Starting phenix.real_space_refine on Tue Jul 29 10:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_6995.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_6995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_6995.map" model { file = "/net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_6995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a90_6995/07_2025/6a90_6995.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.71, per 1000 atoms: 0.61 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.29 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: 3.96 Time building geometry restraints manager: 2.96 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 - 21.38: 6434 21.38 - 42.77: 228 42.77 - 64.15: 38 64.15 - 85.53: 8 85.53 - 106.92: 3 Dihedral angle restraints: 6711 sinusoidal: 2653 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 6708 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 12.073 106.918 4069 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.004 TRP A 624 HIS 0.017 0.004 HIS A 153 PHE 0.041 0.005 PHE A 410 TYR 0.062 0.005 TYR A 933 ARG 0.017 0.002 ARG A1271 Details of bonding type rmsd link_NAG-ASN : bond 0.01228 ( 5) link_NAG-ASN : angle 6.73593 ( 15) link_BETA1-4 : bond 0.01473 ( 2) link_BETA1-4 : angle 6.63520 ( 6) hydrogen bonds : bond 0.31430 ( 557) hydrogen bonds : angle 9.89457 ( 1605) SS BOND : bond 0.00775 ( 8) SS BOND : angle 2.11792 ( 16) covalent geometry : bond 0.01106 (11374) covalent geometry : angle 1.23106 (15462) *********************** 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 : 1.137 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: 1.1780 time to fit residues: 342.0539 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 : 1.156 ------------------------------------------------------------------------------- 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 115 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 291 HIS A 409 ASN A 421 HIS A1118 GLN A1486 HIS B 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115535 restraints weight = 13605.537| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.06 r_work: 0.3050 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11389 Z= 0.142 Angle : 0.732 12.458 15499 Z= 0.375 Chirality : 0.044 0.376 1775 Planarity : 0.005 0.065 1908 Dihedral : 8.486 88.601 1665 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.05 % Allowed : 11.34 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.19), residues: 1372 helix: -1.85 (0.14), residues: 864 sheet: -4.37 (0.72), residues: 22 loop : -2.25 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 PHE 0.018 0.001 PHE A1488 TYR 0.025 0.002 TYR A1313 ARG 0.007 0.001 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 5) link_NAG-ASN : angle 4.96276 ( 15) link_BETA1-4 : bond 0.00535 ( 2) link_BETA1-4 : angle 4.18580 ( 6) hydrogen bonds : bond 0.06348 ( 557) hydrogen bonds : angle 4.68271 ( 1605) SS BOND : bond 0.00319 ( 8) SS BOND : angle 3.26775 ( 16) covalent geometry : bond 0.00278 (11374) covalent geometry : angle 0.70365 (15462) *********************** 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 232 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6979 (mmm160) cc_final: 0.6286 (mmm-85) REVERT: A 236 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8023 (ttt180) REVERT: A 419 TYR cc_start: 0.9214 (t80) cc_final: 0.8994 (t80) REVERT: A 593 PHE cc_start: 0.8175 (m-10) cc_final: 0.7959 (m-10) REVERT: A 597 GLU cc_start: 0.6456 (mt-10) cc_final: 0.6043 (mt-10) REVERT: A 628 ASN cc_start: 0.8655 (t0) cc_final: 0.8405 (t0) REVERT: A 631 MET cc_start: 0.8333 (mmt) cc_final: 0.7943 (mtp) REVERT: A 636 LYS cc_start: 0.7747 (tmmt) cc_final: 0.7269 (tppp) REVERT: A 915 LYS cc_start: 0.7933 (tmtp) cc_final: 0.7437 (pmtt) REVERT: A 999 MET cc_start: 0.8934 (tpt) cc_final: 0.8529 (tpp) REVERT: A 1042 MET cc_start: 0.9233 (mmp) cc_final: 0.8942 (mmm) REVERT: A 1078 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8690 (mttt) REVERT: A 1164 TYR cc_start: 0.8207 (t80) cc_final: 0.7717 (t80) REVERT: A 1174 TYR cc_start: 0.7519 (m-10) cc_final: 0.7212 (m-80) REVERT: A 1200 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6749 (pt0) REVERT: A 1218 VAL cc_start: 0.8266 (p) cc_final: 0.7954 (t) REVERT: A 1230 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7100 (mmtm) REVERT: A 1231 ASP cc_start: 0.8148 (t70) cc_final: 0.7880 (t0) REVERT: A 1283 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7153 (tpp-160) REVERT: A 1300 PHE cc_start: 0.8560 (m-10) cc_final: 0.7435 (t80) REVERT: A 1396 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 1416 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: A 1422 LYS cc_start: 0.7965 (tttm) cc_final: 0.7502 (mtmp) REVERT: A 1450 TYR cc_start: 0.7285 (t80) cc_final: 0.7023 (t80) REVERT: A 1499 ASP cc_start: 0.7894 (t0) cc_final: 0.7260 (m-30) REVERT: A 1501 PHE cc_start: 0.8148 (m-10) cc_final: 0.7880 (m-80) REVERT: B 22 SER cc_start: 0.7985 (t) cc_final: 0.7666 (p) outliers start: 35 outliers final: 10 residues processed: 220 average time/residue: 1.1750 time to fit residues: 284.0290 Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 712 VAL 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 42 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 126 optimal weight: 0.0170 chunk 86 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115597 restraints weight = 13795.519| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3053 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11389 Z= 0.117 Angle : 0.627 11.769 15499 Z= 0.316 Chirality : 0.042 0.341 1775 Planarity : 0.004 0.053 1908 Dihedral : 7.623 77.712 1661 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.14 % Allowed : 13.26 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.22), residues: 1372 helix: -0.37 (0.17), residues: 866 sheet: -4.13 (0.80), residues: 22 loop : -1.98 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 PHE 0.019 0.001 PHE A1279 TYR 0.022 0.001 TYR A1313 ARG 0.007 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 4.34142 ( 15) link_BETA1-4 : bond 0.00621 ( 2) link_BETA1-4 : angle 4.09802 ( 6) hydrogen bonds : bond 0.04878 ( 557) hydrogen bonds : angle 3.98983 ( 1605) SS BOND : bond 0.00848 ( 8) SS BOND : angle 1.92773 ( 16) covalent geometry : bond 0.00240 (11374) covalent geometry : angle 0.60406 (15462) *********************** 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 225 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7610 (mtt) cc_final: 0.7354 (mtp) REVERT: A 158 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7941 (mt) REVERT: A 198 ARG cc_start: 0.6882 (mmm160) cc_final: 0.6325 (mmm-85) REVERT: A 236 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8197 (ttt180) REVERT: A 628 ASN cc_start: 0.8616 (t0) cc_final: 0.8367 (t0) REVERT: A 631 MET cc_start: 0.8438 (mmt) cc_final: 0.7973 (mtp) REVERT: A 636 LYS cc_start: 0.7825 (tmmt) cc_final: 0.6924 (mppt) REVERT: A 661 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8140 (mm-40) REVERT: A 708 ASP cc_start: 0.8547 (p0) cc_final: 0.8255 (m-30) REVERT: A 915 LYS cc_start: 0.8036 (tmtp) cc_final: 0.7464 (pmtt) REVERT: A 999 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8545 (tpp) REVERT: A 1042 MET cc_start: 0.9233 (mmp) cc_final: 0.8948 (mmm) REVERT: A 1078 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8747 (mttt) REVERT: A 1174 TYR cc_start: 0.7678 (m-10) cc_final: 0.7422 (m-80) REVERT: A 1200 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6794 (pt0) REVERT: A 1230 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7053 (mmtt) REVERT: A 1300 PHE cc_start: 0.8585 (m-10) cc_final: 0.7500 (t80) REVERT: A 1369 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7661 (mtp180) REVERT: A 1416 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: A 1422 LYS cc_start: 0.7916 (tttm) cc_final: 0.7406 (mtmp) REVERT: A 1450 TYR cc_start: 0.7267 (t80) cc_final: 0.6949 (t80) REVERT: A 1499 ASP cc_start: 0.7656 (t0) cc_final: 0.7229 (m-30) REVERT: A 1501 PHE cc_start: 0.7992 (m-10) cc_final: 0.7732 (m-10) outliers start: 36 outliers final: 10 residues processed: 211 average time/residue: 1.0506 time to fit residues: 243.6247 Evaluate side-chains 178 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 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 872 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1078 LYS 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 135 