Starting phenix.real_space_refine on Fri Sep 11 18:32:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xsy_6770/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.cif" model { file = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xsy_6770/09_2026/5xsy_6770.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.46, 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: 0.97 Conformation dependent library (CDL) restraints added in 391.1 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: 0.32 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: 1.71 Time building geometry restraints manager: 1.28 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 - 17.73: 5612 17.73 - 35.47: 460 35.47 - 53.20: 119 53.20 - 70.94: 38 70.94 - 88.67: 7 Dihedral angle restraints: 6236 sinusoidal: 2405 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 6233 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 15.038 88.675 3738 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/Z covalent geometry : bond 0.01094 / 0.56 (10874) covalent geometry : angle 1.55406 / 0.94 (14745) SS BOND : bond 0.15513 / 7.54 ( 8) SS BOND : angle 26.36939 / 15.90 ( 16) hydrogen bonds : bond 0.30611 / 20.15 ( 552) hydrogen bonds : angle 9.92518 / 6.91 ( 1593) link_BETA1-3 : bond 0.00488 / 0.33 ( 1) link_BETA1-3 : angle 1.61106 / 1.38 ( 3) link_BETA1-4 : bond 0.01626 / 0.49 ( 9) link_BETA1-4 : angle 3.71734 / 2.07 ( 27) link_BETA1-6 : bond 0.00583 / 0.39 ( 1) link_BETA1-6 : angle 1.04308 / 0.69 ( 3) link_NAG-ASN : bond 0.01304 / 0.72 ( 5) link_NAG-ASN : angle 4.65672 / 2.88 ( 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 : 0.310 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: 0.1029 time to fit residues: 69.3273 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 : 0.478 ------------------------------------------------------------------------------- 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... ** 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 = 0.3672 r_free = 0.3672 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110872 restraints weight = 21914.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113530 restraints weight = 11938.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115214 restraints weight = 7911.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116197 restraints weight = 6079.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116936 restraints weight = 5203.362| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3259 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= 0.193 Angle : 0.878 13.282 14809 Z= 0.459 Chirality : 0.047 0.283 1751 Planarity : 0.006 0.089 1789 Dihedral : 10.729 89.210 1504 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.86 % Favored : 93.44 % Rotamer: Outliers : 6.55 % Allowed : 17.59 % Favored : 75.85 % 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: -2.72 (0.21), residues: 1296 helix: -1.20 (0.16), residues: 840 sheet: -2.58 (0.57), residues: 66 loop : -2.73 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1157 TYR 0.021 0.002 TYR B 110 PHE 0.024 0.002 PHE A 177 TRP 0.032 0.002 TRP A1215 HIS 0.009 0.002 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (10874) covalent geometry : angle 0.85368 / 0.45 (14745) SS BOND : bond 0.01166 / 0.58 ( 8) SS BOND : angle 4.86296 / 3.29 ( 16) hydrogen bonds : bond 0.06135 / 3.95 ( 552) hydrogen bonds : angle 5.58760 / 3.85 ( 1593) link_BETA1-3 : bond 0.00819 / 0.55 ( 1) link_BETA1-3 : angle 1.38495 / 0.99 ( 3) link_BETA1-4 : bond 0.00701 / 0.31 ( 9) link_BETA1-4 : angle 2.15484 / 1.31 ( 27) link_BETA1-6 : bond 0.00333 / 0.22 ( 1) link_BETA1-6 : angle 1.89895 / 1.50 ( 3) link_NAG-ASN : bond 0.00501 / 0.27 ( 5) link_NAG-ASN : angle 3.24415 / 1.93 ( 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 435 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 362 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6905 (mtt90) cc_final: 0.5572 (ptt180) REVERT: A 129 MET cc_start: 0.7699 (ttm) cc_final: 0.7189 (tmm) REVERT: A 139 MET cc_start: 0.8362 (tpp) cc_final: 0.8099 (mtt) REVERT: A 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8257 (ttmt) REVERT: A 232 ARG cc_start: 0.7194 (ttt180) cc_final: 0.6781 (tpt90) REVERT: A 240 GLN cc_start: 0.7477 (tp40) cc_final: 0.7229 (tm-30) REVERT: A 250 PHE cc_start: 0.8123 (t80) cc_final: 0.7407 (m-10) REVERT: A 266 ASN cc_start: 0.8935 (m-40) cc_final: 0.8178 (m110) REVERT: A 300 GLU cc_start: 0.8437 (tt0) cc_final: 0.8195 (tt0) REVERT: A 384 MET cc_start: 0.8380 (mmp) cc_final: 0.8113 (mmm) REVERT: A 407 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7249 (tt0) REVERT: A 690 ASN cc_start: 0.8616 (t0) cc_final: 0.8305 (t0) REVERT: A 771 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6177 (ttt) REVERT: A 1009 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7772 (mmt) REVERT: A 1061 TYR cc_start: 0.8217 (t80) cc_final: 0.7745 (t80) REVERT: A 1071 PHE cc_start: 0.8589 (t80) cc_final: 0.8296 (t80) REVERT: A 1120 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7924 (ttm110) REVERT: A 1156 TYR cc_start: 0.8242 (m-80) cc_final: 0.7701 (m-80) REVERT: A 1203 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8694 (t80) REVERT: A 1240 MET cc_start: 0.8232 (mmp) cc_final: 0.7946 (tpp) REVERT: A 1294 LYS cc_start: 0.7344 (mttt) cc_final: 0.7129 (mmmt) REVERT: A 1325 ASP cc_start: 0.8315 (m-30) cc_final: 0.7816 (t0) REVERT: A 1326 ILE cc_start: 0.8169 (mt) cc_final: 0.7938 (mt) REVERT: A 1368 GLU cc_start: 0.8933 (tt0) cc_final: 0.8648 (mm-30) REVERT: A 1377 ARG cc_start: 0.4915 (tpt170) cc_final: 0.4593 (mmt-90) REVERT: A 1394 VAL cc_start: 0.9436 (m) cc_final: 0.9230 (p) REVERT: B 27 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 96 MET cc_start: 0.7174 (ttm) cc_final: 0.6809 (ttp) REVERT: B 110 TYR cc_start: 0.8093 (m-80) cc_final: 0.7719 (m-10) REVERT: B 164 VAL cc_start: 0.9240 (t) cc_final: 0.9030 (p) REVERT: B 165 MET cc_start: 0.7893 (mmm) cc_final: 0.7685 (tmm) REVERT: B 166 MET cc_start: 0.8766 (tmm) cc_final: 0.8540 (tmm) REVERT: B 183 TYR cc_start: 0.7657 (t80) cc_final: 0.7238 (t80) outliers start: 73 outliers final: 31 residues processed: 399 average time/residue: 0.0933 time to fit residues: 54.2726 Evaluate side-chains 325 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 1120 ARG Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1359 VAL 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 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: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109030 restraints weight = 22058.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111608 restraints weight = 11976.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113287 restraints weight = 7943.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114193 restraints weight = 6107.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114933 restraints weight = 5265.905| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10898 Z= 0.173 Angle : 0.759 9.537 14809 Z= 0.397 Chirality : 0.044 0.230 1751 Planarity : 0.005 0.101 1789 Dihedral : 8.474 89.157 1452 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.48 % Favored : 92.98 % Rotamer: Outliers : 7.36 % Allowed : 20.29 % Favored : 72.35 % 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: -2.06 (0.22), residues: 1296 helix: -0.70 (0.17), residues: 841 sheet: -1.86 (0.63), residues: 54 loop : -2.53 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 663 TYR 0.020 0.002 TYR A 625 PHE 0.021 0.002 PHE B 102 TRP 0.019 0.001 TRP A1507 HIS 0.017 0.003 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10874) covalent geometry : angle 0.74577 / 0.39 (14745) SS BOND : bond 0.00656 / 0.39 ( 8) SS BOND : angle 2.04365 / 1.27 ( 16) hydrogen bonds : bond 0.04803 / 3.09 ( 552) hydrogen bonds : angle 4.97797 / 3.45 ( 1593) link_BETA1-3 : bond 0.00776 / 0.52 ( 1) link_BETA1-3 : angle 1.63990 / 1.32 ( 3) link_BETA1-4 : bond 0.00538 / 0.29 ( 9) link_BETA1-4 : angle 2.16782 / 1.32 ( 27) link_BETA1-6 : bond 0.00116 / 0.08 ( 1) link_BETA1-6 : angle 1.75531 / 1.34 ( 3) link_NAG-ASN : bond 0.00442 / 0.24 ( 5) link_NAG-ASN : angle 2.79413 / 1.67 ( 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 393 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 311 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6723 (mtt90) cc_final: 0.5482 (ptt-90) REVERT: A 129 MET