Starting phenix.real_space_refine on Sun May 3 05:04:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xsy_6770/05_2026/5xsy_6770.map" } resolution = 4.0 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6982 2.51 5 N 1669 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9057 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1110} Chain breaks: 6 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 6, 'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10634 At special positions: 0 Unit cell: (137.814, 131.124, 125.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 1892 8.00 N 1669 7.00 C 6982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 324 " distance=2.00 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=1.98 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS A 725 " distance=2.15 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 766 " distance=1.95 Simple disulfide: pdb=" SG CYS A1158 " - pdb=" SG CYS A1178 " distance=2.38 Simple disulfide: pdb=" SG CYS A1522 " - pdb=" SG CYS A1537 " distance=1.94 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 47 " distance=1.96 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 124 " distance=2.21 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 BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG C 1 " - " ASN A 317 " " NAG D 1 " - " ASN A1174 " " NAG E 1 " - " ASN A1160 " " NAG F 1 " - " ASN B 113 " " NAG G 1 " - " ASN B 117 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 410.8 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 4 sheets defined 71.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.645A pdb=" N ALA A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.638A pdb=" N PHE A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 169 removed outlier: 3.588A pdb=" N GLU A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.622A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.603A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 264 removed outlier: 4.206A pdb=" N ILE A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 242 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.950A pdb=" N THR A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.012A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.700A pdb=" N MET A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.722A pdb=" N ILE A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 431 removed outlier: 3.593A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.801A pdb=" N VAL A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 removed outlier: 4.035A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 618 removed outlier: 3.926A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 removed outlier: 4.051A pdb=" N GLN A 628 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 648 removed outlier: 3.685A pdb=" N SER A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.587A pdb=" N LEU A 656 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 657 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 659 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 660 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 662 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.715A pdb=" N LEU A 667 " --> pdb=" O ARG A 663 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.801A pdb=" N LYS A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 717 removed outlier: 3.801A pdb=" N THR A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS A 712 " --> pdb=" O GLN A 708 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 734 through 747 removed outlier: 3.623A pdb=" N SER A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 4.428A pdb=" N ASP A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 759 " --> pdb=" O TRP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 792 removed outlier: 3.758A pdb=" N CYS A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 999 removed outlier: 3.570A pdb=" N ASN A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 997 " --> pdb=" O CYS A 993 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1018 Processing helix chain 'A' and resid 1019 through 1020 No H-bonds generated for 'chain 'A' and resid 1019 through 1020' Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1028 through 1064 removed outlier: 3.515A pdb=" N ASP A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1040 " --> pdb=" O TYR A1036 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A1053 " --> pdb=" O MET A1049 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N LYS A1059 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A1060 " --> pdb=" O TYR A1056 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A1064 " --> pdb=" O ARG A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.107A pdb=" N ASP A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A1071 " --> pdb=" O CYS A1067 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A1074 " --> pdb=" O ASP A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.922A pdb=" N ARG A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1112 removed outlier: 4.043A pdb=" N ARG A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1152 removed outlier: 3.686A pdb=" N LYS A1116 " --> pdb=" O PHE A1112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1117 " --> pdb=" O GLU A1113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Proline residue: A1127 - end of helix removed outlier: 3.725A pdb=" N ASN A1131 " --> pdb=" O PRO A1127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A1143 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1149 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 4.012A pdb=" N LEU A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1209 Processing helix chain 'A' and resid 1214 through 1224 removed outlier: 3.837A pdb=" N ILE A1218 " --> pdb=" O GLY A1214 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1240 through 1251 removed outlier: 4.355A pdb=" N PHE A1244 " --> pdb=" O MET A1240 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1273 removed outlier: 4.006A pdb=" N ASP A1265 " --> pdb=" O GLY A1261 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A1271 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1272 " --> pdb=" O ASN A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1298 removed outlier: 3.844A pdb=" N LYS A1287 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A1294 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1321 Processing helix chain 'A' and resid 1321 through 1339 removed outlier: 3.720A pdb=" N ASP A1325 " --> pdb=" O GLN A1321 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A1326 " --> pdb=" O PRO A1322 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A1327 " --> pdb=" O PHE A1323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1329 " --> pdb=" O ASP A1325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1342 No H-bonds generated for 'chain 'A' and resid 1340 through 1342' Processing helix chain 'A' and resid 1347 through 1381 removed outlier: 3.531A pdb=" N PHE A1365 " --> pdb=" O PHE A1361 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1406 removed outlier: 3.923A