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111455 restraints weight = 13562.677| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.02 r_work: 0.2984 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11389 Z= 0.155 Angle : 0.662 11.083 15499 Z= 0.333 Chirality : 0.044 0.359 1775 Planarity : 0.004 0.044 1908 Dihedral : 6.905 59.626 1657 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.45 % Allowed : 14.92 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1372 helix: 0.16 (0.18), residues: 875 sheet: -3.98 (0.75), residues: 22 loop : -1.86 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.006 0.001 HIS A 153 PHE 0.023 0.002 PHE A1279 TYR 0.021 0.002 TYR A1313 ARG 0.007 0.001 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 5) link_NAG-ASN : angle 4.44112 ( 15) link_BETA1-4 : bond 0.00464 ( 2) link_BETA1-4 : angle 4.06419 ( 6) hydrogen bonds : bond 0.05070 ( 557) hydrogen bonds : angle 3.88898 ( 1605) SS BOND : bond 0.00524 ( 8) SS BOND : angle 1.88701 ( 16) covalent geometry : bond 0.00360 (11374) covalent geometry : angle 0.64063 (15462) *********************** 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 222 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7691 (mtt) cc_final: 0.7367 (mtp) REVERT: A 198 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6152 (mmt90) REVERT: A 236 ARG cc_start: 0.8779 (ptm160) cc_final: 0.8336 (ttt180) REVERT: A 374 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 628 ASN cc_start: 0.8663 (t0) cc_final: 0.8366 (t0) REVERT: A 631 MET cc_start: 0.8536 (mmt) cc_final: 0.8114 (mtp) REVERT: A 636 LYS cc_start: 0.7886 (tmmt) cc_final: 0.7007 (mppt) REVERT: A 660 MET cc_start: 0.9226 (ttp) cc_final: 0.9022 (ttp) REVERT: A 665 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: A 708 ASP cc_start: 0.8658 (p0) cc_final: 0.8249 (m-30) REVERT: A 915 LYS cc_start: 0.8040 (tmtp) cc_final: 0.7436 (pmtt) REVERT: A 999 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8553 (tpp) REVERT: A 1033 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: A 1042 MET cc_start: 0.9315 (mmp) cc_final: 0.9020 (mmm) REVERT: A 1078 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8688 (mttt) REVERT: A 1083 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 1174 TYR cc_start: 0.7661 (m-10) cc_final: 0.7386 (m-80) REVERT: A 1196 MET cc_start: 0.7128 (tpt) cc_final: 0.6882 (pmm) REVERT: A 1200 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6734 (pt0) REVERT: A 1230 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7048 (mmtt) REVERT: A 1300 PHE cc_start: 0.8585 (m-10) cc_final: 0.7502 (t80) REVERT: A 1416 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: A 1422 LYS cc_start: 0.7955 (tttm) cc_final: 0.7376 (mtmp) REVERT: A 1450 TYR cc_start: 0.7262 (t80) cc_final: 0.6909 (t80) REVERT: A 1499 ASP cc_start: 0.7684 (t0) cc_final: 0.7260 (m-30) REVERT: A 1501 PHE cc_start: 0.7878 (m-10) cc_final: 0.7566 (m-80) REVERT: B 22 SER cc_start: 0.8001 (t) cc_final: 0.7353 (m) outliers start: 51 outliers final: 21 residues processed: 203 average time/residue: 1.0618 time to fit residues: 236.3161 Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 312 ASN 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 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 1108 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1276 LEU 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 B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113044 restraints weight = 13560.274| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.05 r_work: 0.3041 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11389 Z= 0.136 Angle : 0.627 11.101 15499 Z= 0.315 Chirality : 0.043 0.345 1775 Planarity : 0.003 0.040 1908 Dihedral : 6.546 59.606 1657 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.23 % Allowed : 16.58 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1372 helix: 0.45 (0.18), residues: 882 sheet: -3.98 (0.73), residues: 22 loop : -1.77 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.016 0.001 PHE A1279 TYR 0.019 0.002 TYR A 381 ARG 0.005 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 5) link_NAG-ASN : angle 4.54867 ( 15) link_BETA1-4 : bond 0.00553 ( 2) link_BETA1-4 : angle 4.03289 ( 6) hydrogen bonds : bond 0.04691 ( 557) hydrogen bonds : angle 3.73002 ( 1605) SS BOND : bond 0.00435 ( 8) SS BOND : angle 1.59452 ( 16) covalent geometry : bond 0.00313 (11374) covalent geometry : angle 0.60451 (15462) *********************** 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 198 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7678 (mtt) cc_final: 0.7362 (mtp) REVERT: A 198 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6292 (mmm-85) REVERT: A 236 ARG cc_start: 0.8812 (ptm160) cc_final: 0.8605 (ttp80) REVERT: A 374 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 628 ASN cc_start: 0.8642 (t0) cc_final: 0.8330 (t0) REVERT: A 631 MET cc_start: 0.8501 (mmt) cc_final: 0.8082 (mtp) REVERT: A 636 LYS cc_start: 0.7860 (tmmt) cc_final: 0.6909 (mtpt) REVERT: A 649 PHE cc_start: 0.8599 (m-80) cc_final: 0.8342 (m-80) REVERT: A 665 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (mpp) REVERT: A 708 ASP cc_start: 0.8587 (p0) cc_final: 0.8231 (m-30) REVERT: A 915 LYS cc_start: 0.8037 (tmtp) cc_final: 0.7411 (pmtt) REVERT: A 999 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8609 (tpp) REVERT: A 1033 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: A 1042 MET cc_start: 0.9292 (mmp) cc_final: 0.8993 (mmm) REVERT: A 1078 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8746 (mttp) REVERT: A 1083 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 1174 TYR cc_start: 0.7668 (m-10) cc_final: 0.7411 (m-80) REVERT: A 1196 MET cc_start: 0.7197 (tpt) cc_final: 0.6939 (pmm) REVERT: A 1200 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6707 (pt0) REVERT: A 1230 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7133 (mptp) REVERT: A 1300 PHE cc_start: 0.8670 (m-10) cc_final: 0.7539 (t80) REVERT: A 1369 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7645 (mtm110) REVERT: A 1416 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 1422 LYS cc_start: 0.7948 (tttm) cc_final: 0.7392 (mtmp) REVERT: A 1450 TYR cc_start: 0.7274 (t80) cc_final: 0.6745 (t80) REVERT: A 1499 ASP cc_start: 0.7734 (t0) cc_final: 0.7363 (m-30) REVERT: A 1501 PHE cc_start: 0.7886 (m-10) cc_final: 0.7574 (m-80) REVERT: A 1502 SER cc_start: 0.7042 (OUTLIER) cc_final: 0.6647 (m) REVERT: B 22 SER cc_start: 0.7920 (t) cc_final: 0.7318 (m) outliers start: 37 outliers final: 14 residues processed: 187 average time/residue: 1.0705 time to fit residues: 219.0684 Evaluate side-chains 177 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 312 ASN 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 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 941 CYS 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 Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 133 optimal weight: 0.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113608 restraints weight = 13616.203| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.88 r_work: 0.3003 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3335 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= 0.118 Angle : 0.604 10.699 15499 Z= 0.303 Chirality : 0.042 0.328 1775 Planarity : 0.003 0.039 1908 Dihedral : 6.397 59.725 1657 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.23 % Allowed : 16.84 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1372 helix: 0.76 (0.18), residues: 879 sheet: -4.06 (0.69), residues: 22 loop : -1.62 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 PHE 0.016 0.001 PHE A1279 TYR 0.018 0.001 TYR A 381 ARG 0.005 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 5) link_NAG-ASN : angle 4.10687 ( 15) link_BETA1-4 : bond 0.00626 ( 2) link_BETA1-4 : angle 3.92270 ( 6) hydrogen bonds : bond 0.04374 ( 557) hydrogen bonds : angle 3.59471 ( 1605) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.42582 ( 16) covalent geometry : bond 0.00262 (11374) covalent geometry : angle 0.58443 (15462) *********************** 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 201 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7628 (mtt) cc_final: 0.7306 (mtp) REVERT: A 198 ARG cc_start: 0.6984 (mmm160) cc_final: 0.6292 (mmm-85) REVERT: A 213 TYR cc_start: 0.8054 (m-80) cc_final: 0.7764 (m-80) REVERT: A 236 ARG cc_start: 0.8809 (ptm160) cc_final: 0.8607 (ttp80) REVERT: A 628 ASN cc_start: 