cc_start: 0.7956 (ttm) cc_final: 0.7380 (tmm) REVERT: A 166 LYS cc_start: 0.9081 (mttt) cc_final: 0.8679 (mtpt) REVERT: A 228 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8267 (ttmt) REVERT: A 250 PHE cc_start: 0.8176 (t80) cc_final: 0.7500 (m-10) REVERT: A 266 ASN cc_start: 0.8995 (m-40) cc_final: 0.8359 (m-40) REVERT: A 305 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8183 (p90) REVERT: A 335 ARG cc_start: 0.9149 (tmm-80) cc_final: 0.8842 (ptm160) REVERT: A 343 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 590 MET cc_start: 0.6822 (mmm) cc_final: 0.6617 (mmm) REVERT: A 625 TYR cc_start: 0.5108 (t80) cc_final: 0.4821 (t80) REVERT: A 771 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.5983 (ttt) REVERT: A 1009 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7771 (mmt) REVERT: A 1061 TYR cc_start: 0.7982 (t80) cc_final: 0.7612 (t80) REVERT: A 1120 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (ttm110) REVERT: A 1203 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8836 (t80) REVERT: A 1258 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 1292 MET cc_start: 0.6503 (mmp) cc_final: 0.5237 (mtt) REVERT: A 1325 ASP cc_start: 0.8328 (m-30) cc_final: 0.7875 (t0) REVERT: A 1336 MET cc_start: 0.8473 (ttt) cc_final: 0.8113 (tmm) REVERT: A 1361 PHE cc_start: 0.8883 (m-80) cc_final: 0.8301 (m-80) REVERT: A 1368 GLU cc_start: 0.8942 (tt0) cc_final: 0.8671 (mm-30) REVERT: A 1377 ARG cc_start: 0.4809 (tpt170) cc_final: 0.4457 (mmt-90) REVERT: B 96 MET cc_start: 0.7680 (ttm) cc_final: 0.7241 (ttm) REVERT: B 164 VAL cc_start: 0.9325 (t) cc_final: 0.9014 (p) REVERT: B 165 MET cc_start: 0.7870 (mmm) cc_final: 0.7660 (tmm) REVERT: B 166 MET cc_start: 0.8945 (tmm) cc_final: 0.8623 (tmm) REVERT: B 167 TYR cc_start: 0.8384 (m-80) cc_final: 0.8001 (m-80) REVERT: B 183 TYR cc_start: 0.7645 (t80) cc_final: 0.7368 (t80) outliers start: 82 outliers final: 47 residues processed: 360 average time/residue: 0.0854 time to fit residues: 45.8172 Evaluate side-chains 326 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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 1120 ARG 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 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 36 VAL 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: 0.6980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A 999 HIS A1335 ASN A1528 ASN B 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108767 restraints weight = 22503.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111437 restraints weight = 11816.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113161 restraints weight = 7691.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114104 restraints weight = 5864.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114761 restraints weight = 5034.297| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10898 Z= 0.181 Angle : 0.753 10.979 14809 Z= 0.391 Chirality : 0.044 0.252 1751 Planarity : 0.005 0.118 1789 Dihedral : 8.024 85.627 1445 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.64 % Favored : 92.82 % Rotamer: Outliers : 6.91 % Allowed : 22.44 % Favored : 70.65 % 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: -1.68 (0.22), residues: 1296 helix: -0.35 (0.17), residues: 840 sheet: -1.87 (0.63), residues: 54 loop : -2.51 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1429 TYR 0.015 0.002 TYR B 122 PHE 0.021 0.002 PHE B 102 TRP 0.016 0.001 TRP A1507 HIS 0.008 0.002 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (10874) covalent geometry : angle 0.73848 / 0.39 (14745) SS BOND : bond 0.00884 / 0.45 ( 8) SS BOND : angle 2.58556 / 1.69 ( 16) hydrogen bonds : bond 0.04358 / 2.80 ( 552) hydrogen bonds : angle 4.82272 / 3.32 ( 1593) link_BETA1-3 : bond 0.00818 / 0.55 ( 1) link_BETA1-3 : angle 1.71423 / 1.37 ( 3) link_BETA1-4 : bond 0.00493 / 0.26 ( 9) link_BETA1-4 : angle 2.07245 / 1.26 ( 27) link_BETA1-6 : bond 0.00121 / 0.08 ( 1) link_BETA1-6 : angle 1.79485 / 1.37 ( 3) link_NAG-ASN : bond 0.00470 / 0.27 ( 5) link_NAG-ASN : angle 2.73212 / 1.62 ( 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 372 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 295 