Starting phenix.real_space_refine on Tue Nov 18 05:08:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a90_6995/11_2025/6a90_6995.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a90_6995/11_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_6995/11_2025/6a90_6995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a90_6995/11_2025/6a90_6995.map" model { file = "/net/cci-nas-00/data/ceres_data/6a90_6995/11_2025/6a90_6995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a90_6995/11_2025/6a90_6995.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 Na 1 4.78 5 C 7319 2.51 5 N 1780 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10537 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1275} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 2.53, per 1000 atoms: 0.23 Number of scatterers: 11085 At special positions: 0 Unit cell: (133.102, 134.193, 122.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 Na 1 11.00 O 1911 8.00 N 1780 7.00 C 7319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.02 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.05 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 507.0 milliseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 69.0% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.861A pdb=" N ARG A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.751A pdb=" N THR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.552A pdb=" N ALA A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.939A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.905A pdb=" N TYR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.701A pdb=" N ARG A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.838A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.544A pdb=" N ALA A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.543A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.392A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 removed outlier: 3.866A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N THR A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.689A pdb=" N ASN A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.921A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.884A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 435 removed outlier: 3.712A pdb=" N ILE A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.575A pdb=" N LYS A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 538 Processing helix chain 'A' and resid 545 through 571 removed outlier: 3.609A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.263A pdb=" N PHE A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.622A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.645A pdb=" N PHE A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 615 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.443A pdb=" N PHE A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.592A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.562A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 674 Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.729A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.765A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.635A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 736 through 744 removed outlier: 3.672A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.832A pdb=" N ARG A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 removed outlier: 3.746A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.864A pdb=" N GLU A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 883 through 918 removed outlier: 3.669A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 914 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.571A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.583A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 947 through 952' Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.562A pdb=" N ARG A 957 " --> pdb=" O ARG A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.505A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 removed outlier: 4.279A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.648A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.830A pdb=" N GLU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.693A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 3.728A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.790A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 removed outlier: 4.170A pdb=" N VAL A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1123 " --> pdb=" O ARG A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.619A pdb=" N ARG A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1166 Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 