0.8670 (t0) cc_final: 0.8354 (t0) REVERT: A 631 MET cc_start: 0.8502 (mmt) cc_final: 0.7961 (mtp) REVERT: A 636 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7091 (mppt) REVERT: A 649 PHE cc_start: 0.8568 (m-80) cc_final: 0.8329 (m-80) REVERT: A 665 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8120 (mpp) REVERT: A 708 ASP cc_start: 0.8480 (p0) cc_final: 0.8245 (m-30) REVERT: A 915 LYS cc_start: 0.8046 (tmtp) cc_final: 0.7412 (pmtt) REVERT: A 1033 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: A 1042 MET cc_start: 0.9286 (mmp) cc_final: 0.9021 (mmm) REVERT: A 1078 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8743 (mttp) REVERT: A 1083 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 1174 TYR cc_start: 0.7471 (m-10) cc_final: 0.7253 (m-80) REVERT: A 1196 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6958 (pmm) REVERT: A 1200 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6780 (pt0) REVERT: A 1230 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7130 (mmtm) REVERT: A 1300 PHE cc_start: 0.8664 (m-10) cc_final: 0.7565 (t80) REVERT: A 1416 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: A 1422 LYS cc_start: 0.7911 (tttm) cc_final: 0.7360 (mtmp) REVERT: A 1450 TYR cc_start: 0.7229 (t80) cc_final: 0.6832 (t80) REVERT: A 1473 LYS cc_start: 0.6675 (mtmm) cc_final: 0.6334 (ptpt) REVERT: A 1499 ASP cc_start: 0.7784 (t0) cc_final: 0.7492 (m-30) REVERT: A 1501 PHE cc_start: 0.7915 (m-10) cc_final: 0.7581 (m-80) REVERT: A 1502 SER cc_start: 0.7108 (OUTLIER) cc_final: 0.6711 (m) REVERT: B 14 LYS cc_start: 0.7091 (mptm) cc_final: 0.6855 (mptp) outliers start: 37 outliers final: 16 residues processed: 185 average time/residue: 1.2492 time to fit residues: 255.7491 Evaluate side-chains 177 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 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 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 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 1196 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114974 restraints weight = 13736.048| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.04 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.002 0.044 11389 Z= 0.109 Angle : 0.583 10.288 15499 Z= 0.293 Chirality : 0.041 0.314 1775 Planarity : 0.003 0.037 1908 Dihedral : 6.251 58.543 1657 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.62 % Allowed : 17.98 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1372 helix: 0.96 (0.18), residues: 883 sheet: -4.00 (0.68), residues: 22 loop : -1.57 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 PHE 0.016 0.001 PHE A1279 TYR 0.016 0.001 TYR A 381 ARG 0.006 0.000 ARG A1325 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 5) link_NAG-ASN : angle 3.88000 ( 15) link_BETA1-4 : bond 0.00652 ( 2) link_BETA1-4 : angle 3.84813 ( 6) hydrogen bonds : bond 0.04132 ( 557) hydrogen bonds : angle 3.51217 ( 1605) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.26951 ( 16) covalent geometry : bond 0.00235 (11374) covalent geometry : angle 0.56451 (15462) *********************** 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 188 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7535 (mtt) cc_final: 0.7186 (mtp) REVERT: A 198 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6296 (mmm-85) REVERT: A 213 TYR cc_start: 0.8112 (m-80) cc_final: 0.7854 (m-80) REVERT: A 236 ARG cc_start: 0.8809 (ptm160) cc_final: 0.8337 (ttt180) REVERT: A 628 ASN cc_start: 0.8629 (t0) cc_final: 0.8319 (t0) REVERT: A 631 MET cc_start: 0.8487 (mmt) cc_final: 0.7947 (mtp) REVERT: A 636 LYS cc_start: 0.7860 (tmmt) cc_final: 0.7059 (mppt) REVERT: A 649 PHE cc_start: 0.8505 (m-80) cc_final: 0.8288 (m-80) REVERT: A 661 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8235 (mm-40) REVERT: A 665 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8004 (ptp) REVERT: A 708 ASP cc_start: 0.8554 (p0) cc_final: 0.8295 (m-30) REVERT: A 915 LYS cc_start: 0.8043 (tmtp) cc_final: 0.7386 (pmtt) REVERT: A 1042 MET cc_start: 0.9279 (mmp) cc_final: 0.9021 (mmm) REVERT: A 1078 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8715 (mttp) REVERT: A 1083 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 1147 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7696 (mtpp) REVERT: A 1196 MET cc_start: 0.7176 (tpt) cc_final: 0.6947 (pmm) REVERT: A 1200 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6744 (pt0) REVERT: A 1230 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7188 (mmtm) REVERT: A 1300 PHE cc_start: 0.8657 (m-10) cc_final: 0.7531 (t80) REVERT: A 1416 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 1422 LYS cc_start: 0.7886 (tttm) cc_final: 0.7296 (mtmp) REVERT: A 1450 TYR cc_start: 0.7226 (t80) cc_final: 0.6785 (t80) REVERT: A 1499 ASP cc_start: 0.7834 (t0) cc_final: 0.7555 (m-30) REVERT: A 1502 SER cc_start: 0.7055 (OUTLIER) cc_final: 0.6659 (m) REVERT: B 55 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7922 (mtp-110) outliers start: 30 outliers final: 16 residues processed: 174 average time/residue: 1.0598 time to fit residues: 202.5481 Evaluate side-chains 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL 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 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET 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 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 109 optimal weight: 0.0370 chunk 94 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114147 restraints weight = 13601.630| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.70 r_work: 0.3010 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3554 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= 0.116 Angle : 0.592 10.138 15499 Z= 0.295 Chirality : 0.042 0.334 1775 Planarity : 0.003 0.037 1908 Dihedral : 6.177 58.427 1657 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.32 % Allowed : 17.54 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1372 helix: 1.10 (0.18), residues: 877 sheet: -3.67 (0.71), residues: 22 loop : -1.53 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A 392 PHE 0.018 0.001 PHE A1279 TYR 0.017 0.001 TYR A 381 ARG 0.004 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 5) link_NAG-ASN : angle 4.02348 ( 15) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 3.85871 ( 6) hydrogen bonds : bond 0.04203 ( 557) hydrogen bonds : angle 3.47854 ( 1605) SS BOND : bond 0.00300 ( 8) SS BOND : angle 1.22936 ( 16) covalent geometry : bond 0.00260 (11374) covalent geometry : angle 0.57309 (15462) *********************** 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 195 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7587 (mtt) cc_final: 0.7280 (mtp) REVERT: A 198 ARG cc_start: 0.6949 (mmm160) cc_final: 0.6260 (mmm-85) REVERT: A 213 TYR cc_start: 0.8217 (m-80) cc_final: 0.7937 (m-80) REVERT: A 236 ARG cc_start: 0.8771 (ptm160) cc_final: 0.8336 (ttt180) REVERT: A 628 ASN cc_start: 0.8620 (t0) cc_final: 0.8303 (t0) REVERT: A 631 MET cc_start: 0.8442 (mmt) cc_final: 0.8029 (mtp) REVERT: A 636 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7058 (mppt) REVERT: A 661 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8249 (mm-40) REVERT: A 665 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: A 708 ASP cc_start: 0.8526 (p0) cc_final: 0.8260 (m-30) REVERT: A 915 LYS cc_start: 0.8040 (tmtp) cc_final: 0.7388 (pmtt) REVERT: A 1042 MET cc_start: 0.9279 (mmp) cc_final: 0.9015 (mmm) REVERT: A 1078 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8697 (mttp) REVERT: A 1083 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 1147 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7999 (tttm) REVERT: A 1200 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6738 (pt0) REVERT: A 1230 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7181 (mmtm) REVERT: A 1300 PHE cc_start: 0.8616 (m-10) cc_final: 0.7498 (t80) REVERT: A 1416 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 1422 LYS cc_start: 0.7853 (tttm) cc_final: 0.7251 (mtmp) REVERT: A 1450 TYR cc_start: 0.7263 (t80) cc_final: 0.6742 (t80) REVERT: A 1457 LEU cc_start: 0.7275 (mt) cc_final: 0.6886 (mp) REVERT: A 1473 LYS cc_start: 0.6657 (mtmm) cc_final: 0.6293 (ptpt) REVERT: A 1499 ASP cc_start: 0.7796 (t0) cc_final: 0.7568 (m-30) REVERT: A 1502 SER cc_start: 0.7074 (OUTLIER) cc_final: 0.6675 (m) outliers start: 38 outliers final: 18 residues processed: 180 average time/residue: 1.0493 time to fit residues: 207.0711 