.712A pdb=" N ILE A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.575A pdb=" N LYS A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 538 Processing helix chain 'A' and resid 545 through 571 removed outlier: 3.609A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.263A pdb=" N PHE A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.622A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.645A pdb=" N PHE A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 615 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.443A pdb=" N PHE A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.592A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.562A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 674 Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.729A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.765A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.635A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 736 through 744 removed outlier: 3.672A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.832A pdb=" N ARG A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 removed outlier: 3.746A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.864A pdb=" N GLU A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 883 through 918 removed outlier: 3.669A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 914 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.571A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.583A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 947 through 952' Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.562A pdb=" N ARG A 957 " --> pdb=" O ARG A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.505A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 removed outlier: 4.279A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.648A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.830A pdb=" N GLU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.693A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 3.728A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.790A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 removed outlier: 4.170A pdb=" N VAL A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1123 " --> pdb=" O ARG A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.619A pdb=" N ARG A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1166 Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 4.049A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1190 removed outlier: 3.616A pdb=" N ASP A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1187 through 1190' Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 3.665A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 removed outlier: 3.536A pdb=" N LYS A1230 " --> pdb=" O HIS A1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1227 through 1230' Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.623A pdb=" N ILE A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1270 removed outlier: 3.679A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.767A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1322 removed outlier: 3.780A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1308 " --> pdb=" O PHE A1304 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1319 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A1322 " --> pdb=" O MET A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1349 removed outlier: 3.569A pdb=" N LEU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.765A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1399 removed outlier: 4.253A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1423 removed outlier: 3.966A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1423 " --> pdb=" O GLU A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.809A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1433 " --> pdb=" O ASP A1429 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1434 " --> pdb=" O TYR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1460 removed outlier: 4.358A pdb=" N SER A1454 " --> pdb=" O TYR A1450 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A1455 " --> pdb=" O ASP A1451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1478 removed outlier: 3.656A pdb=" N SER A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1505 removed outlier: 3.888A pdb=" N ASP A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1520 removed outlier: 3.607A pdb=" N ASP A1512 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 Processing sheet with id=AA3, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.999A pdb=" N LYS B 28 " --> pdb=" O GLU B 8 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2694 1.33 - 1.45: 2905 1.45 - 1.58: 5656 1.58 - 1.70: 0 1.70 - 1.83: 119 Bond restraints: 11374 Sorted by residual: bond pdb=" C1 NAG A1605 " pdb=" O5 NAG A1605 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C1 NAG A1606 " pdb=" O5 NAG A1606 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C PHE A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.87e+00 bond pdb=" CB VAL A1057 " pdb=" CG2 VAL A1057 