4.049A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1190 removed outlier: 3.616A pdb=" N ASP A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1187 through 1190' Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 3.665A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 removed outlier: 3.536A pdb=" N LYS A1230 " --> pdb=" O HIS A1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1227 through 1230' Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.623A pdb=" N ILE A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1270 removed outlier: 3.679A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.767A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1322 removed outlier: 3.780A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1308 " --> pdb=" O PHE A1304 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1319 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A1322 " --> pdb=" O MET A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1349 removed outlier: 3.569A pdb=" N LEU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.765A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1399 removed outlier: 4.253A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1423 removed outlier: 3.966A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1423 " --> pdb=" O GLU A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.809A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1433 " --> pdb=" O ASP A1429 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1434 " --> pdb=" O TYR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1460 removed outlier: 4.358A pdb=" N SER A1454 " --> pdb=" O TYR A1450 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A1455 " --> pdb=" O ASP A1451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1478 removed outlier: 3.656A pdb=" N SER A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1505 removed outlier: 3.888A pdb=" N ASP A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1520 removed outlier: 3.607A pdb=" N ASP A1512 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 Processing sheet with id=AA3, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.999A pdb=" N LYS B 28 " --> pdb=" O GLU B 8 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.19 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.15), residues: 1372 helix: -4.25 (0.08), residues: 855 sheet: -4.54 (0.70), residues: 22 loop : -2.68 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1271 TYR 0.062 0.005 TYR A 933 PHE 0.041 0.005 PHE A 410 TRP 0.050 0.004 TRP A 624 HIS 0.017 0.004 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.01106 (11374) covalent geometry : angle 1.23106 (15462) SS BOND : bond 0.00775 ( 8) SS BOND : angle 2.11792 ( 16) hydrogen bonds : bond 0.31430 ( 557) hydrogen bonds : angle 9.89457 ( 1605) link_BETA1-4 : bond 0.01473 ( 2) link_BETA1-4 : angle 6.63520 ( 6) link_NAG-ASN : bond 0.01228 ( 5) link_NAG-ASN : angle 6.73593 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6162 (mmm-85) REVERT: A 249 ASP cc_start: 0.8253 (m-30) cc_final: 0.8053 (m-30) REVERT: A 631 MET cc_start: 0.7881 (mmt) cc_final: 0.7674 (mtp) REVERT: A 636 LYS cc_start: 0.7814 (tmmt) cc_final: 0.7405 (ttmt) REVERT: A 886 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 915 LYS cc_start: 0.7914 (tmtp) cc_final: 0.7454 (mttp) REVERT: A 922 TRP cc_start: 0.8269 (m100) cc_final: 0.7906 (m100) REVERT: A 1042 MET cc_start: 0.9099 (mmp) cc_final: 0.8861 (tpt) REVERT: A 1102 PHE cc_start: 0.8562 (t80) cc_final: 0.8225 (t80) REVERT: A 1164 TYR cc_start: 0.8121 (t80) cc_final: 0.7692 (t80) REVERT: A 1174 TYR cc_start: 0.7259 (m-10) cc_final: 0.6921 (m-80) REVERT: A 1218 VAL cc_start: 0.8022 (p) cc_final: 0.7721 (t) REVERT: A 1230 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7094 (mmtt) REVERT: A 1300 PHE cc_start: 0.8135 (m-10) cc_final: 0.7110 (t80) REVERT: A 1422 LYS cc_start: 0.7668 (tttm) cc_final: 0.7431 (mttp) outliers start: 20 outliers final: 7 residues processed: 268 average time/residue: 0.5832 time to fit residues: 168.4416 Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 409 ASN A 421 HIS A1118 GLN A1486 HIS B 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114676 restraints weight = 13701.103| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.09 r_work: 0.3031 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2276 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= 0.149 Angle : 0.734 12.496 15499 Z= 0.377 Chirality : 0.044 0.315 1775 Planarity : 0.005 0.067 1908 Dihedral : 8.471 88.410 1665 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.23 % Allowed : 11.34 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.19), residues: 1372 helix: -1.97 (0.14), residues: 