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 : 1.156 ------------------------------------------------------------------------------- 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 423 VAL 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 941 CYS 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 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1467 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113113 restraints weight = 13673.110| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.07 r_work: 0.3054 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11389 Z= 0.109 Angle : 0.583 10.576 15499 Z= 0.290 Chirality : 0.041 0.302 1775 Planarity : 0.003 0.036 1908 Dihedral : 6.106 59.834 1657 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.79 % Allowed : 17.63 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1372 helix: 1.20 (0.18), residues: 879 sheet: -3.51 (0.72), residues: 22 loop : -1.46 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 PHE 0.017 0.001 PHE A1279 TYR 0.016 0.001 TYR A 381 ARG 0.004 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 5) link_NAG-ASN : angle 3.71055 ( 15) link_BETA1-4 : bond 0.00478 ( 2) link_BETA1-4 : angle 3.87927 ( 6) hydrogen bonds : bond 0.03997 ( 557) hydrogen bonds : angle 3.42735 ( 1605) SS BOND : bond 0.00283 ( 8) SS BOND : angle 1.23541 ( 16) covalent geometry : bond 0.00238 (11374) covalent geometry : angle 0.56526 (15462) *********************** 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: 32 poor density : 158 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7748 (mtt) cc_final: 0.7432 (mtp) REVERT: A 198 ARG cc_start: 0.6973 (mmm160) cc_final: 0.6299 (mmm-85) REVERT: A 213 TYR cc_start: 0.8296 (m-80) cc_final: 0.8069 (m-80) REVERT: A 236 ARG cc_start: 0.8823 (ptm160) cc_final: 0.8370 (ttt180) REVERT: A 628 ASN cc_start: 0.8658 (t0) cc_final: 0.8341 (t0) REVERT: A 631 MET cc_start: 0.8480 (mmt) cc_final: 0.8061 (mtp) REVERT: A 636 LYS cc_start: 0.7906 (tmmt) cc_final: 0.7077 (mtpt) REVERT: A 661 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8309 (mm-40) REVERT: A 665 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8042 (ptp) REVERT: A 708 ASP cc_start: 0.8522 (p0) cc_final: 0.8301 (m-30) REVERT: A 1033 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: A 1042 MET cc_start: 0.9259 (mmp) cc_final: 0.8995 (mmm) REVERT: A 1078 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8755 (mttp) REVERT: A 1083 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 1147 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7984 (tttm) REVERT: A 1200 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6731 (pt0) REVERT: A 1230 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7207 (mmtm) REVERT: A 1300 PHE cc_start: 0.8717 (m-10) cc_final: 0.7621 (t80) REVERT: A 1416 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: A 1422 LYS cc_start: 0.7914 (tttm) cc_final: 0.7322 (mtmp) REVERT: A 1450 TYR cc_start: 0.7272 (t80) cc_final: 0.6771 (t80) REVERT: A 1457 LEU cc_start: 0.7302 (mt) cc_final: 0.6884 (mp) REVERT: A 1473 LYS cc_start: 0.6581 (mtmm) cc_final: 0.6200 (ptpt) REVERT: A 1499 ASP cc_start: 0.7863 (t0) cc_final: 0.7650 (m-30) REVERT: A 1502 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6681 (m) outliers start: 32 outliers final: 17 residues processed: 176 average time/residue: 1.1006 time to fit residues: 211.8165 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 : 1.330 ------------------------------------------------------------------------------- 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 423 VAL 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 941 CYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL 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 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET 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 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 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 = 0.3756 r_free = 0.3756 target = 0.153793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107080 restraints weight = 13585.280| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.76 r_work: 0.2954 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11389 Z= 