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.17e+00 bond pdb=" CB PRO A 980 " pdb=" CG PRO A 980 " ideal model delta sigma weight residual 1.492 1.379 0.113 5.00e-02 4.00e+02 5.10e+00 ... (remaining 11369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14640 2.53 - 5.06: 690 5.06 - 7.59: 104 7.59 - 10.12: 26 10.12 - 12.65: 2 Bond angle restraints: 15462 Sorted by residual: angle pdb=" C PRO A 881 " pdb=" N GLN A 882 " pdb=" CA GLN A 882 " ideal model delta sigma weight residual 121.54 134.19 -12.65 1.91e+00 2.74e-01 4.38e+01 angle pdb=" C MET A1477 " pdb=" N ASN A1478 " pdb=" CA ASN A1478 " ideal model delta sigma weight residual 121.54 133.81 -12.27 1.91e+00 2.74e-01 4.12e+01 angle pdb=" N GLY A 335 " pdb=" CA GLY A 335 " pdb=" C GLY A 335 " ideal model delta sigma weight residual 113.24 120.76 -7.52 1.31e+00 5.83e-01 3.30e+01 angle pdb=" C LYS A1256 " pdb=" N TYR A1257 " pdb=" CA TYR A1257 " ideal model delta sigma weight residual 122.74 130.18 -7.44 1.44e+00 4.82e-01 2.67e+01 angle pdb=" N THR A1132 " pdb=" CA THR A1132 " pdb=" C THR A1132 " ideal model delta sigma weight residual 113.43 107.17 6.26 1.26e+00 6.30e-01 2.47e+01 ... (remaining 15457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 6100 16.06 - 32.13: 373 32.13 - 48.19: 70 48.19 - 64.25: 13 64.25 - 80.31: 8 Dihedral angle restraints: 6564 sinusoidal: 2506 harmonic: 4058 Sorted by residual: dihedral pdb=" CB CYS B 25 " pdb=" SG CYS B 25 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual 93.00 169.68 -76.68 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 343 " pdb=" CB CYS A 343 " ideal model delta sinusoidal sigma weight residual -86.00 -154.30 68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA ASP A 295 " pdb=" C ASP A 295 " pdb=" N GLY A 296 " pdb=" CA GLY A 296 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 6561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1656 0.119 - 0.239: 103 0.239 - 0.358: 11 0.358 - 0.478: 3 0.478 - 0.597: 2 Chirality restraints: 1775 Sorted by residual: chirality pdb=" CG LEU A1054 " pdb=" CB LEU A1054 " pdb=" CD1 LEU A1054 " pdb=" CD2 LEU A1054 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C1 NAG A1607 " pdb=" ND2 ASN A 308 " pdb=" C2 NAG A1607 " pdb=" O5 NAG A1607 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.80e+00 ... (remaining 1772 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 933 " 0.026 2.00e-02 2.50e+03 2.62e-02 1.37e+01 pdb=" CG TYR A 933 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 933 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 933 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 933 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 933 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 933 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 933 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1313 " 0.018 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR A1313 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A1313 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A1313 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A1313 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1313 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A1313 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 624 " -0.030 2.00e-02 2.50e+03 1.93e-02 9.29e+00 pdb=" CG TRP A 624 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 624 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 624 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 624 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 624 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 624 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 624 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 624 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 624 " -0.002 2.00e-02 2.50e+03 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3456 2.82 - 3.34: 9812 3.34 - 3.86: 17322 3.86 - 4.38: 20755 4.38 - 4.90: 34959 Nonbonded interactions: 86304 Sorted by model distance: nonbonded pdb=" O LEU A1346 " pdb=" OH TYR A1394 " model vdw 2.302 3.040 nonbonded pdb=" O ALA A1146 " pdb=" OH TYR A1489 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASP A 686 " pdb=" ND1 HIS A 689 " model vdw 2.359 3.120 nonbonded pdb=" O LYS A1171 " pdb=" OG1 THR A1175 " model vdw 2.373 3.040 nonbonded pdb=" OG SER B 1 " pdb=" N ALA B 2 " model vdw 2.379 3.120 ... (remaining 86299 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 'C' selection = chain 'D' } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.011 0.113 11389 Z= 0.465 Angle : 1.256 15.905 15499 Z= 0.658 Chirality : 0.072 0.597 1775 Planarity : 0.007 0.065 1908 Dihedral : 11.484 80.311 3922 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.58 % Favored : 92.13 % Rotamer: Outliers : 1.75 % Allowed : 5.15 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.15), residues: 1372 helix: -4.25 (0.08), residues: 855 sheet: -4.54 (0.70), residues: 22 loop : -2.68 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1271 TYR 0.062 0.005 TYR A 933 PHE 0.041 0.005 PHE A 410 TRP 0.050 0.004 TRP A 624 HIS 0.017 0.004 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01106 / 0.46 (11374) covalent geometry : angle 1.23106 / 0.65 (15462) SS BOND : bond 0.00775 / 0.42 ( 8) SS BOND : angle 2.11792 / 1.37 ( 16) hydrogen bonds : bond 0.31430 / 22.75 ( 557) hydrogen bonds : angle 9.89457 / 6.98 ( 1605) link_BETA1-4 : bond 0.01473 / 0.70 ( 2) link_BETA1-4 : angle 6.63520 / 3.70 ( 6) link_NAG-ASN : bond 0.01228 / 0.63 ( 5) link_NAG-ASN : angle 6.73593 / 4.