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6781 (mtt90) cc_final: 0.5458 (ptt180) REVERT: A 129 MET cc_start: 0.7913 (ttm) cc_final: 0.7354 (tmm) REVERT: A 166 LYS cc_start: 0.9078 (mttt) cc_final: 0.8807 (mmmt) REVERT: A 228 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8211 (mtmm) REVERT: A 232 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6404 (tpt90) REVERT: A 250 PHE cc_start: 0.8251 (t80) cc_final: 0.7662 (m-10) REVERT: A 305 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8145 (p90) REVERT: A 335 ARG cc_start: 0.9184 (tmm-80) cc_final: 0.8900 (ptm160) REVERT: A 625 TYR cc_start: 0.4835 (t80) cc_final: 0.4564 (t80) REVERT: A 759 GLU cc_start: 0.8180 (tt0) cc_final: 0.7950 (tt0) REVERT: A 771 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6327 (ttt) REVERT: A 1009 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7844 (mmt) REVERT: A 1203 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8890 (t80) REVERT: A 1258 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8754 (tp) REVERT: A 1281 MET cc_start: 0.8679 (mpp) cc_final: 0.8409 (mpp) REVERT: A 1292 MET cc_start: 0.6533 (mmp) cc_final: 0.5353 (mtt) REVERT: A 1316 TYR cc_start: 0.7172 (t80) cc_final: 0.6914 (t80) REVERT: A 1325 ASP cc_start: 0.8237 (m-30) cc_final: 0.7828 (t0) REVERT: A 1368 GLU cc_start: 0.8973 (tt0) cc_final: 0.8673 (mm-30) REVERT: A 1377 ARG cc_start: 0.4543 (tpt170) cc_final: 0.3916 (mmt-90) REVERT: A 1475 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.6584 (p90) REVERT: B 96 MET cc_start: 0.7731 (ttm) cc_final: 0.7494 (ttm) REVERT: B 125 TYR cc_start: 0.6551 (t80) cc_final: 0.6057 (t80) REVERT: B 130 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7219 (pp) REVERT: B 140 ASN cc_start: 0.7955 (p0) cc_final: 0.7565 (p0) REVERT: B 164 VAL cc_start: 0.9319 (t) cc_final: 0.8997 (p) REVERT: B 166 MET cc_start: 0.9021 (tmm) cc_final: 0.8644 (tmm) REVERT: B 167 TYR cc_start: 0.8406 (m-80) cc_final: 0.7796 (m-80) outliers start: 77 outliers final: 53 residues processed: 344 average time/residue: 0.0904 time to fit residues: 46.0683 Evaluate side-chains 343 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 331 MET 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 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 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 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 1317 ASP 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 1448 LEU 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 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 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 162 SER 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: 6.9990 chunk 6 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN ** 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** B 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111690 restraints weight = 22419.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114432 restraints weight = 11969.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116142 restraints weight = 7865.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117074 restraints weight = 6047.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117848 restraints weight = 5220.066| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5062 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= 0.143 Angle : 0.700 9.272 14809 Z= 0.361 Chirality : 0.042 0.206 1751 Planarity : 0.005 0.103 1789 Dihedral : 7.564 85.054 1441 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 6.91 % Allowed : 23.34 % Favored : 69.75 % 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: -1.35 (0.23), residues: 1296 helix: -0.07 (0.18), residues: 847 sheet: -1.85 (0.58), residues: 64 loop : -2.45 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1120 TYR 0.018 0.001 TYR A 392 PHE 0.021 0.001 PHE B 102 TRP 0.013 0.001 TRP A1507 HIS 0.009 0.002 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10874) covalent geometry : angle 0.68841 / 0.36 (14745) SS BOND : bond 0.00695 / 0.43 ( 8) SS BOND : angle 1.77448 / 1.03 ( 16) hydrogen bonds : bond 0.04010 / 2.60 ( 552) hydrogen bonds : angle 4.60380 / 3.19 ( 1593) link_BETA1-3 : bond 0.00890 / 0.59 ( 1) link_BETA1-3 : angle 1.72974 / 1.37 ( 3) link_BETA1-4 : bond 0.00465 / 0.23 ( 9) link_BETA1-4 : angle 1.94322 / 1.19 ( 27) link_BETA1-6 : bond 0.00240 / 0.16 ( 1) link_BETA1-6 : angle 1.69088 / 1.28 ( 3) link_NAG-ASN : bond 0.00370 / 0.20 ( 5) link_NAG-ASN : angle 2.48778 / 1.49 ( 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 380 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6792 (mtt90) cc_final: 0.5441 (ptt180) REVERT: A 129 MET cc_start: 0.7840 (ttm) cc_final: 0.7308 (tmm) REVERT: A 166 LYS cc_start: 0.9037 (mttt) cc_final: 0.8823 (mmmt) REVERT: A 335 ARG cc_start: 0.9136 (tmm-80) cc_final: 0.8590 (ptm160) REVERT: A 563 MET cc_start: 0.6769 (tmm) cc_final: 0.6450 (tmm) REVERT: A 647 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2594 (tt) REVERT: A 702 PHE cc_start: 0.9426 (m-80) cc_final: 0.9173 (m-80) REVERT: A 759 GLU cc_start: 0.8210 (tt0) cc_final: 0.7937 (tt0) REVERT: A 771 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6134 (ttt) REVERT: A 993 CYS cc_start: 0.8541 (m) cc_final: 0.8220 (m) REVERT: A 1009 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7835 (mmt) REVERT: A 1048 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: A 1064 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: A 1203 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8765 (t80) REVERT: A 1240 MET cc_start: 0.8562 (mmp) cc_final: 0.8222 (tpp) REVERT: A 1258 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 1292 MET cc_start: 0.6568 (mmp) cc_final: 0.5431 (mtt) REVERT: A 1325 ASP cc_start: 0.8228 (m-30) cc_final: 0.7845 (t0) REVERT: A 1336 MET cc_start: 0.8443 (ttt) cc_final: 0.8227 (tmm) REVERT: A 1368 GLU cc_start: 0.8944 (tt0) cc_final: 0.8697 (mm-30) REVERT: A 1377 ARG cc_start: 0.4413 (tpt170) cc_final: 0.3801 (mmt-90) REVERT: A 1456 LEU cc_start: 0.9290 (tp) cc_final: 0.8949 (tp) REVERT: A 1475 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6358 (p90) REVERT: A 1485 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 125 TYR cc_start: 0.6535 (t80) cc_final: 0.6038 (t80) REVERT: B 130 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6955 (pp) REVERT: B 148 ASN cc_start: 0.8654 (p0) cc_final: 0.8328 (p0) REVERT: B 163 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 164 VAL cc_start: 0.9297 (t) cc_final: 0.8988 (p) REVERT: B 166 MET cc_start: 0.9003 (tmm) cc_final: 0.8598 (tmm) REVERT: B 167 TYR cc_start: 0.8279 (m-80) cc_final: 0.7722 (m-80) outliers start: 77 outliers final: 50 residues processed: 349 average time/residue: 0.0856 time to fit residues: 45.2631 Evaluate side-chains 341 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 173 CYS 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 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 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 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 1064 ASP 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 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 1461 ILE 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 1498 LEU 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 81 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1472 ASN B 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108665 restraints weight = 22981.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111324 restraints weight = 12336.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112876 restraints weight = 8135.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114033 restraints weight = 6343.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114609 restraints weight = 5391.673| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10898 Z= 0.208 Angle : 0.749 13.632 14809 Z= 0.387 Chirality : 0.045 0.203 1751 Planarity : 0.005 0.104 1789 Dihedral : 7.358 84.859 1435 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.79 % Favored : 92.67 % Rotamer: Outliers : 7.18 % Allowed : 23.97 % Favored : 68.85 % 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: -1.33 (0.23), residues: 1296 helix: -0.05 (0.17), residues: 845 sheet: -1.62 (0.61), residues: 60 loop : -2.49 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1120 TYR 0.024 