pdb=" N VAL A1394 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A1398 " --> pdb=" O VAL A1394 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1400 " --> pdb=" O SER A1396 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1401 " --> pdb=" O ILE A1397 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1403 " --> pdb=" O GLY A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1421 removed outlier: 3.796A pdb=" N VAL A1418 " --> pdb=" O THR A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.562A pdb=" N ARG A1426 " --> pdb=" O ARG A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1435 removed outlier: 3.515A pdb=" N ALA A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A1435 " --> pdb=" O ILE A1431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1430 through 1435' Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 4.192A pdb=" N LEU A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1444 " --> pdb=" O LEU A1440 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1474 removed outlier: 3.687A pdb=" N ILE A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A1472 " --> pdb=" O PHE A1468 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A1474 " --> pdb=" O MET A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1503 removed outlier: 3.552A pdb=" N SER A1494 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A1495 " --> pdb=" O PHE A1491 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A1496 " --> pdb=" O GLY A1492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A1500 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A1501 " --> pdb=" O CYS A1497 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A1503 " --> pdb=" O PHE A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1516 removed outlier: 3.518A pdb=" N LEU A1512 " --> pdb=" O ASP A1508 " (cutoff:3.500A) Proline residue: A1513 - end of helix Processing helix chain 'A' and resid 1539 through 1570 removed outlier: 3.719A pdb=" N THR A1545 " --> pdb=" O GLY A1541 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1546 " --> pdb=" O LYS A1542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1552 " --> pdb=" O CYS A1548 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1559 " --> pdb=" O PHE A1555 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU A1568 " --> pdb=" O ALA A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1578 removed outlier: 4.148A pdb=" N GLU A1575 " --> pdb=" O GLY A1571 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 160 through 191 removed outlier: 3.876A pdb=" N TYR B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 273 Processing sheet with id=AA2, first strand: chain 'A' and resid 1157 through 1160 Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.355A pdb=" N ALA B 34 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 126 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 143 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 75 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 45 552 hydrogen bonds defined for protein. 1593 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: 1.44 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1903 1.32 - 1.45: 2916 1.45 - 1.57: 5904 1.57 - 1.69: 1 1.69 - 1.81: 150 Bond restraints: 10874 Sorted by residual: bond pdb=" CA GLU B 136 " pdb=" C GLU B 136 " ideal model delta sigma weight residual 1.523 1.681 -0.159 1.28e-02 6.10e+03 1.54e+02 bond pdb=" C GLY A1518 " pdb=" N PRO A1519 " ideal model delta sigma weight residual 1.329 1.403 -0.073 1.18e-02 7.18e+03 3.87e+01 bond pdb=" N PRO A1520 " pdb=" CD PRO A1520 " ideal model delta sigma weight residual 1.474 1.554 -0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 1.473 1.550 -0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" N PRO A1519 " pdb=" CD PRO A1519 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.63: 14585 5.63 - 11.26: 134 11.26 - 16.90: 19 16.90 - 22.53: 3 22.53 - 28.16: 4 Bond angle restraints: 14745 Sorted by residual: angle pdb=" N LEU B 130 " pdb=" CA LEU B 130 " pdb=" C LEU B 130 " ideal model delta sigma weight residual 109.46 81.30 28.16 1.66e+00 3.63e-01 2.88e+02 angle pdb=" C TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta sigma weight residual 109.48 83.04 26.44 1.68e+00 3.54e-01 2.48e+02 angle pdb=" C LEU B 130 " pdb=" CA LEU B 130 " pdb=" CB LEU B 130 " ideal model delta sigma weight residual 109.80 134.63 -24.83 1.64e+00 3.72e-01 2.29e+02 angle pdb=" C SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta sigma weight residual 109.38 82.35 27.03 2.03e+00 2.43e-01 1.77e+02 angle pdb=" C MET B 83 " pdb=" CA MET B 83 " pdb=" CB MET B 83 " ideal model delta sigma weight residual 110.19 92.25 17.94 1.62e+00 3.81e-01 1.23e+02 ... (remaining 14740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 6041 23.10 - 46.21: 355 46.21 - 69.31: 100 69.31 - 92.41: 35 92.41 - 115.52: 29 Dihedral angle restraints: 6560 sinusoidal: 2729 harmonic: 3831 Sorted by residual: dihedral pdb=" C SER B 76 " pdb=" N SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta harmonic sigma weight residual -122.60 -94.64 -27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR B 110 " pdb=" N TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta harmonic sigma weight residual -122.60 -95.89 -26.71 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -168.70 82.70 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1482 0.095 - 0.190: 217 0.190 - 0.285: 39 0.285 - 0.380: 8 0.380 - 0.475: 5 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA ALA A1573 " pdb=" N ALA A1573 " pdb=" C ALA A1573 " pdb=" CB ALA A1573 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA GLU B 136 " pdb=" N GLU B 136 " pdb=" C GLU B 136 " pdb=" CB GLU B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA GLU A 586 " pdb=" N GLU A 586 " pdb=" C GLU A 586 " pdb=" CB GLU A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 1748 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 213 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 268 " -1.014 9.50e-02 1.11e+02 4.55e-01 1.25e+02 pdb=" NE ARG A 268 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 268 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 268 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 268 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 336 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO A 337 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.064 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 27 2.37 - 3.00: 6081 3.00 - 3.63: 15491 3.63 - 4.27: 22949 4.27 - 4.90: 36672 Nonbonded interactions: 81220 Sorted by model distance: nonbonded pdb=" CG1 VAL A1016 " pdb=" CD1 LEU A1034 " model vdw 1.735 3.880 nonbonded pdb=" O GLN A1346 " pdb=" OG SER A1347 " model vdw 1.915 3.040 nonbonded pdb=" O LEU A 620 " pdb=" O ASP A 621 " model vdw 1.993 3.040 nonbonded pdb=" O THR A 629 " pdb=" CG2 ILE A 632 " model vdw 2.137 3.460 nonbonded pdb=" O ASP A1483 " pdb=" OD1 ASP A1484 " model vdw 2.176 3.040 ... (remaining 81215 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 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.780 Find NCS groups from input