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6162 (mmm-85) REVERT: A 249 ASP cc_start: 0.8253 (m-30) cc_final: 0.8053 (m-30) REVERT: A 631 MET cc_start: 0.7881 (mmt) cc_final: 0.7674 (mtp) REVERT: A 636 LYS cc_start: 0.7814 (tmmt) cc_final: 0.7405 (ttmt) REVERT: A 886 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 915 LYS cc_start: 0.7914 (tmtp) cc_final: 0.7454 (mttp) REVERT: A 922 TRP cc_start: 0.8269 (m100) cc_final: 0.7906 (m100) REVERT: A 1042 MET cc_start: 0.9099 (mmp) cc_final: 0.8861 (tpt) REVERT: A 1102 PHE cc_start: 0.8562 (t80) cc_final: 0.8225 (t80) REVERT: A 1164 TYR cc_start: 0.8121 (t80) cc_final: 0.7692 (t80) REVERT: A 1174 TYR cc_start: 0.7259 (m-10) cc_final: 0.6921 (m-80) REVERT: A 1218 VAL cc_start: 0.8022 (p) cc_final: 0.7721 (t) REVERT: A 1230 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7094 (mmtt) REVERT: A 1300 PHE cc_start: 0.8135 (m-10) cc_final: 0.7110 (t80) REVERT: A 1422 LYS cc_start: 0.7668 (tttm) cc_final: 0.7431 (mttp) outliers start: 20 outliers final: 7 residues processed: 268 average time/residue: 0.5627 time to fit residues: 163.2655 Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 409 ASN A 421 HIS A1118 GLN A1486 HIS B 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114540 restraints weight = 13696.306| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.01 r_work: 0.3073 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11389 Z= 0.148 Angle : 0.729 12.413 15499 Z= 0.375 Chirality : 0.044 0.301 1775 Planarity : 0.005 0.065 1908 Dihedral : 6.500 73.854 1518 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.05 % Allowed : 11.52 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.19), residues: 1372 helix: -1.90 (0.14), residues: 875 sheet: -4.34 (0.72), residues: 22 loop : -2.27 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1137 TYR 0.028 0.002 TYR A1313 PHE 0.020 0.001 PHE A1488 TRP 0.030 0.002 TRP A 624 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (11374) covalent geometry : angle 0.70251 / 0.37 (15462) SS BOND : bond 0.00556 / 0.29 ( 8) SS BOND : angle 3.14694 / 2.17 ( 16) hydrogen bonds : bond 0.06241 / 4.53 ( 557) hydrogen bonds : angle 4.67943 / 3.24 ( 1605) link_BETA1-4 : bond 0.00472 / 0.23 ( 2) link_BETA1-4 : angle 3.92841 / 2.25 ( 6) link_NAG-ASN : bond 0.00923 / 0.51 ( 5) link_NAG-ASN : angle 4.94033 / 3.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6950 (mmm160) cc_final: 0.6259 (mmm-85) REVERT: A 236 ARG cc_start: 0.8592 (ptm160) cc_final: 0.8063 (ttt180) REVERT: A 419 TYR cc_start: 0.9181 (t80) cc_final: 0.8967 (t80) REVERT: A 597 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6133 (mt-10) REVERT: A 628 ASN cc_start: 0.8649 (t0) cc_final: 0.8400 (t0) REVERT: A 631 MET cc_start: 0.8345 (mmt) cc_final: 0.7979 (mtp) REVERT: A 636 LYS cc_start: 0.7749 (tmmt) cc_final: 0.7256 (tppp) REVERT: A 915 LYS cc_start: 0.7956 (tmtp) cc_final: 0.7472 (pmtt) REVERT: A 999 MET cc_start: 0.8938 (tpt) cc_final: 0.8521 (tpp) REVERT: A 1042 MET cc_start: 0.9235 (mmp) cc_final: 0.8945 (mmm) REVERT: A 1078 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8696 (mttt) REVERT: A 1102 PHE cc_start: 0.8805 (t80) cc_final: 0.8591 (t80) REVERT: A 1164 TYR cc_start: 0.8213 (t80) cc_final: 0.7719 (t80) REVERT: A 1174 TYR cc_start: 0.7530 (m-10) cc_final: 0.7223 (m-80) REVERT: A 1200 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6795 (pt0) REVERT: A 1218 VAL cc_start: 0.8278 (p) cc_final: 0.7972 (t) REVERT: A 1230 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7109 (mmtm) REVERT: A 1231 ASP cc_start: 0.8159 (t70) cc_final: 0.7877 (t0) REVERT: A 1283 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7160 (tpp-160) REVERT: A 1300 PHE cc_start: 0.8568 (m-10) cc_final: 0.7441 (t80) REVERT: A 1396 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8608 (mt) REVERT: A 1416 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: A 1422 LYS cc_start: 0.7976 (tttm) cc_final: 0.7495 (mtmp) REVERT: A 1450 TYR cc_start: 0.7288 (t80) cc_final: 0.7022 (t80) REVERT: A 1499 ASP cc_start: 0.7923 (t0) cc_final: 0.7288 (m-30) REVERT: A 1501 PHE cc_start: 0.8175 (m-10) cc_final: 0.7903 (m-80) REVERT: B 22 SER cc_start: 0.8002 (t) cc_final: 0.7649 (p) outliers start: 35 outliers final: 13 residues processed: 222 average time/residue: 0.4875 time to fit residues: 118.6210 Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 0.0770 chunk 118 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114523 restraints weight = 13786.246| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.18 r_work: 0.3004 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11389 Z= 0.123 Angle : 0.633 11.455 15499 Z= 0.322 Chirality : 0.043 0.364 1775 Planarity : 0.004 0.052 1908 Dihedral : 5.767 