0.002 TYR A 625 PHE 0.021 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/Z covalent geometry : bond 0.00477 / 0.21 (10874) covalent geometry : angle 0.73788 / 0.38 (14745) SS BOND : bond 0.00602 / 0.33 ( 8) SS BOND : angle 1.78722 / 1.08 ( 16) hydrogen bonds : bond 0.04073 / 2.63 ( 552) hydrogen bonds : angle 4.75273 / 3.29 ( 1593) link_BETA1-3 : bond 0.00769 / 0.51 ( 1) link_BETA1-3 : angle 1.94975 / 1.60 ( 3) link_BETA1-4 : bond 0.00488 / 0.21 ( 9) link_BETA1-4 : angle 2.03086 / 1.26 ( 27) link_BETA1-6 : bond 0.00029 / 0.02 ( 1) link_BETA1-6 : angle 1.96369 / 1.53 ( 3) link_NAG-ASN : bond 0.00518 / 0.32 ( 5) link_NAG-ASN : angle 2.56795 / 1.55 ( 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 364 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 284 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6829 (mtt90) cc_final: 0.5342 (ptt180) REVERT: A 129 MET cc_start: 0.7854 (ttm) cc_final: 0.7315 (tmm) REVERT: A 166 LYS cc_start: 0.9076 (mttt) cc_final: 0.8857 (mmmt) REVERT: A 232 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6300 (tpt90) REVERT: A 250 PHE cc_start: 0.8318 (t80) cc_final: 0.7630 (m-10) REVERT: A 305 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8162 (p90) REVERT: A 335 ARG cc_start: 0.9136 (tmm-80) cc_final: 0.8582 (ptm160) REVERT: A 357 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9320 (tp) REVERT: A 563 MET cc_start: 0.6770 (tmm) cc_final: 0.6429 (tmm) REVERT: A 759 GLU cc_start: 0.8275 (tt0) cc_final: 0.7972 (tt0) REVERT: A 771 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6295 (ttt) REVERT: A 779 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8114 (tm) REVERT: A 993 CYS cc_start: 0.8468 (m) cc_final: 0.8154 (m) REVERT: A 1009 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (mmt) REVERT: A 1203 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8863 (t80) REVERT: A 1258 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 1292 MET cc_start: 0.6672 (mmp) cc_final: 0.5697 (mtt) REVERT: A 1325 ASP cc_start: 0.8260 (m-30) cc_final: 0.7967 (t0) REVERT: A 1368 GLU cc_start: 0.8962 (tt0) cc_final: 0.8724 (mm-30) REVERT: A 1377 ARG cc_start: 0.4361 (tpt170) cc_final: 0.3832 (mmt-90) REVERT: A 1456 LEU cc_start: 0.9338 (tp) cc_final: 0.9045 (tp) REVERT: A 1475 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.6458 (p90) REVERT: B 81 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8191 (t) REVERT: B 125 TYR cc_start: 0.6614 (t80) cc_final: 0.6023 (t80) REVERT: B 130 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7115 (pp) REVERT: B 148 ASN cc_start: 0.8706 (p0) cc_final: 0.8394 (p0) REVERT: B 164 VAL cc_start: 0.9318 (t) cc_final: 0.8989 (p) REVERT: B 166 MET cc_start: 0.9036 (tmm) cc_final: 0.8627 (tmm) outliers start: 80 outliers final: 56 residues processed: 335 average time/residue: 0.0862 time to fit residues: 43.8643 Evaluate side-chains 342 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 357 LEU 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 603 LEU Chi-restraints excluded: chain A residue 643 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 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 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 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 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 1461 ILE 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 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1559 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 81 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 150 VAL 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: 2.9990 chunk 12 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.0050 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112254 restraints weight = 22496.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114948 restraints weight = 11996.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116700 restraints weight = 7902.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117788 restraints weight = 6072.