model: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.012 0.354 10898 Z= 0.594 Angle : 1.790 55.668 14809 Z= 1.024 Chirality : 0.077 0.475 1751 Planarity : 0.017 0.482 1789 Dihedral : 18.877 115.517 4062 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 1.54 % Allowed : 6.64 % Favored : 91.82 % Rotamer: Outliers : 7.45 % Allowed : 8.35 % Favored : 84.20 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.53 (0.20), residues: 1296 helix: -1.95 (0.17), residues: 784 sheet: -2.65 (0.52), residues: 68 loop : -2.74 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1027 TYR 0.035 0.004 TYR A 714 PHE 0.031 0.003 PHE B 63 TRP 0.055 0.003 TRP A1215 HIS 0.022 0.004 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.01094 (10874) covalent geometry : angle 1.55406 (14745) SS BOND : bond 0.15513 ( 8) SS BOND : angle 26.36939 ( 16) hydrogen bonds : bond 0.30611 ( 552) hydrogen bonds : angle 9.92518 ( 1593) link_BETA1-3 : bond 0.00488 ( 1) link_BETA1-3 : angle 1.61106 ( 3) link_BETA1-4 : bond 0.01626 ( 9) link_BETA1-4 : angle 3.71734 ( 27) link_BETA1-6 : bond 0.00583 ( 1) link_BETA1-6 : angle 1.04308 ( 3) link_NAG-ASN : bond 0.01304 ( 5) link_NAG-ASN : angle 4.65672 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 428 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5322 (ptt180) REVERT: A 129 MET cc_start: 0.8068 (ttm) cc_final: 0.7512 (tmm) REVERT: A 133 PHE cc_start: 0.7602 (t80) cc_final: 0.7374 (t80) REVERT: A 139 MET cc_start: 0.8688 (tpp) cc_final: 0.8264 (mtt) REVERT: A 194 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6167 (mmp) REVERT: A 232 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6816 (tpt170) REVERT: A 250 PHE cc_start: 0.8270 (t80) cc_final: 0.7235 (m-10) REVERT: A 255 PHE cc_start: 0.9090 (m-80) cc_final: 0.8886 (m-80) REVERT: A 266 ASN cc_start: 0.9021 (m-40) cc_final: 0.8093 (m110) REVERT: A 268 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7643 (ttm170) REVERT: A 298 GLU cc_start: 0.9374 (tt0) cc_final: 0.8655 (pt0) REVERT: A 372 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7376 (ttm170) REVERT: A 386 ILE cc_start: 0.9043 (mm) cc_final: 0.8799 (mt) REVERT: A 405 TYR cc_start: 0.6925 (m-10) cc_final: 0.6689 (m-10) REVERT: A 590 MET cc_start: 0.7093 (mtp) cc_final: 0.6780 (mmm) REVERT: A 647 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2823 (tp) REVERT: A 679 LYS cc_start: 0.8843 (tttt) cc_final: 0.8530 (tppt) REVERT: A 717 TYR cc_start: 0.8402 (m-80) cc_final: 0.8170 (m-10) REVERT: A 725 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6976 (t) REVERT: A 726 GLU cc_start: 0.8725 (tt0) cc_final: 0.7512 (tm-30) REVERT: A 732 MET cc_start: 0.8640 (mmt) cc_final: 0.8430 (mmm) REVERT: A 771 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7010 (ttt) REVERT: A 999 HIS cc_start: 0.7853 (t-90) cc_final: 0.7477 (t-170) REVERT: A 1002 PHE cc_start: 0.8329 (t80) cc_final: 0.8111 (t80) REVERT: A 1059 LYS cc_start: 0.7619 (tttp) cc_final: 0.7179 (mptt) REVERT: A 1064 ASP cc_start: 0.7845 (m-30) cc_final: 0.7549 (t0) REVERT: A 1067 CYS cc_start: 0.8568 (m) cc_final: 0.8224 (m) REVERT: A 1071 PHE cc_start: 0.8683 (t80) cc_final: 0.8454 (t80) REVERT: A 1110 SER cc_start: 0.8704 (t) cc_final: 0.8450 (m) REVERT: A 1120 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7897 (ttm110) REVERT: A 1165 GLU cc_start: 0.8720 (tt0) cc_final: 0.8117 (mm-30) REVERT: A 1192 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7894 (tm) REVERT: A 1231 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 1240 MET cc_start: 0.9257 (mmp) cc_final: 0.8768 (tpp) REVERT: A 1288 TYR cc_start: 0.8283 (m-10) cc_final: 0.7851 (m-10) REVERT: A 1294 LYS cc_start: 0.6906 (mttt) cc_final: 0.6479 (mmmt) REVERT: A 1325 ASP cc_start: 0.8607 (m-30) cc_final: 0.8362 (t0) REVERT: A 1326 ILE cc_start: 0.8148 (mt) cc_final: 0.7777 (mt) REVERT: A 1329 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: A 1340 MET cc_start: 0.9063 (mtp) cc_final: 0.8601 (ttt) REVERT: A 1368 GLU cc_start: 0.8882 (tt0) cc_final: 0.8590 (mm-30) REVERT: A 1377 ARG cc_start: 0.3999 (tpt170) cc_final: 0.3649 (mmt-90) REVERT: A 1398 ILE cc_start: 0.8453 (mt) cc_final: 0.8251 (mt) REVERT: A 1419 ILE cc_start: 0.9035 (mm) cc_final: 0.8788 (mm) REVERT: A 1446 MET cc_start: 0.8183 (ttt) cc_final: 0.7971 (ttm) REVERT: A 1468 PHE cc_start: 0.8617 (t80) cc_final: 0.8351 (t80) REVERT: A 1499 PHE cc_start: 0.8835 (t80) cc_final: 0.8602 (t80) REVERT: A 1523 ASP cc_start: 0.7661 (m-30) cc_final: 0.7260 (t70) REVERT: B 27 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8370 (pt0) REVERT: B 28 VAL cc_start: 0.8886 (p) cc_final: 0.8599 (p) REVERT: B 38 HIS cc_start: 0.8160 (t-90) cc_final: 0.7861 (t-90) REVERT: B 49 MET cc_start: 0.8393 (ttt) cc_final: 0.8066 (ttp) REVERT: B 62 TRP cc_start: 0.8178 (m100) cc_final: 0.7414 (m-10) REVERT: B 72 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9034 (t) REVERT: B 75 TYR cc_start: 0.8686 (t80) cc_final: 0.8178 (t80) REVERT: B 81 THR cc_start: 0.9063 (m) cc_final: 0.8854 (m) REVERT: B 94 ASN cc_start: 0.8316 (t0) cc_final: 0.7872 (t0) REVERT: B 114 VAL cc_start: 0.9382 (t) cc_final: 0.8937 (p) REVERT: B 121 THR cc_start: 0.7770 (m) cc_final: 0.7538 (m) REVERT: B 125 TYR cc_start: 0.7672 (t80) cc_final: 0.6963 (t80) REVERT: B 155 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8155 (mtt180) REVERT: B 163 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: B 165 MET cc_start: 0.8112 (mmm) cc_final: 0.7350 (tmm) REVERT: B 177 LEU cc_start: 0.8981 (mt) cc_final: 0.8745 (mt) REVERT: B 183 TYR cc_start: 0.8035 (t80) cc_final: 0.7558 (t80) REVERT: B 194 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7278 (mp0) outliers start: 83 outliers final: 28 residues processed: 477 average time/residue: 0.0977 time to fit residues: 65.5666 Evaluate side-chains 351 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1329 MET Chi-restraints excluded: chain A residue 1364 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1534 ARG Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 346 ASN A 560 HIS A 628 GLN A 631 ASN A 690 ASN A1270 GLN B 73 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110945 restraints weight = 21902.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113585 restraints weight = 12011.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115304 restraints weight = 7946.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116287 restraints weight = 6077.