53.919 1514 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.88 % Allowed : 14.05 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1372 helix: -0.47 (0.17), residues: 877 sheet: -4.24 (0.73), residues: 22 loop : -2.00 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1137 TYR 0.022 0.001 TYR A1313 PHE 0.020 0.001 PHE A1279 TRP 0.025 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11374) covalent geometry : angle 0.61056 / 0.32 (15462) SS BOND : bond 0.00304 / 0.18 ( 8) SS BOND : angle 2.17573 / 1.41 ( 16) hydrogen bonds : bond 0.04988 / 3.64 ( 557) hydrogen bonds : angle 4.02235 / 2.77 ( 1605) link_BETA1-4 : bond 0.00545 / 0.26 ( 2) link_BETA1-4 : angle 3.92949 / 2.24 ( 6) link_NAG-ASN : bond 0.00607 / 0.35 ( 5) link_NAG-ASN : angle 4.26240 / 2.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7631 (mtt) cc_final: 0.7345 (mtp) REVERT: A 158 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7913 (mt) REVERT: A 198 ARG cc_start: 0.6878 (mmm160) cc_final: 0.6142 (mmm-85) REVERT: A 236 ARG cc_start: 0.8645 (ptm160) cc_final: 0.8162 (ttt180) REVERT: A 628 ASN cc_start: 0.8607 (t0) cc_final: 0.8332 (t0) REVERT: A 631 MET cc_start: 0.8433 (mmt) cc_final: 0.7893 (mtp) REVERT: A 636 LYS cc_start: 0.7757 (tmmt) cc_final: 0.6829 (mppt) REVERT: A 661 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8126 (mm-40) REVERT: A 708 ASP cc_start: 0.8595 (p0) cc_final: 0.8251 (m-30) REVERT: A 872 LEU cc_start: 0.8627 (mm) cc_final: 0.8341 (tm) REVERT: A 915 LYS cc_start: 0.8016 (tmtp) cc_final: 0.7425 (pmtt) REVERT: A 999 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8570 (tpp) REVERT: A 1042 MET cc_start: 0.9267 (mmp) cc_final: 0.8981 (mmm) REVERT: A 1078 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8710 (mttt) REVERT: A 1174 TYR cc_start: 0.7646 (m-10) cc_final: 0.7400 (m-80) REVERT: A 1200 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6747 (pt0) REVERT: A 1230 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7041 (mmtt) REVERT: A 1300 PHE cc_start: 0.8552 (m-10) cc_final: 0.7409 (t80) REVERT: A 1369 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7709 (mtp180) REVERT: A 1416 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: A 1422 LYS cc_start: 0.7918 (tttm) cc_final: 0.7396 (mtmp) REVERT: A 1450 TYR cc_start: 0.7261 (t80) cc_final: 0.6901 (t80) REVERT: A 1499 ASP cc_start: 0.7688 (t0) cc_final: 0.7222 (m-30) REVERT: A 1501 PHE cc_start: 0.7972 (m-10) cc_final: 0.7720 (m-10) outliers start: 33 outliers final: 11 residues processed: 201 average time/residue: 0.4953 time to fit residues: 109.0611 Evaluate side-chains 178 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 HIS A1465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110201 restraints weight = 13710.741| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.87 r_work: 0.2973 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11389 Z= 0.176 Angle : 0.681 11.583 15499 Z= 0.345 Chirality : 0.046 0.355 1775 Planarity : 0.004 0.047 1908 Dihedral : 5.559 57.721 1510 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.97 % Allowed : 14.05 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1372 helix: 0.08 (0.17), residues: 875 sheet: -4.14 (0.63), residues: 22 loop : -1.87 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1137 TYR 0.023 0.002 TYR A1313 PHE 0.025 0.002 PHE A1279 TRP 0.023 0.002 TRP A 624 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11374) covalent geometry : angle 0.66114 / 0.34 (15462) SS BOND : bond 0.00722 / 0.53 ( 8) SS BOND : angle 2.07438 / 1.28 ( 16) hydrogen bonds : bond 0.05343 / 3.88 ( 557) hydrogen bonds : angle 3.94936 / 2.73 ( 1605) link_BETA1-4 : bond 0.00635 / 0.30 ( 2) link_BETA1-4 : angle 3.81179 / 2.14 ( 6) link_NAG-ASN : bond 0.00583 / 0.31 ( 5) link_NAG-ASN : angle 4.32991 / 3.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7779 (mtt) cc_final: 0.7457 (mtp) REVERT: A 198 ARG cc_start: 0.6914 (mmm160) cc_final: 0.6190 (mmt90) REVERT: A 236 ARG cc_start: 0.8797 (ptm160) cc_final: 0.8336 (ttt180) REVERT: A 371 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8850 (tp) REVERT: A 374 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8708 (mp) REVERT: A 628 ASN cc_start: 0.8712 (t0) cc_final: 0.8404 (t0) REVERT: A 631 MET cc_start: 0.8533 (mmt) cc_final: 0.8120 (mtp) REVERT: A 636 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7047 (mppt) REVERT: A 665 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: A 708 ASP cc_start: 0.8689 (p0) cc_final: 0.8238 (m-30) REVERT: A 915 LYS cc_start: 0.8076 (tmtp) cc_final: 0.7475 (pmtt) REVERT: A 982 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 999 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8558 (tpp) REVERT: A 1033 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: A 1042 MET cc_start: 0.9315 (mmp) cc_final: 0.9006 (mmm) REVERT: A 1078 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8990 (mttm) REVERT: A 1083 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 1174 TYR cc_start: 0.7690 (m-10) cc_final: 0.7418 (m-80) REVERT: A 1200 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6862 (pt0) REVERT: A 1230 