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118300 restraints weight = 5187.523| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10898 Z= 0.138 Angle : 0.726 12.205 14809 Z= 0.367 Chirality : 0.043 0.255 1751 Planarity : 0.004 0.099 1789 Dihedral : 7.029 82.948 1430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.86 % Favored : 93.60 % Rotamer: Outliers : 7.00 % Allowed : 25.40 % Favored : 67.59 % 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: -0.98 (0.23), residues: 1296 helix: 0.20 (0.18), residues: 840 sheet: -1.67 (0.59), residues: 64 loop : -2.23 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1120 TYR 0.019 0.001 TYR A 625 PHE 0.021 0.001 PHE B 102 TRP 0.016 0.001 TRP A1507 HIS 0.006 0.001 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10874) covalent geometry : angle 0.71586 / 0.36 (14745) SS BOND : bond 0.00527 / 0.28 ( 8) SS BOND : angle 1.91641 / 1.25 ( 16) hydrogen bonds : bond 0.03873 / 2.53 ( 552) hydrogen bonds : angle 4.54423 / 3.17 ( 1593) link_BETA1-3 : bond 0.00835 / 0.56 ( 1) link_BETA1-3 : angle 1.76470 / 1.41 ( 3) link_BETA1-4 : bond 0.00445 / 0.23 ( 9) link_BETA1-4 : angle 1.83906 / 1.11 ( 27) link_BETA1-6 : bond 0.00357 / 0.24 ( 1) link_BETA1-6 : angle 1.66642 / 1.27 ( 3) link_NAG-ASN : bond 0.00343 / 0.18 ( 5) link_NAG-ASN : angle 2.38791 / 1.44 ( 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 381 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 303 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6794 (mtt90) cc_final: 0.5299 (ptt180) REVERT: A 129 MET cc_start: 0.7876 (ttm) cc_final: 0.7357 (tmm) REVERT: A 166 LYS cc_start: 0.9057 (mttt) cc_final: 0.8839 (mmmt) REVERT: A 335 ARG cc_start: 0.9112 (tmm-80) cc_final: 0.8561 (ptm160) REVERT: A 354 LEU cc_start: 0.9051 (mt) cc_final: 0.8835 (mt) REVERT: A 357 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9310 (tp) REVERT: A 383 ILE cc_start: 0.8913 (mm) cc_final: 0.8706 (mm) REVERT: A 563 MET cc_start: 0.6746 (tmm) cc_final: 0.6435 (tmm) REVERT: A 759 GLU cc_start: 0.8210 (tt0) cc_final: 0.7883 (tt0) REVERT: A 771 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6229 (ttt) REVERT: A 779 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8310 (tm) REVERT: A 993 CYS cc_start: 0.8404 (m) cc_final: 0.8110 (m) REVERT: A 1009 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7876 (mmt) REVERT: A 1048 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: A 1064 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: A 1203 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8708 (t80) REVERT: A 1240 MET cc_start: 0.8489 (mmp) cc_final: 0.8266 (tpp) REVERT: A 1258 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 1292 MET cc_start: 0.6596 (mmp) cc_final: 0.5602 (mtt) REVERT: A 1325 ASP cc_start: 0.8279 (m-30) cc_final: 0.7913 (t0) REVERT: A 1368 GLU cc_start: 0.8912 (tt0) cc_final: 0.8683 (mm-30) REVERT: A 1377 ARG cc_start: 0.4142 (tpt170) cc_final: 0.3379 (mmt-90) REVERT: A 1421 LEU cc_start: 0.8348 (tt) cc_final: 0.8078 (tp) REVERT: A 1451 LEU cc_start: 0.9361 (tp) cc_final: 0.9156 (tt) REVERT: A 1456 LEU cc_start: 0.9290 (tp) cc_final: 0.8913 (tp) REVERT: A 1475 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6177 (p90) REVERT: A 1539 ASN cc_start: 0.7709 (t0) cc_final: 0.7480 (m-40) REVERT: B 125 TYR cc_start: 0.6469 (t80) cc_final: 0.5997 (t80) REVERT: B 130 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6661 (pp) REVERT: B 140 ASN cc_start: 0.7875 (p0) cc_final: 0.7548 (p0) REVERT: B 148 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8471 (p0) REVERT: B 163 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 164 VAL cc_start: 0.9281 (t) cc_final: 0.8971 (p) REVERT: B 166 MET cc_start: 0.9020 (tmm) cc_final: 0.8626 (tmm) outliers start: 78 outliers final: 45 residues processed: 347 average time/residue: 0.0870 time to fit residues: 45.5787 Evaluate side-chains 340 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 324 CYS Chi-restraints excluded: chain A residue 357 LEU 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 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 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 1064 ASP 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 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 1497 CYS 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 38 HIS Chi-restraints excluded: chain B residue 59 VAL 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 148 ASN Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.0010 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 560 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113499 restraints weight = 22434.