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117030 restraints weight = 5203.815| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10898 Z= 0.197 Angle : 0.891 13.812 14809 Z= 0.462 Chirality : 0.048 0.261 1751 Planarity : 0.006 0.080 1789 Dihedral : 15.809 89.064 1828 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.02 % Favored : 93.29 % Rotamer: Outliers : 6.55 % Allowed : 17.68 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.21), residues: 1296 helix: -1.16 (0.16), residues: 834 sheet: -2.60 (0.57), residues: 66 loop : -2.69 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 213 TYR 0.025 0.002 TYR B 110 PHE 0.024 0.002 PHE A 177 TRP 0.033 0.002 TRP A1215 HIS 0.008 0.002 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00420 (10874) covalent geometry : angle 0.86642 (14745) SS BOND : bond 0.01361 ( 8) SS BOND : angle 4.50218 ( 16) hydrogen bonds : bond 0.06124 ( 552) hydrogen bonds : angle 5.58969 ( 1593) link_BETA1-3 : bond 0.01288 ( 1) link_BETA1-3 : angle 1.80198 ( 3) link_BETA1-4 : bond 0.00806 ( 9) link_BETA1-4 : angle 2.66345 ( 27) link_BETA1-6 : bond 0.00388 ( 1) link_BETA1-6 : angle 2.57647 ( 3) link_NAG-ASN : bond 0.00483 ( 5) link_NAG-ASN : angle 3.16610 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 359 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6909 (mtt90) cc_final: 0.5576 (ptt180) REVERT: A 129 MET cc_start: 0.7741 (ttm) cc_final: 0.7239 (tmm) REVERT: A 139 MET cc_start: 0.8362 (tpp) cc_final: 0.8108 (mtt) REVERT: A 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8254 (ttmt) REVERT: A 232 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6777 (tpt90) REVERT: A 240 GLN cc_start: 0.7559 (tp40) cc_final: 0.7187 (tm-30) REVERT: A 250 PHE cc_start: 0.8118 (t80) cc_final: 0.7427 (m-10) REVERT: A 266 ASN cc_start: 0.8935 (m-40) cc_final: 0.8180 (m110) REVERT: A 300 GLU cc_start: 0.8443 (tt0) cc_final: 0.8197 (tt0) REVERT: A 324 CYS cc_start: 0.5525 (t) cc_final: 0.5312 (t) REVERT: A 382 PHE cc_start: 0.8916 (m-10) cc_final: 0.8701 (m-80) REVERT: A 384 MET cc_start: 0.8380 (mmp) cc_final: 0.8110 (mmm) REVERT: A 407 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7254 (tt0) REVERT: A 690 ASN cc_start: 0.8611 (t0) cc_final: 0.8305 (t0) REVERT: A 771 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6174 (ttt) REVERT: A 1009 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7778 (mmt) REVERT: A 1061 TYR cc_start: 0.8214 (t80) cc_final: 0.7745 (t80) REVERT: A 1071 PHE cc_start: 0.8578 (t80) cc_final: 0.8279 (t80) REVERT: A 1156 TYR cc_start: 0.8242 (m-80) cc_final: 0.7714 (m-80) REVERT: A 1203 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8710 (t80) REVERT: A 1240 MET cc_start: 0.8229 (mmp) cc_final: 0.7946 (tpp) REVERT: A 1294 LYS cc_start: 0.7333 (mttt) cc_final: 0.7114 (mmmt) REVERT: A 1325 ASP cc_start: 0.8311 (m-30) cc_final: 0.7814 (t0) REVERT: A 1326 ILE cc_start: 0.8171 (mt) cc_final: 0.7931 (mt) REVERT: A 1368 GLU cc_start: 0.8934 (tt0) cc_final: 0.8652 (mm-30) REVERT: A 1377 ARG cc_start: 0.4961 (tpt170) cc_final: 0.4568 (mmt-90) REVERT: A 1394 VAL cc_start: 0.9441 (m) cc_final: 0.9238 (p) REVERT: B 27 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: B 96 MET cc_start: 0.7133 (ttm) cc_final: 0.6740 (ttp) REVERT: B 110 TYR cc_start: 0.8095 (m-80) cc_final: 0.7692 (m-10) REVERT: B 183 TYR cc_start: 0.7654 (t80) cc_final: 0.7233 (t80) outliers start: 73 outliers final: 29 residues processed: 399 average time/residue: 0.0885 time to fit residues: 50.6323 Evaluate side-chains 319 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1537 CYS Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110202 restraints weight = 22012.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112839 restraints weight = 11956.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114511 restraints weight = 7862.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115411 restraints weight = 6038.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116164 restraints weight = 5209.220| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10898 Z= 0.163 Angle : 0.773 9.612 14809 Z= 0.398 Chirality : 0.045 0.231 1751 Planarity : 0.005 0.098 1789 Dihedral : 11.699 89.260 1772 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.56 % Favored : 92.90 % Rotamer: Outliers : 6.73 % Allowed : 20.29 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.22), residues: 1296 helix: -0.66 (0.17), residues: 839 sheet: -1.87 (0.62), residues: 54 loop : -2.59 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 663 TYR 0.021 0.002 TYR A 625 PHE 0.022 0.002 PHE B 102 TRP 0.020 0.002 TRP A1507 HIS 0.018 0.003 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00354 (10874) covalent geometry : angle 0.75621 (14745) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.99143 ( 16) hydrogen bonds : bond 0.04775 ( 552) hydrogen bonds : angle 4.96396 ( 1593) link_BETA1-3 : bond 0.01287 ( 1) link_BETA1-3 : angle 2.48172 ( 3) link_BETA1-4 : bond 0.00687 ( 9) link_BETA1-4 : angle 2.68664 ( 27) link_BETA1-6 : bond 0.00055 ( 1) link_BETA1-6 : angle 3.01620 ( 3) link_NAG-ASN : bond 0.00408 ( 5) link_NAG-ASN : angle 2.65375 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 307 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6700 (mtt90) cc_final: 0.5482 (ptt-90) REVERT: A 129 MET cc_start: 0.7921 (ttm) cc_final: 0.7335 (tmm) REVERT: A 139 MET cc_start: 0.8374 (tpp) cc_final: 0.8128 (mtt) REVERT: A 228 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8236 (ttmt) REVERT: A 250 PHE cc_start: 0.8153 (t80) cc_final: 0.7485 (m-10) REVERT: A 266 ASN cc_start: 0.8963 (m-40) cc_final: 0.8378 (m-40) REVERT: A 305 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8185 (p90) REVERT: A 324 CYS cc_start: 0.5730 (t) cc_final: 0.5376 (t) REVERT: A 335 ARG cc_start: 0.9152 (tmm-80) cc_final: 0.8866 (ptm160) REVERT: A 343 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 369 MET cc_start: 0.8856 (mtm) cc_final: 0.8636 (mtm) REVERT: A 382 PHE cc_start: 0.8911 (m-10) cc_final: 0.8687 (m-80) REVERT: A 625 TYR cc_start: 0.4958 (t80) cc_final: 0.4657 (t80) REVERT: A 771 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.5975 (ttt) REVERT: A 1009 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7747 (mmt) REVERT: A 1061 TYR cc_start: 0.7952 (t80) cc_final: 0.7610 (t80) REVERT: A 1203 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8829 (t80) REVERT: A 1258 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 1292 MET cc_start: 0.6494 (mmp) cc_final: 0.5225 (mtt) REVERT: A 1325 ASP cc_start: 0.8328 (m-30) cc_final: 0.7858 (t0) REVERT: A 1336 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: A 1361 PHE cc_start: 0.8851 (m-80) cc_final: 0.8199 (m-80) REVERT: A 1368 GLU cc_start: 0.8949 (tt0) cc_final: 0.8668 (mm-30) REVERT: A 1377 ARG cc_start: 0.4782 (tpt170) cc_final: 0.4452 (mmt-90) REVERT: A 1448 LEU cc_start: 0.9334 (tt) cc_final: 0.9107 (tp) REVERT: B 96 MET cc_start: 0.7605 (ttm) cc_final: 0.7185 (ttm) REVERT: B 166 MET cc_start: 0.8987 (tmm) cc_final: 0.8597 (tmm) REVERT: B 167 TYR cc_start: 0.8231 (m-80) cc_final: 0.7836 (m-80) REVERT: B 183 TYR cc_start: 0.7735 (t80) cc_final: 0.7455 (t80) outliers start: 75 outliers final: 44 residues processed: 351 average time/residue: 0.0743 time to fit residues: 39.0030 Evaluate side-chains 323 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 HIS A1335 ASN A1528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108343 restraints weight = 22380.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110907 restraints weight = 11987.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112565 restraints weight = 7878.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113446 restraints weight = 6006.