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7154 (mptp) REVERT: A 1277 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6359 (ptp90) REVERT: A 1300 PHE cc_start: 0.8627 (m-10) cc_final: 0.7592 (t80) REVERT: A 1369 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7709 (mtm110) REVERT: A 1416 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: A 1422 LYS cc_start: 0.7939 (tttm) cc_final: 0.7384 (mtmp) REVERT: A 1450 TYR cc_start: 0.7268 (t80) cc_final: 0.6923 (t80) REVERT: A 1471 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.6071 (tttm) REVERT: A 1499 ASP cc_start: 0.7672 (t0) cc_final: 0.7346 (m-30) REVERT: A 1501 PHE cc_start: 0.7936 (m-10) cc_final: 0.7641 (m-80) REVERT: A 1502 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6753 (m) outliers start: 57 outliers final: 24 residues processed: 204 average time/residue: 0.5247 time to fit residues: 116.5656 Evaluate side-chains 193 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 839 GLN A1467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112220 restraints weight = 13576.005| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.03 r_work: 0.2981 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11389 Z= 0.139 Angle : 0.630 11.361 15499 Z= 0.318 Chirality : 0.044 0.371 1775 Planarity : 0.003 0.041 1908 Dihedral : 5.382 59.179 1510 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.23 % Allowed : 16.67 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1372 helix: 0.44 (0.18), residues: 880 sheet: -4.08 (0.65), residues: 22 loop : -1.72 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1137 TYR 0.019 0.001 TYR A 381 PHE 0.017 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11374) covalent geometry : angle 0.60994 / 0.31 (15462) SS BOND : bond 0.00443 / 0.32 ( 8) SS BOND : angle 1.61224 / 1.02 ( 16) hydrogen bonds : bond 0.04786 / 3.49 ( 557) hydrogen bonds : angle 3.76666 / 2.60 ( 1605) link_BETA1-4 : bond 0.00519 / 0.25 ( 2) link_BETA1-4 : angle 3.79161 / 2.14 ( 6) link_NAG-ASN : bond 0.00578 / 0.31 ( 5) link_NAG-ASN : angle 4.31167 / 2.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7680 (mtt) cc_final: 0.7349 (mtp) REVERT: A 198 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6259 (mmm-85) REVERT: A 213 TYR cc_start: 0.8026 (m-80) cc_final: 0.7776 (m-80) REVERT: A 236 ARG cc_start: 0.8807 (ptm160) cc_final: 0.8381 (ttt180) REVERT: A 628 ASN cc_start: 0.8672 (t0) cc_final: 0.8362 (t0) REVERT: A 631 MET cc_start: 0.8521 (mmt) cc_final: 0.8112 (mtp) REVERT: A 636 LYS cc_start: 0.7861 (tmmt) cc_final: 0.6932 (mppt) REVERT: A 649 PHE cc_start: 0.8616 (m-80) cc_final: 0.8333 (m-80) REVERT: A 665 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8151 (mpp) REVERT: A 708 ASP cc_start: 0.8604 (p0) cc_final: 0.8241 (m-30) REVERT: A 915 LYS cc_start: 0.8043 (tmtp) cc_final: 0.7399 (pmtt) REVERT: A 999 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8633 (tpp) REVERT: A 1033 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: A 1042 MET cc_start: 0.9318 (mmp) cc_final: 0.9031 (mmm) REVERT: A 1078 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8747 (mttp) REVERT: A 1083 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: A 1174 TYR cc_start: 0.7681 (m-10) cc_final: 0.7433 (m-80) REVERT: A 1196 MET cc_start: 0.7220 (tpt) cc_final: 0.6946 (pmm) REVERT: A 1200 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6742 (pt0) REVERT: A 1230 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7134 (mptp) REVERT: A 1300 PHE cc_start: 0.8693 (m-10) cc_final: 0.7574 (t80) REVERT: A 1369 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7642 (mtm110) REVERT: A 1416 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: A 1422 LYS cc_start: 0.7968 (tttm) cc_final: 0.7382 (mtmp) REVERT: A 1450 TYR cc_start: 0.7173 (t80) cc_final: 0.6764 (t80) REVERT: A 1499 ASP cc_start: 0.7684 (t0) cc_final: 0.7237 (m-30) REVERT: A 1501 PHE cc_start: 0.7920 (m-10) cc_final: 0.7623 (m-80) REVERT: B 22 SER cc_start: 0.7922 (t) cc_final: 0.7384 (m) outliers start: 37 outliers final: 15 residues processed: 188 average time/residue: 0.5017 time to fit residues: 103.0447 Evaluate side-chains 176 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111276 restraints weight = 13667.969| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.02 r_work: 0.3041 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11389 Z= 0.126 Angle : 0.617 11.088 15499 Z= 0.309 Chirality : 0.043 0.363 1775 Planarity : 0.003 0.039 1908 Dihedral : 5.276 58.032 1510 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.58 % Allowed : 16.75 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1372 helix: 0.72 (0.18), residues: 880 sheet: -3.97 (0.68), residues: 22 loop : -1.60 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1325 TYR 0.018 0.001 TYR A 381 PHE 0.017 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11374) covalent geometry : angle 0.59812 / 0.30 (15462) SS BOND : bond 0.00360 / 0.26 ( 8) SS BOND : angle 1.41372 / 0.93 ( 16) hydrogen bonds : bond 0.04520 / 3.29 ( 557) hydrogen bonds : angle 3.64198 / 2.50 ( 1605) link_BETA1-4 : bond 0.00656 / 0.32 ( 2) link_BETA1-4 : angle 3.66632 / 2.07 ( 6) link_NAG-ASN : bond 0.00654 / 0.35 ( 5) link_NAG-ASN : angle 4.11964 / 2.