875 sheet: -4.34 (0.72), residues: 22 loop : -2.27 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1137 TYR 0.026 0.002 TYR A1313 PHE 0.019 0.001 PHE A1488 TRP 0.029 0.002 TRP A 624 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00308 (11374) covalent geometry : angle 0.70695 (15462) SS BOND : bond 0.00310 ( 8) SS BOND : angle 3.12306 ( 16) hydrogen bonds : bond 0.06452 ( 557) hydrogen bonds : angle 4.71334 ( 1605) link_BETA1-4 : bond 0.00755 ( 2) link_BETA1-4 : angle 4.06610 ( 6) link_NAG-ASN : bond 0.00993 ( 5) link_NAG-ASN : angle 4.94593 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6931 (mmm160) cc_final: 0.6243 (mmm-85) REVERT: A 236 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8018 (ttt180) REVERT: A 419 TYR cc_start: 0.9177 (t80) cc_final: 0.8952 (t80) REVERT: A 597 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6144 (mt-10) REVERT: A 628 ASN cc_start: 0.8643 (t0) cc_final: 0.8395 (t0) REVERT: A 631 MET cc_start: 0.8364 (mmt) cc_final: 0.7921 (mtp) REVERT: A 636 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7253 (tppp) REVERT: A 638 TYR cc_start: 0.8132 (p90) cc_final: 0.7932 (p90) REVERT: A 915 LYS cc_start: 0.7938 (tmtp) cc_final: 0.7431 (pmtt) REVERT: A 999 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8533 (tpp) REVERT: A 1042 MET cc_start: 0.9245 (mmp) cc_final: 0.8958 (mmm) REVERT: A 1078 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8674 (mttt) REVERT: A 1102 PHE cc_start: 0.8794 (t80) cc_final: 0.8587 (t80) REVERT: A 1164 TYR cc_start: 0.8216 (t80) cc_final: 0.7725 (t80) REVERT: A 1174 TYR cc_start: 0.7510 (m-10) cc_final: 0.7202 (m-80) REVERT: A 1200 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6800 (pt0) REVERT: A 1218 VAL cc_start: 0.8269 (p) cc_final: 0.7964 (t) REVERT: A 1230 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7097 (mmtm) REVERT: A 1231 ASP cc_start: 0.8147 (t70) cc_final: 0.7869 (t0) REVERT: A 1283 ARG cc_start: 0.7949 (tpt90) cc_final: 0.7146 (tpp-160) REVERT: A 1300 PHE cc_start: 0.8533 (m-10) cc_final: 0.7402 (t80) REVERT: A 1396 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 1416 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: A 1422 LYS cc_start: 0.7954 (tttm) cc_final: 0.7479 (mtmp) REVERT: A 1450 TYR cc_start: 0.7263 (t80) cc_final: 0.7007 (t80) REVERT: A 1499 ASP cc_start: 0.7925 (t0) cc_final: 0.7293 (m-30) REVERT: A 1501 PHE cc_start: 0.8152 (m-10) cc_final: 0.7888 (m-80) REVERT: B 22 SER cc_start: 0.7970 (t) cc_final: 0.7617 (p) outliers start: 37 outliers final: 13 residues processed: 223 average time/residue: 0.5121 time to fit residues: 124.5615 Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 126 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114528 restraints weight = 13769.350| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.11 r_work: 0.3024 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11389 Z= 0.124 Angle : 0.640 11.501 15499 Z= 0.323 Chirality : 0.042 0.380 1775 Planarity : 0.004 0.052 1908 Dihedral : 7.582 75.077 1661 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.97 % Allowed : 14.14 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.22), residues: 1372 helix: -0.49 (0.17), residues: 875 sheet: -4.26 (0.73), residues: 22 loop : -2.00 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1137 TYR 0.022 0.001 TYR A1313 PHE 0.020 0.001 PHE A1279 TRP 0.024 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00264 (11374) covalent geometry : angle 0.61762 (15462) SS BOND : bond 0.00300 ( 8) SS BOND : angle 2.18108 ( 16) hydrogen bonds : bond 0.04972 ( 557) hydrogen bonds : angle 4.01167 ( 1605) link_BETA1-4 : bond 0.00683 ( 2) link_BETA1-4 : angle 4.11288 ( 6) link_NAG-ASN : bond 0.00563 ( 5) link_NAG-ASN : angle 4.23471 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7613 (mtt) cc_final: 0.7327 (mtp) REVERT: A 158 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 198 ARG cc_start: 0.6879 (mmm160) cc_final: 0.6165 (mmm-85) REVERT: A 236 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8179 (ttt180) REVERT: A 628 ASN cc_start: 0.8582 (t0) cc_final: 0.8336 (t0) REVERT: A 631 MET cc_start: 0.8454 (mmt) cc_final: 0.7928 (mtp) REVERT: A 636 LYS cc_start: 0.7795 (tmmt) cc_final: 0.6893 (mppt) REVERT: A 661 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8129 (mm-40) REVERT: A 708 ASP cc_start: 0.8570 (p0) cc_final: 0.8238 (m-30) REVERT: A 872 LEU cc_start: 0.8612 (mm) cc_final: 0.8344 (tm) REVERT: A 915 LYS cc_start: 0.8011 (tmtp) cc_final: 0.7423 (pmtt) REVERT: A 1042 MET cc_start: 0.9264 (mmp) cc_final: 0.8981 (mmm) REVERT: A 1078 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8697 (mttt) REVERT: A 1174 TYR cc_start: 0.7637 (m-10) cc_final: 0.7384 (m-80) REVERT: A 1200 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6730 (pt0) REVERT: A 1230 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7128 (mmtm) REVERT: A 1300 PHE cc_start: 0.8542 (m-10) cc_final: 0.7399 (t80) REVERT: A 1416 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: A 1422 LYS cc_start: 0.7905 (tttm) cc_final: 0.7388 (mtmp) REVERT: A 1450 TYR cc_start: 0.7262 (t80) cc_final: 0.6904 (t80) REVERT: A 1499 ASP cc_start: 0.7649 (t0) cc_final: 0.7174 (m-30) REVERT: A 1501 PHE cc_start: 0.7918 (m-10) cc_final: 0.7665 (m-10) outliers start: 34 outliers final: 12 residues processed: 205 average time/residue: 0.4916 time to fit residues: 110.0574 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.156337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113733 restraints weight = 13732.936| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.89 r_work: 0.3019 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11389 Z= 0.131 Angle : 0.633 10.906 15499 Z= 0.317 Chirality : 0.042 0.302 1775 Planarity : 0.003 0.045 1908 Dihedral : 6.839 58.108 1657 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.93 % Allowed : 14.92 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1372 helix: 0.21 (0.18), residues: 874 sheet: -4.15 (0.68), residues: 22 loop : -1.83 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1137 TYR 0.019 0.002 TYR A1313 PHE 0.022 0.001 PHE A1198 TRP 0.021 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00294 (11374) covalent geometry : angle 0.61073 (15462) SS BOND : bond 0.00436 ( 8) SS BOND : angle 1.80945 ( 16) hydrogen bonds : bond 0.04695 ( 557) hydrogen bonds : angle 3.80924 ( 1605) link_BETA1-4 : bond 0.00534 ( 2) link_BETA1-4 : angle 4.04209 ( 6) link_NAG-ASN : bond 0.00586 ( 5) link_NAG-ASN : angle 4.44799 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7670 (mtt) cc_final: 0.7361 (mtp) REVERT: A 198 ARG cc_start: 0.6827 (mmm160) cc_final: 0.6160 (mmm-85) REVERT: A 236 ARG cc_start: 0.8701 (ptm160) cc_final: 0.8307 (ttt180) REVERT: A 374 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 628 ASN cc_start: 0.8652 (t0) cc_final: 0.8356 (t0) REVERT: A 631 MET cc_start: 0.8536 (mmt) cc_final: 0.8080 (mtp) REVERT: A 636 LYS cc_start: 0.7760 (tmmt) cc_final: 0.6909 (mppt) REVERT: A 660 MET cc_start: 0.9157 (ttp) cc_final: 0.8941 (ttp) REVERT: A 665 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (mpp) REVERT: A 708 ASP cc_start: 0.8588 (p0) cc_final: 0.8259 (m-30) REVERT: A 872 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8464 (tm) REVERT: A 915 LYS cc_start: 0.8054 (tmtp) cc_final: 0.7456 (pmtt) REVERT: A 1033 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: A 1042 MET cc_start: 0.9279 (mmp) cc_final: 0.8992 (mmm) REVERT: A 1078 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8737 (mttt) REVERT: A 1083 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 1174 TYR cc_start: 0.7672 (m-10) cc_final: 0.7396 (m-80) REVERT: A 1196 MET cc_start: 0.7128 (tpt) cc_final: 0.6890 (pmm) REVERT: A 1200 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6795 (pt0) REVERT: A 1230 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7076 (mmtt) REVERT: A 1300 PHE cc_start: 0.8579 (m-10) cc_final: 0.7485 (t80) REVERT: A 1416 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: A 1422 LYS cc_start: 0.7931 (tttm) cc_final: 0.7375 (mtmp) REVERT: A 1450 TYR cc_start: 0.7249 (t80) cc_final: 0.6913 (t80) REVERT: A 1499 ASP cc_start: 0.7653 (t0) cc_final: 0.7267 (m-30) REVERT: A 1501 PHE cc_start: 0.7938 (m-10) cc_final: 0.7661 (m-10) REVERT: B 22 SER cc_start: 0.7948 (t) cc_final: 0.7367 (m) outliers start: 45 outliers final: 22 residues processed: 199 average time/residue: 0.5177 time to fit residues: 112.0396 Evaluate side-chains 185 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER 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 373 THR 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 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 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 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS A1467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112745 restraints weight = 13570.540| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.90 r_work: 0.3014 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3206 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= 0.141 Angle : 0.629 11.044 15499 Z= 0.317 Chirality : 0.043 0.361 1775 Planarity : 0.003 0.040 1908 Dihedral : 6.541 59.442 1657 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.01 % Allowed : 15.53 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1372 helix: 0.50 (0.18), residues: 876 sheet: -4.07 (0.65), residues: 22 loop : -1.69 