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114182 restraints weight = 5164.246| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10898 Z= 0.174 Angle : 0.745 11.264 14809 Z= 0.383 Chirality : 0.045 0.253 1751 Planarity : 0.005 0.115 1789 Dihedral : 10.108 86.171 1765 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.56 % Favored : 92.90 % Rotamer: Outliers : 6.01 % Allowed : 23.07 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -1.66 (0.22), residues: 1296 helix: -0.33 (0.17), residues: 840 sheet: -1.78 (0.60), residues: 58 loop : -2.51 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1429 TYR 0.015 0.002 TYR B 122 PHE 0.022 0.002 PHE B 102 TRP 0.014 0.001 TRP A1507 HIS 0.008 0.002 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00391 (10874) covalent geometry : angle 0.72677 (14745) SS BOND : bond 0.00932 ( 8) SS BOND : angle 2.55485 ( 16) hydrogen bonds : bond 0.04294 ( 552) hydrogen bonds : angle 4.78884 ( 1593) link_BETA1-3 : bond 0.01240 ( 1) link_BETA1-3 : angle 2.48881 ( 3) link_BETA1-4 : bond 0.00585 ( 9) link_BETA1-4 : angle 2.59089 ( 27) link_BETA1-6 : bond 0.00361 ( 1) link_BETA1-6 : angle 2.85111 ( 3) link_NAG-ASN : bond 0.00426 ( 5) link_NAG-ASN : angle 2.60377 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6762 (mtt90) cc_final: 0.5491 (ptt180) REVERT: A 129 MET cc_start: 0.7916 (ttm) cc_final: 0.7379 (tmm) REVERT: A 139 MET cc_start: 0.8421 (tpp) cc_final: 0.7990 (mtt) REVERT: A 228 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8283 (mtmm) REVERT: A 232 ARG cc_start: 0.7097 (ttt180) cc_final: 0.6340 (tpt90) REVERT: A 250 PHE cc_start: 0.8236 (t80) cc_final: 0.7627 (m-10) REVERT: A 266 ASN cc_start: 0.9035 (m-40) cc_final: 0.8344 (m-40) REVERT: A 305 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8162 (p90) REVERT: A 324 CYS cc_start: 0.5862 (t) cc_final: 0.5515 (t) REVERT: A 335 ARG cc_start: 0.9191 (tmm-80) cc_final: 0.8912 (ptm160) REVERT: A 343 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7752 (p0) REVERT: A 382 PHE cc_start: 0.8928 (m-10) cc_final: 0.8588 (m-80) REVERT: A 625 TYR cc_start: 0.4803 (t80) cc_final: 0.4578 (t80) REVERT: A 759 GLU cc_start: 0.8174 (tt0) cc_final: 0.7933 (tt0) REVERT: A 771 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6189 (ttt) REVERT: A 1009 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (mmt) REVERT: A 1203 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8860 (t80) REVERT: A 1258 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 1292 MET cc_start: 0.6506 (mmp) cc_final: 0.5351 (mtt) REVERT: A 1325 ASP cc_start: 0.8212 (m-30) cc_final: 0.7822 (t0) REVERT: A 1368 GLU cc_start: 0.8923 (tt0) cc_final: 0.8656 (mm-30) REVERT: A 1377 ARG cc_start: 0.4572 (tpt170) cc_final: 0.4031 (mmt-90) REVERT: A 1475 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.6479 (p90) REVERT: A 1508 ASP cc_start: 0.8077 (p0) cc_final: 0.7868 (p0) REVERT: B 96 MET cc_start: 0.7747 (ttm) cc_final: 0.7511 (ttm) REVERT: B 125 TYR cc_start: 0.6611 (t80) cc_final: 0.6110 (t80) REVERT: B 130 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7100 (pp) REVERT: B 166 MET cc_start: 0.9072 (tmm) cc_final: 0.8631 (tmm) outliers start: 67 outliers final: 49 residues processed: 339 average time/residue: 0.0810 time to fit residues: 40.7507 Evaluate side-chains 341 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1210 SER Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1317 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108701 restraints weight = 22454.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111150 restraints weight = 12417.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112727 restraints weight = 8414.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113571 restraints weight = 6562.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114253 restraints weight = 5717.515| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10898 Z= 0.187 Angle : 0.728 9.329 14809 Z= 0.377 Chirality : 0.044 0.218 1751 Planarity : 0.005 0.103 1789 Dihedral : 9.318 84.887 1765 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.40 % Favored : 93.06 % Rotamer: Outliers : 6.82 % Allowed : 23.70 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % 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: -1.38 (0.23), residues: 1296 helix: -0.09 (0.17), residues: 845 sheet: -1.69 (0.60), residues: 60 loop : -2.49 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 123 TYR 0.021 0.002 TYR A1316 PHE 0.021 0.002 PHE A1499 TRP 0.012 0.001 TRP A1507 HIS 0.008 0.002 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00429 (10874) covalent geometry : angle 0.71445 (14745) SS BOND : bond 0.00561 ( 8) SS BOND : angle 1.64600 ( 16) hydrogen bonds : bond 0.04097 ( 552) hydrogen bonds : angle 4.74461 ( 1593) link_BETA1-3 : bond 0.01151 ( 1) link_BETA1-3 : angle 2.34061 ( 3) link_BETA1-4 : bond 0.00525 ( 9) link_BETA1-4 : angle 2.35816 ( 27) link_BETA1-6 : bond 0.00043 ( 1) link_BETA1-6 : angle 2.56634 ( 3) link_NAG-ASN : bond 0.00435 ( 5) link_NAG-ASN : angle 2.51081 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6856 (mtt90) cc_final: 0.5477 (ptt180) REVERT: A 129 MET cc_start: 0.7862 (ttm) cc_final: 0.7323 (tmm) REVERT: A 250 PHE cc_start: 0.8240 (t80) cc_final: 0.7626 (m-10) REVERT: A 305 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8140 (p90) REVERT: A 324 CYS cc_start: 0.5995 (t) cc_final: 0.5703 (t) REVERT: A 335 ARG cc_start: 0.9183 (tmm-80) cc_final: 0.8660 (ptm160) REVERT: A 382 PHE cc_start: 0.8935 (m-10) cc_final: 0.8658 (m-80) REVERT: A 702 PHE cc_start: 0.9432 (m-80) cc_final: 0.9222 (m-80) REVERT: A 759 GLU cc_start: 0.8221 (tt0) cc_final: 0.7967 (tt0) REVERT: A 771 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6223 (ttt) REVERT: A 993 CYS cc_start: 0.8482 (m) cc_final: 0.8178 (m) REVERT: A 1009 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7865 (mmt) REVERT: A 1048 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: A 1070 ASP cc_start: 0.7150 (t70) cc_final: 0.6918 (t70) REVERT: A 1203 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8865 (t80) REVERT: A 1258 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8768 (tp) REVERT: A 1292 MET cc_start: 0.6565 (mmp) cc_final: 0.5425 (mtt) REVERT: A 1325 ASP cc_start: 0.8216 (m-30) cc_final: 0.7847 (t0) REVERT: A 1368 GLU cc_start: 0.8915 (tt0) cc_final: 0.8688 (mm-30) REVERT: A 1377 ARG cc_start: 0.4453 (tpt170) cc_final: 0.3862 (mmt-90) REVERT: A 1456 LEU cc_start: 0.9311 (tp) cc_final: 0.9011 (tp) REVERT: A 1475 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.6549 (p90) REVERT: A 1485 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8957 (mp) REVERT: B 125 TYR cc_start: 0.6532 (t80) cc_final: 0.6091 (t80) REVERT: B 130 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7228 (pp) REVERT: B 148 ASN cc_start: 0.8619 (p0) cc_final: 0.8276 (p0) REVERT: B 163 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 166 MET cc_start: 0.9068 (tmm) cc_final: 0.8646 (tmm) outliers start: 76 outliers final: 53 residues processed: 340 average time/residue: 0.0813 time to fit residues: 41.6549 Evaluate side-chains 341 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1048 GLU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1210 SER Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1329 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109572 restraints weight = 22782.