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7633 (mtt) cc_final: 0.7312 (mtp) REVERT: A 198 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6312 (mmm-85) REVERT: A 213 TYR cc_start: 0.8116 (m-80) cc_final: 0.7878 (m-80) REVERT: A 236 ARG cc_start: 0.8801 (ptm160) cc_final: 0.8596 (ttp80) REVERT: A 429 GLU cc_start: 0.6805 (tt0) cc_final: 0.6427 (tt0) REVERT: A 628 ASN cc_start: 0.8689 (t0) cc_final: 0.8378 (t0) REVERT: A 631 MET cc_start: 0.8508 (mmt) cc_final: 0.7978 (mtp) REVERT: A 636 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7106 (mppt) REVERT: A 649 PHE cc_start: 0.8582 (m-80) cc_final: 0.8339 (m-80) REVERT: A 665 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (mpp) REVERT: A 708 ASP cc_start: 0.8611 (p0) cc_final: 0.8215 (m-30) REVERT: A 915 LYS cc_start: 0.8059 (tmtp) cc_final: 0.7420 (pmtt) REVERT: A 1042 MET cc_start: 0.9287 (mmp) cc_final: 0.9013 (mmm) REVERT: A 1078 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8769 (mttp) REVERT: A 1083 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: A 1174 TYR cc_start: 0.7544 (m-10) cc_final: 0.7328 (m-80) REVERT: A 1196 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6962 (pmm) REVERT: A 1200 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6736 (pt0) REVERT: A 1230 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7186 (mptp) REVERT: A 1300 PHE cc_start: 0.8673 (m-10) cc_final: 0.7615 (t80) REVERT: A 1369 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7653 (mtm110) REVERT: A 1416 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: A 1422 LYS cc_start: 0.7957 (tttm) cc_final: 0.7395 (mtmp) REVERT: A 1450 TYR cc_start: 0.7263 (t80) cc_final: 0.6825 (t80) REVERT: A 1473 LYS cc_start: 0.6634 (mtmm) cc_final: 0.6306 (ptpt) REVERT: A 1499 ASP cc_start: 0.7809 (t0) cc_final: 0.7490 (m-30) REVERT: A 1501 PHE cc_start: 0.7871 (m-10) cc_final: 0.7604 (m-80) REVERT: A 1502 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6703 (m) outliers start: 41 outliers final: 18 residues processed: 183 average time/residue: 0.4919 time to fit residues: 98.6369 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 HIS A 839 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112052 restraints weight = 13575.798| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.07 r_work: 0.2964 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11389 Z= 0.148 Angle : 0.638 11.193 15499 Z= 0.318 Chirality : 0.044 0.350 1775 Planarity : 0.003 0.042 1908 Dihedral : 5.282 57.650 1510 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.40 % Allowed : 17.36 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1372 helix: 0.77 (0.18), residues: 880 sheet: -3.97 (0.66), residues: 22 loop : -1.55 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1325 TYR 0.019 0.002 TYR A 381 PHE 0.021 0.001 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11374) covalent geometry : angle 0.61789 / 0.31 (15462) SS BOND : bond 0.00374 / 0.26 ( 8) SS BOND : angle 1.44700 / 0.95 ( 16) hydrogen bonds : bond 0.04721 / 3.43 ( 557) hydrogen bonds : angle 3.64915 / 2.51 ( 1605) link_BETA1-4 : bond 0.00436 / 0.21 ( 2) link_BETA1-4 : angle 3.70805 / 2.09 ( 6) link_NAG-ASN : bond 0.00651 / 0.34 ( 5) link_NAG-ASN : angle 4.34125 / 2.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7690 (mtt) cc_final: 0.7397 (mtp) REVERT: A 198 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6204 (mmt90) REVERT: A 236 ARG cc_start: 0.8811 (ptm160) cc_final: 0.8602 (ttp80) REVERT: A 428 GLU cc_start: 0.7390 (pp20) cc_final: 0.7150 (pp20) REVERT: A 628 ASN cc_start: 0.8692 (t0) cc_final: 0.8378 (t0) REVERT: A 631 MET cc_start: 0.8512 (mmt) cc_final: 0.8000 (mtp) REVERT: A 636 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7158 (mppt) REVERT: A 649 PHE cc_start: 0.8606 (m-80) cc_final: 0.8352 (m-80) REVERT: A 665 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8131 (mpp) REVERT: A 708 ASP cc_start: 0.8703 (p0) cc_final: 0.8231 (m-30) REVERT: A 1042 MET cc_start: 0.9323 (mmp) cc_final: 0.9040 (mmm) REVERT: A 1078 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8759 (mttp) REVERT: A 1083 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: A 1147 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8051 (tttm) REVERT: A 1174 TYR cc_start: 0.7504 (m-10) cc_final: 0.7279 (m-80) REVERT: A 1196 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6963 (pmm) REVERT: A 1200 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6727 (pt0) REVERT: A 1230 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7137 (mptp) REVERT: A 1300 PHE cc_start: 0.8747 (m-10) cc_final: 0.7723 (t80) REVERT: A 1416 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: A 1422 LYS cc_start: 0.7982 (tttm) cc_final: 0.7382 (mtmp) REVERT: A 1450 TYR cc_start: 0.7222 (t80) cc_final: 0.6766 (t80) REVERT: A 1499 ASP cc_start: 0.7834 (t0) cc_final: 0.7545 (m-30) REVERT: A 1502 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6697 (m) outliers start: 39 outliers final: 20 residues processed: 176 average time/residue: 0.4861 