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1137 TYR 0.018 0.002 TYR A 381 PHE 0.017 0.001 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00327 (11374) covalent geometry : angle 0.60704 (15462) SS BOND : bond 0.00439 ( 8) SS BOND : angle 1.59402 ( 16) hydrogen bonds : bond 0.04708 ( 557) hydrogen bonds : angle 3.70800 ( 1605) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 4.01231 ( 6) link_NAG-ASN : bond 0.00723 ( 5) link_NAG-ASN : angle 4.44105 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7664 (mtt) cc_final: 0.7332 (mtp) REVERT: A 198 ARG cc_start: 0.7000 (mmm160) cc_final: 0.6317 (mmm-85) REVERT: A 236 ARG cc_start: 0.8810 (ptm160) cc_final: 0.8593 (ttp80) REVERT: A 374 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 628 ASN cc_start: 0.8672 (t0) cc_final: 0.8366 (t0) REVERT: A 631 MET cc_start: 0.8506 (mmt) cc_final: 0.8103 (mtp) REVERT: A 636 LYS cc_start: 0.7841 (tmmt) cc_final: 0.6941 (mppt) REVERT: A 649 PHE cc_start: 0.8605 (m-80) cc_final: 0.8352 (m-80) REVERT: A 665 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: A 708 ASP cc_start: 0.8601 (p0) cc_final: 0.8270 (m-30) REVERT: A 915 LYS cc_start: 0.8049 (tmtp) cc_final: 0.7438 (pmtt) REVERT: A 1033 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: A 1042 MET cc_start: 0.9290 (mmp) cc_final: 0.9010 (mmm) REVERT: A 1078 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8717 (mttt) REVERT: A 1083 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 1174 TYR cc_start: 0.7695 (m-10) cc_final: 0.7439 (m-80) REVERT: A 1196 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6967 (pmm) REVERT: A 1200 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6809 (pt0) REVERT: A 1230 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7150 (mptp) REVERT: A 1300 PHE cc_start: 0.8681 (m-10) cc_final: 0.7594 (t80) REVERT: A 1416 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: A 1422 LYS cc_start: 0.7948 (tttm) cc_final: 0.7405 (mtmp) REVERT: A 1450 TYR cc_start: 0.7279 (t80) cc_final: 0.6736 (t80) REVERT: A 1499 ASP cc_start: 0.7735 (t0) cc_final: 0.7367 (m-30) REVERT: A 1501 PHE cc_start: 0.7922 (m-10) cc_final: 0.7606 (m-80) REVERT: A 1502 SER cc_start: 0.7105 (OUTLIER) cc_final: 0.6721 (m) REVERT: B 22 SER cc_start: 0.7866 (t) cc_final: 0.7323 (m) outliers start: 46 outliers final: 19 residues processed: 190 average time/residue: 0.5019 time to fit residues: 104.3644 Evaluate side-chains 183 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 218 VAL 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 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 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 1218 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.156988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114419 restraints weight = 13741.448| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.87 r_work: 0.3020 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11389 Z= 0.112 Angle : 0.590 10.497 15499 Z= 0.296 Chirality : 0.041 0.295 1775 Planarity : 0.003 0.038 1908 Dihedral : 6.344 59.428 1657 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.88 % Allowed : 16.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1372 helix: 0.75 (0.18), residues: 889 sheet: -4.07 (0.67), residues: 22 loop : -1.68 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1325 TYR 0.016 0.001 TYR A 381 PHE 0.016 0.001 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00243 (11374) covalent geometry : angle 0.57143 (15462) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.30223 ( 16) hydrogen bonds : bond 0.04183 ( 557) hydrogen bonds : angle 3.54961 ( 1605) link_BETA1-4 : bond 0.00582 ( 2) link_BETA1-4 : angle 3.92553 ( 6) link_NAG-ASN : bond 0.00627 ( 5) link_NAG-ASN : angle 3.94921 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7593 (mtt) cc_final: 0.7280 (mtp) REVERT: A 198 ARG cc_start: 0.6979 (mmm160) cc_final: 0.6297 (mmm-85) REVERT: A 213 TYR cc_start: 0.7999 (m-80) cc_final: 0.7710 (m-80) REVERT: A 628 ASN cc_start: 0.8672 (t0) cc_final: 0.8360 (t0) REVERT: A 631 MET cc_start: 0.8501 (mmt) cc_final: 0.7946 (mtp) REVERT: A 636 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7068 (mppt) REVERT: A 649 PHE cc_start: 0.8575 (m-80) cc_final: 0.8313 (m-80) REVERT: A 665 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: A 708 ASP cc_start: 0.8447 (p0) cc_final: 0.8242 (m-30) REVERT: A 915 LYS cc_start: 0.8045 (tmtp) cc_final: 0.7418 (pmtt) REVERT: A 1042 MET cc_start: 0.9270 (mmp) cc_final: 0.9011 (mmm) REVERT: A 1078 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8724 (mttt) REVERT: A 1083 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 1196 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6956 (pmm) REVERT: A 1200 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6776 (pt0) REVERT: A 1230 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7139 (mmtm) REVERT: A 1300 PHE cc_start: 0.8669 (m-10) cc_final: 0.7580 (t80) REVERT: A 1416 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: A 1422 LYS cc_start: 0.7909 (tttm) cc_final: 0.7349 (mtmp) REVERT: A 1450 TYR cc_start: 0.7219 (t80) cc_final: 0.6826 (t80) REVERT: A 1473 LYS cc_start: 0.6682 (mtmm) cc_final: 0.6372 (ptpt) REVERT: A 1499 ASP cc_start: 0.7749 (t0) cc_final: 0.7432 (m-30) REVERT: A 1501 PHE cc_start: 0.7905 (m-10) cc_final: 0.7569 (m-80) REVERT: A 1502 SER cc_start: 0.7090 (OUTLIER) cc_final: 0.6699 (m) outliers start: 33 outliers final: 14 residues processed: 181 average time/residue: 0.5373 time to fit residues: 106.2257 Evaluate side-chains 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111586 restraints weight = 13586.017| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.83 r_work: 0.2972 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11389 Z= 0.161 Angle : 0.637 10.927 15499 Z= 0.320 Chirality : 0.044 0.323 1775 Planarity : 0.003 0.042 1908 Dihedral : 6.347 59.011 1657 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.75 % Allowed : 16.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1372 helix: 0.76 (0.18), residues: 886 sheet: -3.93 (0.66), residues: 22 loop : -1.67 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1325 TYR 0.019 0.002 TYR A 381 PHE 0.022 0.002 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00385 (11374) covalent geometry : angle 0.61808 (15462) SS BOND : bond 0.00379 ( 8) SS BOND : angle 1.43751 ( 16) hydrogen bonds : bond 0.04755 ( 557) hydrogen bonds : angle 3.63854 ( 1605) link_BETA1-4 : bond 0.00535 ( 2) link_BETA1-4 : angle 3.95805 ( 6) link_NAG-ASN : bond 0.00585 ( 5) link_NAG-ASN : angle 4.18871 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6988 (mmm160) cc_final: 0.6212 (mmt90) REVERT: A 213 TYR cc_start: 0.8179 (m-80) cc_final: 0.7944 (m-80) REVERT: A 236 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8306 (ttt180) REVERT: A 374 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 628 ASN cc_start: 0.8682 (t0) cc_final: 0.8367 (t0) REVERT: A 631 MET cc_start: 0.8511 (mmt) cc_final: 0.7980 (mtp) REVERT: A 636 LYS cc_start: 0.7881 (tmmt) cc_final: 0.7094 (mppt) REVERT: A 649 PHE cc_start: 0.8577 (m-80) cc_final: 0.8324 (m-80) REVERT: A 665 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8152 (mpp) REVERT: A 708 ASP cc_start: 0.8596 (p0) cc_final: 0.8269 (m-30) REVERT: A 915 LYS cc_start: 0.8054 (tmtp) cc_final: 0.7410 (pmtt) REVERT: A 1019 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 1042 MET cc_start: 0.9300 (mmp) cc_final: 0.9018 (mmm) REVERT: A 1078 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8703 (mttt) REVERT: A 1083 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 1147 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7670 (mtpp) REVERT: A 1196 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6962 (pmm) REVERT: A 1200 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6781 (pt0) REVERT: A 1230 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7131 (mptp) REVERT: A 1300 PHE cc_start: 0.8661 (m-10) cc_final: 0.7571 (t80) REVERT: A 1416 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: A 1422 LYS cc_start: 0.7938 (tttm) cc_final: 0.7358 (mtmp) REVERT: A 1450 TYR cc_start: 0.7216 (t80) cc_final: 0.6782 (t80) REVERT: A 1499 ASP cc_start: 0.7805 (t0) cc_final: 0.7523 (m-30) REVERT: A 1502 SER cc_start: 0.7099 (OUTLIER) cc_final: 0.6690 (m) outliers start: 43 outliers final: 21 residues processed: 178 average time/residue: 0.4891 time to fit residues: 95.3499 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 236 ARG Chi-restraints excluded: chain A residue 240 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 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113788 restraints weight = 13551.102| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.98 r_work: 0.2979 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3473 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= 0.128 Angle : 0.614 10.787 15499 Z= 0.307 Chirality : 0.042 0.304 1775 Planarity : 0.003 0.041 1908 Dihedral : 6.287 58.266 1657 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.40 % Allowed : 17.36 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1372 helix: 0.88 (0.18), residues: 885 sheet: -3.82 (0.68), residues: 22 loop : -1.62 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1325 TYR 0.018 0.001 TYR A 381 PHE 0.019 0.001 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00291 (11374) covalent geometry : angle 0.59621 (15462) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.29685 ( 16) hydrogen bonds : bond 0.04462 ( 557) hydrogen bonds : angle 3.58237 ( 1605) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 3.93064 ( 6) link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 3.92022 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7718 (mtt) cc_final: 0.7410 (mtp) REVERT: A 198 ARG cc_start: 0.6983 (mmm160) cc_final: 0.6286 (mmm-85) REVERT: A 213 TYR cc_start: 0.8152 (m-80) cc_final: 0.7891 (m-80) REVERT: A 628 ASN cc_start: 0.8675 (t0) cc_final: 0.8356 (t0) REVERT: A 631 MET cc_start: 0.8517 (mmt) cc_final: 0.7990 (mtp) REVERT: A 636 LYS cc_start: 0.7880 (tmmt) cc_final: 0.7087 (mppt) REVERT: A 649 PHE cc_start: 0.8558 (m-80) cc_final: 0.8333 (m-80) REVERT: A 665 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8157 (mpp) REVERT: A 708 ASP cc_start: 0.8615 (p0) cc_final: 0.8260 (m-30) REVERT: A 1019 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 1042 MET cc_start: 0.9294 (mmp) cc_final: 0.9019 (mmm) REVERT: A 1078 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8700 (mttt) REVERT: A 1083 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 1147 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7704 (mtpp) REVERT: A 1196 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6957 (pmm) REVERT: A 1200 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6793 (pt0) REVERT: A 1230 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7121 (mptp) REVERT: A 1300 PHE cc_start: 0.8654 (m-10) cc_final: 0.7545 (t80) REVERT: A 1416 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 1422 LYS cc_start: 0.7958 (tttm) cc_final: 0.7357 (mtmp) REVERT: A 1450 TYR cc_start: 0.7257 (t80) cc_final: 0.6759 (t80) REVERT: A 1473 LYS cc_start: 0.6639 (mtmm) cc_final: 0.6213 (ptpt) REVERT: A 1499 ASP cc_start: 0.7824 (t0) cc_final: 0.7545 (m-30) REVERT: A 1502 SER cc_start: 0.7079 (OUTLIER) cc_final: 0.6677 (m) outliers start: 39 outliers final: 20 residues processed: 177 average time/residue: 0.4968 time to fit residues: 96.4875 Evaluate side-chains 173 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.153808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110646 restraints weight = 13535.984| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.88 r_work: 0.2957 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11389 Z= 0.165 Angle : 0.655 10.959 15499 Z= 0.328 Chirality : 0.044 0.343 1775 Planarity : 0.003 0.043 1908 Dihedral : 6.358 57.634 1657 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.14 % Allowed : 17.89 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1372 helix: 0.80 (0.18), residues: 888 sheet: -3.87 (0.65), residues: 22 loop : -1.60 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1325 TYR 0.019 0.002 TYR A 381 PHE 0.024 0.002 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00394 (11374) covalent geometry : angle 0.63583 (15462) SS BOND : bond 0.00368 ( 8) SS BOND : angle 1.40415 ( 16) hydrogen bonds : bond 0.04908 ( 557) hydrogen bonds : angle 3.66566 ( 1605) link_BETA1-4 : bond 0.00542 ( 2) link_BETA1-4 : angle 3.96150 ( 6) link_NAG-ASN : bond 0.00604 ( 5) link_NAG-ASN : angle 4.33935 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7797 (mtt) cc_final: 0.7471 (mtp) REVERT: A 198 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6249 (mmt90) REVERT: A 429 GLU cc_start: 0.6809 (tt0) cc_final: 0.6491 (tt0) REVERT: A 628 ASN cc_start: 0.8685 (t0) cc_final: 0.8368 (t0) REVERT: A 631 MET cc_start: 0.8497 (mmt) cc_final: 0.7998 (mtp) REVERT: A 636 LYS cc_start: 0.7901 (tmmt) cc_final: 0.7108 (mppt) REVERT: A 649 PHE cc_start: 0.8553 (m-80) cc_final: 0.8289 (m-80) REVERT: A 665 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (mpp) REVERT: A 708 ASP cc_start: 0.8600 (p0) cc_final: 0.8218 (m-30) REVERT: A 1019 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 1042 MET cc_start: 0.9324 (mmp) cc_final: 0.9046 (mmm) REVERT: A 1078 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.9008 (mttm) REVERT: A 1083 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 1147 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8035 (tttm) REVERT: A 1174 TYR cc_start: 0.7280 (m-80) cc_final: 0.6953 (m-80) REVERT: A 1196 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6974 (pmm) REVERT: A 1200 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6668 (pt0) REVERT: A 1230 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7088 (mptp) REVERT: A 1277 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6259 (ptp90) REVERT: A 1300 PHE cc_start: 0.8704 (m-10) cc_final: 0.7672 (t80) REVERT: A 1416 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: A 1422 LYS cc_start: 0.7968 (tttm) cc_final: 0.7580 (ttmp) REVERT: A 1450 TYR cc_start: 0.7298 (t80) cc_final: 0.6702 (t80) REVERT: A 1499 ASP cc_start: 0.7889 (t0) cc_final: 0.7625 (m-30) REVERT: A 1502 SER cc_start: 0.7107 (OUTLIER) cc_final: 0.6698 (m) outliers start: 36 outliers final: 18 residues processed: 171 average time/residue: 0.5043 time to fit residues: 94.6309 Evaluate side-chains 172 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 940 MET Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108527 restraints weight = 13684.011| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.76 r_work: 0.2982 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3572 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= 0.130 Angle : 0.620 10.905 15499 Z= 0.310 Chirality : 0.043 0.305 1775 Planarity : 0.003 0.040 1908 Dihedral : 6.324 58.462 1657 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.79 % Allowed : 18.32 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1372 helix: 0.99 (0.18), residues: 880 sheet: -3.79 (0.66), residues: 22 loop : -1.58 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1325 TYR 0.018 0.001 TYR A 381 PHE 0.020 0.001 PHE A1279 TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00297 (11374) covalent geometry : angle 0.60204 (15462) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.22084 ( 16) hydrogen bonds : bond 0.04479 ( 557) hydrogen bonds : angle 3.56712 ( 1605) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 3.92999 ( 6) link_NAG-ASN : bond 0.00616 ( 5) link_NAG-ASN : angle 4.05428 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7730 (mtt) cc_final: 0.7381 (mtp) REVERT: A 159 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: A 198 ARG cc_start: 0.7015 (mmm160) cc_final: 0.6210 (mmt90) REVERT: A 628 ASN cc_start: 0.8675 (t0) cc_final: 0.8355 (t0) REVERT: A 631 MET cc_start: 0.8502 (mmt) cc_final: 0.7989 (mtp) REVERT: A 636 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7154 (mppt) REVERT: A 649 PHE cc_start: 0.8517 (m-80) cc_final: 0.8273 (m-80) REVERT: A 661 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8194 (mm-40) REVERT: A 665 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: A 708 ASP cc_start: 0.8597 (p0) cc_final: 0.8244 (m-30) REVERT: A 1019 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 1042 MET cc_start: 0.9307 (mmp) cc_final: 0.9037 (mmm) REVERT: A 1078 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8999 (mttm) REVERT: A 1083 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 1147 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: A 1174 TYR cc_start: 0.7224 (m-80) cc_final: 0.6997 (m-80) REVERT: A 1200 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6794 (pt0) REVERT: A 1230 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7077 (mptp) REVERT: A 1277 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6260 (ptp90) REVERT: A 1300 PHE cc_start: 0.8753 (m-10) cc_final: 0.7696 (t80) REVERT: A 1416 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 1422 LYS cc_start: 0.7967 (tttm) cc_final: 0.7351 (mtmp) REVERT: A 1450 TYR cc_start: 0.7395 (t80) cc_final: 0.6928 (t80) REVERT: A 1473 LYS cc_start: 0.6603 (mtmm) cc_final: 0.6171 (ptpt) REVERT: A 1499 ASP cc_start: 0.7836 (t0) cc_final: 0.7608 (m-30) outliers start: 32 outliers final: 21 residues processed: 166 average time/residue: 0.5036 time to fit residues: 91.7279 Evaluate side-chains 175 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 13 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.156995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110790 restraints weight = 13637.669| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.76 r_work: 0.3014 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3741 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= 0.107 Angle : 0.590 11.036 15499 Z= 0.295 Chirality : 0.042 0.290 1775 Planarity : 0.003 0.038 1908 Dihedral : 6.186 59.104 1657 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.62 % Allowed : 18.50 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1372 helix: 1.20 (0.18), residues: 878 sheet: -3.67 (0.70), residues: 22 loop : -1.45 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 846 TYR 0.017 0.001 TYR A1447 PHE 0.016 0.001 PHE A1279 TRP 0.021 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00227 (11374) covalent geometry : angle 0.57412 (15462) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.01585 ( 16) hydrogen bonds : bond 0.04000 ( 557) hydrogen bonds : angle 3.46632 ( 1605) link_BETA1-4 : bond 0.00503 ( 2) link_BETA1-4 : angle 3.83743 ( 6) link_NAG-ASN : bond 0.00643 ( 5) link_NAG-ASN : angle 3.63107 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.05 seconds wall clock time: 84 minutes 57.17 seconds (5097.17 seconds total)