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112124 restraints weight = 12521.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113681 restraints weight = 8397.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114688 restraints weight = 6580.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115197 restraints weight = 5671.940| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10898 Z= 0.158 Angle : 0.719 13.207 14809 Z= 0.368 Chirality : 0.043 0.213 1751 Planarity : 0.005 0.101 1789 Dihedral : 8.508 83.303 1759 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.48 % Favored : 92.98 % Rotamer: Outliers : 6.64 % Allowed : 25.22 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -1.19 (0.23), residues: 1296 helix: 0.06 (0.18), residues: 847 sheet: -1.60 (0.61), residues: 60 loop : -2.45 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1157 TYR 0.021 0.002 TYR A 625 PHE 0.021 0.002 PHE B 102 TRP 0.013 0.001 TRP A1507 HIS 0.007 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00357 (10874) covalent geometry : angle 0.70793 (14745) SS BOND : bond 0.00444 ( 8) SS BOND : angle 1.30940 ( 16) hydrogen bonds : bond 0.03921 ( 552) hydrogen bonds : angle 4.63540 ( 1593) link_BETA1-3 : bond 0.00972 ( 1) link_BETA1-3 : angle 2.14304 ( 3) link_BETA1-4 : bond 0.00549 ( 9) link_BETA1-4 : angle 2.20487 ( 27) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 2.51786 ( 3) link_NAG-ASN : bond 0.00369 ( 5) link_NAG-ASN : angle 2.34588 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6817 (mtt90) cc_final: 0.5350 (ptt180) REVERT: A 129 MET cc_start: 0.7871 (ttm) cc_final: 0.7390 (tmm) REVERT: A 166 LYS cc_start: 0.9006 (mttt) cc_final: 0.8785 (mmmt) REVERT: A 250 PHE cc_start: 0.8289 (t80) cc_final: 0.7594 (m-10) REVERT: A 305 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8068 (p90) REVERT: A 324 CYS cc_start: 0.5965 (t) cc_final: 0.5762 (t) REVERT: A 335 ARG cc_start: 0.9155 (tmm-80) cc_final: 0.8604 (ptm160) REVERT: A 382 PHE cc_start: 0.8867 (m-10) cc_final: 0.8530 (m-80) REVERT: A 398 LEU cc_start: 0.9369 (mt) cc_final: 0.9155 (mt) REVERT: A 563 MET cc_start: 0.6756 (tmm) cc_final: 0.6424 (tmm) REVERT: A 702 PHE cc_start: 0.9406 (m-80) cc_final: 0.9164 (m-80) REVERT: A 754 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8831 (ttm) REVERT: A 759 GLU cc_start: 0.8212 (tt0) cc_final: 0.7905 (tt0) REVERT: A 771 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6141 (ttt) REVERT: A 993 CYS cc_start: 0.8423 (m) cc_final: 0.8118 (m) REVERT: A 1009 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7872 (mmt) REVERT: A 1203 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8824 (t80) REVERT: A 1240 MET cc_start: 0.8591 (mmp) cc_final: 0.8254 (tpp) REVERT: A 1258 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8738 (tp) REVERT: A 1281 MET cc_start: 0.8596 (mpp) cc_final: 0.8319 (mpp) REVERT: A 1292 MET cc_start: 0.6596 (mmp) cc_final: 0.5587 (mtt) REVERT: A 1325 ASP cc_start: 0.8205 (m-30) cc_final: 0.7857 (t0) REVERT: A 1368 GLU cc_start: 0.8899 (tt0) cc_final: 0.8670 (mm-30) REVERT: A 1377 ARG cc_start: 0.4469 (tpt170) cc_final: 0.3812 (mmt-90) REVERT: A 1451 LEU cc_start: 0.9333 (tp) cc_final: 0.9101 (tt) REVERT: A 1456 LEU cc_start: 0.9270 (tp) cc_final: 0.8917 (tp) REVERT: A 1475 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.6439 (p90) REVERT: A 1548 CYS cc_start: 0.8320 (m) cc_final: 0.7857 (m) REVERT: B 125 TYR cc_start: 0.6497 (t80) cc_final: 0.6064 (t80) REVERT: B 130 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7090 (pp) REVERT: B 148 ASN cc_start: 0.8682 (p0) cc_final: 0.8385 (p0) REVERT: B 166 MET cc_start: 0.9138 (tmm) cc_final: 0.8732 (tmm) outliers start: 74 outliers final: 52 residues processed: 345 average time/residue: 0.0765 time to fit residues: 40.1707 Evaluate side-chains 340 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1210 SER Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1329 MET Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 0.0470 chunk 30 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 395 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111406 restraints weight = 22275.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113916 restraints weight = 12252.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115501 restraints weight = 8191.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116393 restraints weight = 6385.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117007 restraints weight = 5550.299| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10898 Z= 0.140 Angle : 0.713 11.259 14809 Z= 0.362 Chirality : 0.043 0.218 1751 Planarity : 0.004 0.098 1789 Dihedral : 7.873 82.103 1755 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.17 % Favored : 93.29 % Rotamer: Outliers : 6.28 % Allowed : 26.12 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % 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: -1.02 (0.23), residues: 1296 helix: 0.21 (0.18), residues: 847 sheet: -1.63 (0.59), residues: 64 loop : -2.42 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 123 TYR 0.019 0.001 TYR A 625 PHE 0.021 0.001 PHE B 102 TRP 0.016 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00309 (10874) covalent geometry : angle 0.70177 (14745) SS BOND : bond 0.00535 ( 8) SS BOND : angle 1.45353 ( 16) hydrogen bonds : bond 0.03758 ( 552) hydrogen bonds : angle 4.50746 ( 1593) link_BETA1-3 : bond 0.00983 ( 1) link_BETA1-3 : angle 1.99941 ( 3) link_BETA1-4 : bond 0.00527 ( 9) link_BETA1-4 : angle 2.10782 ( 27) link_BETA1-6 : bond 0.00387 ( 1) link_BETA1-6 : angle 2.35102 ( 3) link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 2.25133 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 298 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6833 (mtt90) cc_final: 0.5313 (ptt180) REVERT: A 129 MET cc_start: 0.8007 (ttm) cc_final: 0.7391 (tmm) REVERT: A 166 LYS cc_start: 0.8947 (mttt) cc_final: 0.8717 (mmmm) REVERT: A 335 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8589 (ptm160) REVERT: A 369 MET cc_start: 0.8872 (mtp) cc_final: 0.8471 (mtm) REVERT: A 398 LEU cc_start: 0.9343 (mt) cc_final: 0.9099 (mt) REVERT: A 563 MET cc_start: 0.6833 (tmm) cc_final: 0.6539 (tmm) REVERT: A 661 LEU cc_start: 0.9208 (mt) cc_final: 0.8979 (mp) REVERT: A 702 PHE cc_start: 0.9367 (m-80) cc_final: 0.9102 (m-80) REVERT: A 759 GLU cc_start: 0.8190 (tt0) cc_final: 0.7891 (tt0) REVERT: A 771 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6126 (ttt) REVERT: A 779 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8377 (tm) REVERT: A 993 CYS cc_start: 0.8381 (m) cc_final: 0.8102 (m) REVERT: A 1009 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7881 (mmt) REVERT: A 1048 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: A 1203 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8745 (t80) REVERT: A 1240 MET cc_start: 0.8619 (mmp) cc_final: 0.8325 (tpp) REVERT: A 1258 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (tp) REVERT: A 1292 MET cc_start: 0.6623 (mmp) cc_final: 0.5600 (mtt) REVERT: A 1325 ASP