time to fit residues: 93.9518 Evaluate side-chains 177 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111988 restraints weight = 13551.210| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.79 r_work: 0.2968 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11389 Z= 0.134 Angle : 0.630 11.051 15499 Z= 0.311 Chirality : 0.044 0.374 1775 Planarity : 0.003 0.041 1908 Dihedral : 5.243 57.194 1510 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.40 % Allowed : 17.98 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1372 helix: 0.87 (0.18), residues: 880 sheet: -3.87 (0.66), residues: 22 loop : -1.53 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1325 TYR 0.019 0.001 TYR A 381 PHE 0.020 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (11374) covalent geometry : angle 0.61129 / 0.31 (15462) SS BOND : bond 0.00337 / 0.24 ( 8) SS BOND : angle 1.35790 / 0.90 ( 16) hydrogen bonds : bond 0.04518 / 3.29 ( 557) hydrogen bonds : angle 3.59828 / 2.48 ( 1605) link_BETA1-4 : bond 0.00440 / 0.21 ( 2) link_BETA1-4 : angle 3.65854 / 2.07 ( 6) link_NAG-ASN : bond 0.00662 / 0.35 ( 5) link_NAG-ASN : angle 4.21412 / 2.84 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6979 (mmm160) cc_final: 0.6280 (mmm-85) REVERT: A 236 ARG cc_start: 0.8809 (ptm160) cc_final: 0.8604 (ttp80) REVERT: A 428 GLU cc_start: 0.7335 (pp20) cc_final: 0.7071 (pp20) REVERT: A 628 ASN cc_start: 0.8682 (t0) cc_final: 0.8363 (t0) REVERT: A 631 MET cc_start: 0.8510 (mmt) cc_final: 0.8000 (mtp) REVERT: A 636 LYS cc_start: 0.7928 (tmmt) cc_final: 0.7129 (mppt) REVERT: A 649 PHE cc_start: 0.8573 (m-80) cc_final: 0.8322 (m-80) REVERT: A 665 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8123 (mpp) REVERT: A 708 ASP cc_start: 0.8650 (p0) cc_final: 0.8215 (m-30) REVERT: A 1042 MET cc_start: 0.9316 (mmp) cc_final: 0.9036 (mmm) REVERT: A 1078 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8744 (mttp) REVERT: A 1083 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 1147 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: A 1174 TYR cc_start: 0.7504 (m-10) cc_final: 0.7282 (m-80) REVERT: A 1176 MET cc_start: 0.8363 (mmt) cc_final: 0.8129 (mmm) REVERT: A 1196 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6968 (pmm) REVERT: A 1200 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6720 (pt0) REVERT: A 1230 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7149 (mptp) REVERT: A 1300 PHE cc_start: 0.8663 (m-10) cc_final: 0.7550 (t80) REVERT: A 1416 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 1422 LYS cc_start: 0.7988 (tttm) cc_final: 0.7372 (mtmp) REVERT: A 1450 TYR cc_start: 0.7344 (t80) cc_final: 0.6723 (t80) REVERT: A 1473 LYS cc_start: 0.6636 (mtmm) cc_final: 0.6266 (ptpt) REVERT: A 1499 ASP cc_start: 0.7830 (t0) cc_final: 0.7540 (m-30) outliers start: 39 outliers final: 21 residues processed: 172 average time/residue: 0.4930 time to fit residues: 92.9807 Evaluate side-chains 176 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110643 restraints weight = 13565.980| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.10 r_work: 0.2966 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11389 Z= 0.139 Angle : 0.634 11.081 15499 Z= 0.314 Chirality : 0.044 0.332 1775 Planarity : 0.003 0.041 1908 Dihedral : 5.204 57.069 1510 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.97 % Allowed : 18.50 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1372 helix: 0.94 (0.18), residues: 880 sheet: -3.89 (0.65), residues: 22 loop : -1.51 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1137 TYR 0.018 0.001 TYR A 381 PHE 0.021 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11374) covalent geometry : angle 0.61662 / 0.31 (15462) SS BOND : bond 0.00335 / 0.24 ( 8) SS BOND : angle 1.36489 / 0.91 ( 16) hydrogen bonds : bond 0.04563 / 3.32 ( 557) hydrogen bonds : angle 3.58584 / 2.47 ( 1605) link_BETA1-4 : bond 0.00494 / 0.24 ( 2) link_BETA1-4 : angle 3.60758 / 2.03 ( 6) link_NAG-ASN : bond 0.00601 / 0.32 ( 5) link_NAG-ASN : angle 4.04198 / 2.77 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7695 (mtt) cc_final: 0.7358 (mtp) REVERT: A 198 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6190 (mmt90) REVERT: A 236 ARG cc_start: 0.8808 (ptm160) cc_final: 0.8600 (ttp80) REVERT: A 428 GLU cc_start: 0.7310 (pp20) cc_final: 0.7037 (pp20) REVERT: A 628 ASN cc_start: 0.8654 (t0) cc_final: 0.8335 (t0) REVERT: A 631 MET cc_start: 0.8488 (mmt) cc_final: 0.7985 (mtp) REVERT: A 636 LYS cc_start: 0.7951 (tmmt) cc_final: 0.7164 (mppt) REVERT: A 649 PHE cc_start: 0.8559 (m-80) cc_final: 0.8290 (m-80) REVERT: A 665 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (mpp) REVERT: A 708 ASP cc_start: 0.8661 (p0) cc_final: 0.8217 (m-30) REVERT: A 1019 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 1042 MET cc_start: 0.9314 (mmp) cc_final: 0.9030 (mmm) REVERT: A 1078 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8707 (mttp) REVERT: A 1083 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 1147 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (tttm) REVERT: A 1174 TYR cc_start: 0.7479 (m-10) cc_final: 0.7250 (m-80) REVERT: A 1196 