0.177 Angle : 0.658 10.930 15499 Z= 0.329 Chirality : 0.044 0.305 1775 Planarity : 0.004 0.043 1908 Dihedral : 6.259 58.742 1657 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.44 % Allowed : 18.24 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1372 helix: 0.99 (0.18), residues: 876 sheet: -3.61 (0.63), residues: 22 loop : -1.49 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 32 HIS 0.006 0.001 HIS A 153 PHE 0.025 0.002 PHE A1279 TYR 0.019 0.002 TYR A 381 ARG 0.004 0.000 ARG A1271 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 5) link_NAG-ASN : angle 3.86755 ( 15) link_BETA1-4 : bond 0.00504 ( 2) link_BETA1-4 : angle 3.96545 ( 6) hydrogen bonds : bond 0.04879 ( 557) hydrogen bonds : angle 3.61026 ( 1605) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.64364 ( 16) covalent geometry : bond 0.00426 (11374) covalent geometry : angle 0.64058 (15462) ********************** 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 183 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7090 (mmm160) cc_final: 0.6230 (mmt90) REVERT: A 628 ASN cc_start: 0.8662 (t0) cc_final: 0.8334 (t0) REVERT: A 631 MET cc_start: 0.8592 (mmt) cc_final: 0.8080 (mtp) REVERT: A 636 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7117 (mtpt) REVERT: A 665 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8096 (mpp) REVERT: A 708 ASP cc_start: 0.8624 (p0) cc_final: 0.8229 (m-30) REVERT: A 1033 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: A 1042 MET cc_start: 0.9331 (mmp) cc_final: 0.9048 (mmm) REVERT: A 1078 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8733 (mttp) REVERT: A 1083 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 1147 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8012 (tttm) REVERT: A 1174 TYR cc_start: 0.7525 (m-10) cc_final: 0.7318 (m-80) REVERT: A 1200 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6725 (pt0) REVERT: A 1230 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7070 (mptp) REVERT: A 1300 PHE cc_start: 0.8741 (m-10) cc_final: 0.7660 (t80) REVERT: A 1416 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: A 1422 LYS cc_start: 0.7960 (tttm) cc_final: 0.7565 (ttmp) REVERT: A 1450 TYR cc_start: 0.7305 (t80) cc_final: 0.6697 (t80) REVERT: A 1451 ASP cc_start: 0.7298 (m-30) cc_final: 0.7073 (p0) REVERT: A 1457 LEU cc_start: 0.7315 (mt) cc_final: 0.6952 (mp) REVERT: A 1499 ASP cc_start: 0.7833 (t0) cc_final: 0.7600 (m-30) REVERT: A 1502 SER cc_start: 0.7059 (OUTLIER) cc_final: 0.6635 (m) outliers start: 28 outliers final: 15 residues processed: 170 average time/residue: 1.6769 time to fit residues: 316.8836 Evaluate side-chains 169 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 423 VAL Chi-restraints excluded: chain A residue 595 ILE 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 948 GLN Chi-restraints excluded: chain A residue 970 VAL 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 1147 LYS 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 Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110937 restraints weight = 13534.435| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.04 r_work: 0.3026 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3662 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= 0.129 Angle : 0.618 11.091 15499 Z= 0.308 Chirality : 0.043 0.296 1775 Planarity : 0.004 0.076 1908 Dihedral : 6.234 59.895 1657 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.36 % Allowed : 18.50 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1372 helix: 1.14 (0.18), residues: 875 sheet: -3.58 (0.67), residues: 22 loop : -1.46 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.020 0.001 PHE A1279 TYR 0.019 0.001 TYR A 381 ARG 0.004 0.000 ARG A1137 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 5) link_NAG-ASN : angle 3.73938 ( 15) link_BETA1-4 : bond 0.00453 ( 2) link_BETA1-4 : angle 3.93561 ( 6) hydrogen bonds : bond 0.04431 ( 557) hydrogen bonds : angle 3.53177 ( 1605) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.61499 ( 16) covalent geometry : bond 0.00296 (11374) covalent geometry : angle 0.60017 (15462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11094.02 seconds wall clock time: 196 minutes 31.20 seconds (11791.20 seconds total)