cc_start: 0.8263 (m-30) cc_final: 0.7907 (t0) REVERT: A 1377 ARG cc_start: 0.4110 (tpt170) cc_final: 0.3364 (mmt-90) REVERT: A 1456 LEU cc_start: 0.9252 (tp) cc_final: 0.8872 (tp) REVERT: A 1468 PHE cc_start: 0.7950 (t80) cc_final: 0.7721 (t80) REVERT: A 1475 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.6240 (p90) REVERT: A 1523 ASP cc_start: 0.8090 (t70) cc_final: 0.7832 (t70) REVERT: A 1539 ASN cc_start: 0.7825 (t0) cc_final: 0.7564 (m-40) REVERT: A 1548 CYS cc_start: 0.8310 (m) cc_final: 0.7823 (m) REVERT: B 125 TYR cc_start: 0.6470 (t80) cc_final: 0.5992 (t80) REVERT: B 130 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6728 (pp) REVERT: B 148 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8471 (p0) REVERT: B 166 MET cc_start: 0.9154 (tmm) cc_final: 0.8735 (tmm) outliers start: 70 outliers final: 52 residues processed: 338 average time/residue: 0.0785 time to fit residues: 39.9436 Evaluate side-chains 340 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1048 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1317 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112627 restraints weight = 22256.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115178 restraints weight = 12268.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116810 restraints weight = 8229.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117667 restraints weight = 6398.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118371 restraints weight = 5571.104| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10898 Z= 0.137 Angle : 0.730 12.827 14809 Z= 0.369 Chirality : 0.044 0.227 1751 Planarity : 0.004 0.096 1789 Dihedral : 7.449 80.775 1753 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 6.01 % Allowed : 27.11 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -0.85 (0.23), residues: 1296 helix: 0.27 (0.18), residues: 847 sheet: -0.95 (0.69), residues: 51 loop : -2.25 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 123 TYR 0.016 0.001 TYR A 625 PHE 0.024 0.001 PHE A 161 TRP 0.015 0.001 TRP A1507 HIS 0.004 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00297 (10874) covalent geometry : angle 0.71928 (14745) SS BOND : bond 0.00494 ( 8) SS BOND : angle 1.58225 ( 16) hydrogen bonds : bond 0.03665 ( 552) hydrogen bonds : angle 4.45412 ( 1593) link_BETA1-3 : bond 0.01220 ( 1) link_BETA1-3 : angle 2.06002 ( 3) link_BETA1-4 : bond 0.00437 ( 9) link_BETA1-4 : angle 2.06739 ( 27) link_BETA1-6 : bond 0.00514 ( 1) link_BETA1-6 : angle 2.17824 ( 3) link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 2.21441 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 292 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6810 (mtt90) cc_final: 0.5270 (ptt180) REVERT: A 129 MET cc_start: 0.7926 (ttm) cc_final: 0.7342 (tmm) REVERT: A 166 LYS cc_start: 0.8938 (mttt) cc_final: 0.8702 (mmmm) REVERT: A 266 ASN cc_start: 0.8987 (m-40) cc_final: 0.8363 (m-40) REVERT: A 398 LEU cc_start: 0.9275 (mt) cc_final: 0.9004 (mt) REVERT: A 563 MET cc_start: 0.6827 (tmm) cc_final: 0.6580 (tmm) REVERT: A 702 PHE cc_start: 0.9342 (m-80) cc_final: 0.9047 (m-80) REVERT: A 771 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6344 (ttt) REVERT: A 779 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8370 (tm) REVERT: A 993 CYS cc_start: 0.8364 (m) cc_final: 0.8110 (m) REVERT: A 1009 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7885 (mmt) REVERT: A 1048 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: A 1203 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 1240 MET cc_start: 0.8609 (mmp) cc_final: 0.8311 (tpp) REVERT: A 1258 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 1292 MET cc_start: 0.6611 (mmp) cc_final: 0.5617 (mtt) REVERT: A 1325 ASP cc_start: 0.8278 (m-30) cc_final: 0.7891 (t0) REVERT: A 1377 ARG cc_start: 0.4175 (tpt170) cc_final: 0.3424 (mmt-90) REVERT: A 1456 LEU cc_start: 0.9239 (tp) cc_final: 0.8878 (tp) REVERT: A 1475 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6146 (p90) REVERT: A 1539 ASN cc_start: 0.7720 (t0) cc_final: 0.7479 (m-40) REVERT: A 1548 CYS cc_start: 0.8281 (m) cc_final: 0.7794 (m) REVERT: B 125 TYR cc_start: 0.6464 (t80) cc_final: 0.5918 (t80) REVERT: B 148 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8510 (p0) REVERT: B 166 MET cc_start: 0.9161 (tmm) cc_final: 0.8835 (tmm) REVERT: B 167 TYR cc_start: 0.8234 (m-80) cc_final: 0.7657 (m-80) outliers start: 67 outliers final: 46 residues processed: 333 average time/residue: 0.0803 time to fit residues: 40.5129 Evaluate side-chains 339 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1048 GLU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1317 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1472 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113040 restraints weight = 22352.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115579 restraints weight = 12261.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117209 restraints weight = 8217.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117854 restraints weight = 6401.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118510 restraints weight = 5675.405| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10898 Z= 0.143 Angle : 0.748 12.786 14809 Z= 0.375 Chirality : 0.044 0.244 1751 Planarity : 0.005 0.097 1789 Dihedral : 7.270 80.923 1753 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.86 % Favored : 93.60 % Rotamer: Outliers : 5.30 % Allowed : 27.56 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1296 helix: 0.41 (0.18), residues: 842 sheet: -0.78 (0.72), residues: 49 loop : -2.04 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.016 0.001 TYR B 110 PHE 0.025 0.001 PHE A 161 TRP 0.014 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00320 (10874) covalent geometry : angle 0.73765 (14745) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.68005 ( 16) hydrogen bonds : bond 0.03627 ( 552) hydrogen bonds : angle 4.48616 ( 1593) link_BETA1-3 : bond 0.00902 ( 1) link_BETA1-3 : angle 1.91512 ( 3) link_BETA1-4 : bond 0.00458 ( 9) link_BETA1-4 : angle 2.02793 ( 27) link_BETA1-6 : bond 0.00290 ( 1) link_BETA1-6 : angle 1.93378 ( 3) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 2.23304 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 294 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6832 (mtt90) cc_final: 0.5278 (ptt180) REVERT: A 129 MET cc_start: 0.7901 (ttm) cc_final: 0.7387 (tmm) REVERT: A 166 LYS cc_start: 0.8948 (mttt) cc_final: 0.8696 (mmmm) REVERT: A 266 ASN cc_start: 0.8920 (m-40) cc_final: 0.8343 (m-40) REVERT: A 343 ASN cc_start: 0.8117 (p0) cc_final: 0.7481 (p0) REVERT: A 369 MET cc_start: 0.8909 (mtp) cc_final: 0.8536 (mtm) REVERT: A 391 PHE cc_start: 0.9131 (t80) cc_final: 0.8759 (t80) REVERT: A 398 LEU cc_start: 0.9280 (mt) cc_final: 0.9047 (mt) REVERT: A 563 MET cc_start: 0.6801 (tmm) cc_final: 0.6564 (tmm) REVERT: A 771 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6340 (ttt) REVERT: A 779 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8360 (tm) REVERT: A 993 CYS cc_start: 0.8290 (m) cc_final: 0.8033 (m) REVERT: A 1009 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7873 (mmt) REVERT: A 1048 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: A 1144 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 1201 MET cc_start: 0.8236 (tpp) cc_final: 0.8033 (tpp) REVERT: A 1203 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8716 (t80) REVERT: A 1240 MET cc_start: 0.8554 (mmp) cc_final: 0.8279 (tpp) REVERT: A 1258 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 1292 MET cc_start: 0.6727 (mmp) cc_final: 0.5733 (mtt) REVERT: A 1325 ASP cc_start: 0.8268 (m-30) cc_final: 0.7969 (t0) REVERT: A 1456 LEU cc_start: 0.9248 (tp) cc_final: 0.8867 (tp) REVERT: A 1475 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.6336 (p90) REVERT: A 1487 ASN cc_start: 0.9305 (p0) cc_final: 0.9087 (p0) REVERT: A 1534 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7580 (mtm180) REVERT: A 1539 ASN cc_start: 0.7704 (t0) cc_final: 0.7482 (m-40) REVERT: A 1548 CYS cc_start: 0.8282 (m) cc_final: 0.7814 (m) REVERT: B 125 TYR cc_start: 0.6848 (t80) cc_final: 0.5878 (t80) REVERT: B 148 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8609 (p0) REVERT: B 166 MET cc_start: 0.9178 (tmm) cc_final: 0.8842 (tmm) REVERT: B 167 TYR cc_start: 0.8219 (m-80) cc_final: 0.7635 (m-80) outliers start: 59 outliers final: 43 residues processed: 328 average time/residue: 0.0757 time to fit residues: 38.2337 Evaluate side-chains 338 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1048 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1317 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 130 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112363 restraints weight = 22548.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114878 restraints weight = 12306.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116517 restraints weight = 8239.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117371 restraints weight = 6385.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118085 restraints weight = 5555.557| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10898 Z= 0.145 Angle : 0.741 11.463 14809 Z= 0.373 Chirality : 0.044 0.241 1751 Planarity : 0.005 0.094 1789 Dihedral : 7.125 80.680 1753 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.33 % Favored : 93.13 % Rotamer: Outliers : 4.85 % Allowed : 28.82 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -0.46 (0.23), residues: 1296 helix: 0.53 (0.18), residues: 843 sheet: -0.49 (0.70), residues: 51 loop : -2.02 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.018 0.001 TYR B 125 PHE 0.025 0.001 PHE A 161 TRP 0.013 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00333 (10874) covalent geometry : angle 0.73130 (14745) SS BOND : bond 0.00374 ( 8) SS BOND : angle 1.53007 ( 16) hydrogen bonds : bond 0.03607 ( 552) hydrogen bonds : angle 4.49837 ( 1593) link_BETA1-3 : bond 0.00872 ( 1) link_BETA1-3 : angle 1.84944 ( 3) link_BETA1-4 : bond 0.00505 ( 9) link_BETA1-4 : angle 2.00108 ( 27) link_BETA1-6 : bond 0.00384 ( 1) link_BETA1-6 : angle 1.73783 ( 3) link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 2.23201 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6888 (mtt90) cc_final: 0.5247 (ptt180) REVERT: A 129 MET cc_start: 0.7935 (ttm) cc_final: 0.7411 (tmm) REVERT: A 166 LYS cc_start: 0.9014 (mttt) cc_final: 0.8701 (mmmm) REVERT: A 266 ASN cc_start: 0.8937 (m-40) cc_final: 0.8343 (m-40) REVERT: A 343 ASN cc_start: 0.7956 (p0) cc_final: 0.7363 (p0) REVERT: A 344 TYR cc_start: 0.8706 (m-80) cc_final: 0.8349 (m-80) REVERT: A 369 MET cc_start: 0.9029 (mtp) cc_final: 0.8706 (mtm) REVERT: A 391 PHE cc_start: 0.9122 (t80) cc_final: 0.8850 (t80) REVERT: A 393 LEU cc_start: 0.8496 (mt) cc_final: 0.8272 (mp) REVERT: A 398 LEU cc_start: 0.9281 (mt) cc_final: 0.9049 (mt) REVERT: A 582 PHE cc_start: 0.8739 (t80) cc_final: 0.8252 (t80) REVERT: A 634 ASP cc_start: 0.8707 (m-30) cc_final: 0.8130 (p0) REVERT: A 702 PHE cc_start: 0.9358 (m-80) cc_final: 0.9057 (m-80) REVERT: A 771 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6248 (ttt) REVERT: A 779 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7955 (tm) REVERT: A 993 CYS cc_start: 0.8413 (m) cc_final: 0.8117 (m) REVERT: A 1144 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 1195 ASN cc_start: 0.8487 (p0) cc_final: 0.8270 (p0) REVERT: A 1201 MET cc_start: 0.8251 (tpp) cc_final: 0.7976 (tpp) REVERT: A 1203 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8690 (t80) REVERT: A 1240 MET cc_start: 0.8588 (mmp) cc_final: 0.8272 (tpp) REVERT: A 1258 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 1292 MET cc_start: 0.6787 (mmp) cc_final: 0.5790 (mtt) REVERT: A 1325 ASP cc_start: 0.8273 (m-30) cc_final: 0.7969 (t0) REVERT: A 1475 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.6441 (p90) REVERT: A 1487 ASN cc_start: 0.9325 (p0) cc_final: 0.9054 (p0) REVERT: A 1534 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7515 (mtp180) REVERT: A 1539 ASN cc_start: 0.7735 (t0) cc_final: 0.7489 (m-40) REVERT: A 1548 CYS cc_start: 0.8353 (m) cc_final: 0.7844 (m) REVERT: B 64 MET cc_start: 0.8160 (tpp) cc_final: 0.7720 (tpt) REVERT: B 148 ASN cc_start: 0.8862 (p0) cc_final: 0.8608 (p0) REVERT: B 166 MET cc_start: 0.9182 (tmm) cc_final: 0.8884 (tmm) outliers start: 54 outliers final: 39 residues processed: 323 average time/residue: 0.0817 time to fit residues: 39.9360 Evaluate side-chains 330 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1317 ASP Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.0050 chunk 101 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113171 restraints weight = 22636.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115978 restraints weight = 11697.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117706 restraints weight = 7486.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118833 restraints weight = 5660.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119281 restraints weight = 4772.748| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10898 Z= 0.137 Angle : 0.733 11.440 14809 Z= 0.367 Chirality : 0.044 0.263 1751 Planarity : 0.004 0.094 1789 Dihedral : 6.976 79.230 1753 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.94 % Favored : 93.52 % Rotamer: Outliers : 4.13 % Allowed : 29.26 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -0.30 (0.23), residues: 1296 helix: 0.67 (0.18), residues: 840 sheet: -0.42 (0.70), residues: 51 loop : -1.97 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.018 0.001 TYR B 110 PHE 0.028 0.001 PHE A1499 TRP 0.014 0.001 TRP A1507 HIS 0.005 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00308 (10874) covalent geometry : angle 0.72397 (14745) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.35058 ( 16) hydrogen bonds : bond 0.03568 ( 552) hydrogen bonds : angle 4.46207 ( 1593) link_BETA1-3 : bond 0.00886 ( 1) link_BETA1-3 : angle 1.74439 ( 3) link_BETA1-4 : bond 0.00522 ( 9) link_BETA1-4 : angle 1.96593 ( 27) link_BETA1-6 : bond 0.00420 ( 1) link_BETA1-6 : angle 1.66526 ( 3) link_NAG-ASN : bond 0.00347 ( 5) link_NAG-ASN : angle 2.12762 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.41 seconds wall clock time: 32 minutes 39.18 seconds (1959.18 seconds total)