MET cc_start: 0.7171 (tpt) cc_final: 0.6943 (pmm) REVERT: A 1200 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6680 (pt0) REVERT: A 1230 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7068 (mptp) REVERT: A 1277 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6273 (ptp90) REVERT: A 1300 PHE cc_start: 0.8753 (m-10) cc_final: 0.7650 (t80) REVERT: A 1416 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: A 1422 LYS cc_start: 0.7982 (tttm) cc_final: 0.7534 (ttmp) REVERT: A 1450 TYR cc_start: 0.7425 (t80) cc_final: 0.6880 (t80) REVERT: A 1499 ASP cc_start: 0.7876 (t0) cc_final: 0.7573 (m-30) outliers start: 34 outliers final: 22 residues processed: 177 average time/residue: 0.5111 time to fit residues: 98.8961 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 123 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 839 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113997 restraints weight = 13732.386| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11389 Z= 0.115 Angle : 0.606 11.199 15499 Z= 0.300 Chirality : 0.043 0.316 1775 Planarity : 0.003 0.039 1908 Dihedral : 5.101 57.563 1510 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.27 % Allowed : 19.20 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1372 helix: 1.12 (0.18), residues: 877 sheet: -3.83 (0.66), residues: 22 loop : -1.42 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 846 TYR 0.018 0.001 TYR A 381 PHE 0.018 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11374) covalent geometry : angle 0.59026 / 0.30 (15462) SS BOND : bond 0.00297 / 0.21 ( 8) SS BOND : angle 1.20107 / 0.81 ( 16) hydrogen bonds : bond 0.04209 / 3.07 ( 557) hydrogen bonds : angle 3.50779 / 2.41 ( 1605) link_BETA1-4 : bond 0.00401 / 0.20 ( 2) link_BETA1-4 : angle 3.60147 / 2.05 ( 6) link_NAG-ASN : bond 0.00634 / 0.34 ( 5) link_NAG-ASN : angle 3.75654 / 2.58 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7726 (mtt) cc_final: 0.7382 (mtp) REVERT: A 198 ARG cc_start: 0.7001 (mmm160) cc_final: 0.6315 (mmm-85) REVERT: A 236 ARG cc_start: 0.8802 (ptm160) cc_final: 0.8447 (ttt180) REVERT: A 428 GLU cc_start: 0.7398 (pp20) cc_final: 0.7149 (pp20) REVERT: A 628 ASN cc_start: 0.8696 (t0) cc_final: 0.8367 (t0) REVERT: A 631 MET cc_start: 0.8513 (mmt) cc_final: 0.8022 (mtp) REVERT: A 636 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7154 (mppt) REVERT: A 649 PHE cc_start: 0.8551 (m-80) cc_final: 0.8321 (m-80) REVERT: A 661 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8305 (mm-40) REVERT: A 665 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8135 (mpp) REVERT: A 708 ASP cc_start: 0.8550 (p0) cc_final: 0.8236 (m-30) REVERT: A 999 MET cc_start: 0.8867 (tpt) cc_final: 0.8612 (tpp) REVERT: A 1042 MET cc_start: 0.9281 (mmp) cc_final: 0.9007 (mmm) REVERT: A 1078 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8761 (mttp) REVERT: A 1083 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 1147 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7952 (tttm) REVERT: A 1174 TYR cc_start: 0.7618 (m-10) cc_final: 0.7369 (m-80) REVERT: A 1200 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6766 (pt0) REVERT: A 1230 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7101 (mptp) REVERT: A 1277 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6292 (ptp90) REVERT: A 1300 PHE cc_start: 0.8716 (m-10) cc_final: 0.7618 (t80) REVERT: A 1416 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 1422 LYS cc_start: 0.8015 (tttm) cc_final: 0.7399 (mtmp) REVERT: A 1450 TYR cc_start: 0.7389 (t80) cc_final: 0.6913 (t80) REVERT: A 1473 LYS cc_start: 0.6734 (mtmm) cc_final: 0.6311 (ptpt) REVERT: A 1499 ASP cc_start: 0.7950 (t0) cc_final: 0.7688 (m-30) outliers start: 26 outliers final: 18 residues processed: 173 average time/residue: 0.5277 time to fit residues: 99.4124 Evaluate side-chains 174 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 82 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113740 restraints weight = 13640.215| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.03 r_work: 0.2992 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11389 Z= 0.114 Angle : 0.602 9.747 15499 Z= 0.299 Chirality : 0.043 0.314 1775 Planarity : 0.003 0.038 1908 Dihedral : 5.055 58.291 1510 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.53 % Allowed : 19.02 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1372 helix: 1.19 (0.18), residues: 875 sheet: -3.74 (0.66), residues: 22 loop : -1.40 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1325 TYR 0.017 0.001 TYR A 381 PHE 0.019 0.001 PHE A1279 TRP 0.014 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11374) covalent geometry : angle 0.58658 / 0.30 (15462) SS BOND : bond 0.00268 / 0.19 ( 8) SS BOND : angle 1.31729 / 0.90 ( 16) hydrogen bonds : bond 0.04209 / 3.07 ( 557) hydrogen bonds : angle 3.48457 / 2.39 ( 1605) link_BETA1-4 : bond 0.00533 / 0.26 ( 2) link_BETA1-4 : angle 3.47780 / 1.97 ( 6) link_NAG-ASN : bond 0.00630 / 0.34 ( 5) link_NAG-ASN : angle 3.62114 / 2.48 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.42 seconds wall clock time: 80 minutes 5.74 seconds (4805.74 seconds total)