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116177 restraints weight = 11956.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117935 restraints weight = 7868.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118857 restraints weight = 6027.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119635 restraints weight = 5206.692| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10898 Z= 0.135 Angle : 0.725 13.328 14809 Z= 0.365 Chirality : 0.043 0.283 1751 Planarity : 0.004 0.098 1789 Dihedral : 6.840 80.188 1430 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.48 % Favored : 93.98 % Rotamer: Outliers : 5.66 % Allowed : 27.02 % Favored : 67.32 % 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: -0.82 (0.23), residues: 1296 helix: 0.30 (0.18), residues: 849 sheet: -1.67 (0.57), residues: 74 loop : -2.14 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1120 TYR 0.017 0.001 TYR A 625 PHE 0.021 0.001 PHE A 391 TRP 0.016 0.001 TRP A1507 HIS 0.006 0.001 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10874) covalent geometry : angle 0.71625 / 0.36 (14745) SS BOND : bond 0.00341 / 0.17 ( 8) SS BOND : angle 1.60977 / 1.06 ( 16) hydrogen bonds : bond 0.03709 / 2.40 ( 552) hydrogen bonds : angle 4.46214 / 3.11 ( 1593) link_BETA1-3 : bond 0.00908 / 0.61 ( 1) link_BETA1-3 : angle 1.98483 / 1.62 ( 3) link_BETA1-4 : bond 0.00439 / 0.22 ( 9) link_BETA1-4 : angle 1.77864 / 1.09 ( 27) link_BETA1-6 : bond 0.00295 / 0.20 ( 1) link_BETA1-6 : angle 1.64039 / 1.26 ( 3) link_NAG-ASN : bond 0.00252 / 0.13 ( 5) link_NAG-ASN : angle 2.27822 / 1.40 ( 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: 63 poor density : 296 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6767 (mtt90) cc_final: 0.5245 (ptt180) REVERT: A 129 MET cc_start: 0.7922 (ttm) cc_final: 0.7337 (tmm) REVERT: A 166 LYS cc_start: 0.9086 (mttt) cc_final: 0.8886 (mmmt) REVERT: A 241 MET cc_start: 0.7873 (mmm) cc_final: 0.7289 (mmt) REVERT: A 305 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7890 (p90) REVERT: A 354 LEU cc_start: 0.9066 (mt) cc_final: 0.8851 (mt) REVERT: A 357 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9281 (tp) REVERT: A 358 MET cc_start: 0.9126 (tmm) cc_final: 0.8892 (tmm) REVERT: A 563 MET cc_start: 0.6823 (tmm) cc_final: 0.6580 (tmm) REVERT: A 759 GLU cc_start: 0.8196 (tt0) cc_final: 0.7853 (tt0) REVERT: A 771 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6398 (ttt) REVERT: A 779 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8258 (tm) REVERT: A 993 CYS cc_start: 0.8385 (m) cc_final: 0.8089 (m) REVERT: A 1009 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7875 (mmt) REVERT: A 1064 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: A 1112 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: A 1144 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 1203 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8701 (t80) REVERT: A 1240 MET cc_start: 0.8529 (mmp) cc_final: 0.8303 (tpp) REVERT: A 1258 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 1292 MET cc_start: 0.6715 (mmp) cc_final: 0.5711 (mtt) REVERT: A 1325 ASP cc_start: 0.8297 (m-30) cc_final: 0.7882 (t0) REVERT: A 1368 GLU cc_start: 0.8923 (tt0) cc_final: 0.8684 (mm-30) REVERT: A 1377 ARG cc_start: 0.4038 (tpt170) cc_final: 0.3330 (mmt-90) REVERT: A 1438 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7495 (ptm-80) REVERT: A 1451 LEU cc_start: 0.9363 (tp) cc_final: 0.9149 (tt) REVERT: A 1456 LEU cc_start: 0.9274 (tp) cc_final: 0.8895 (tp) REVERT: A 1475 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.6253 (p90) REVERT: A 1534 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7498 (mtp180) REVERT: A 1539 ASN cc_start: 0.7677 (t0) cc_final: 0.7457 (m-40) REVERT: B 42 LEU cc_start: 0.7526 (mp) cc_final: 0.7033 (pp) REVERT: B 125 TYR cc_start: 0.6488 (t80) cc_final: 0.5905 (t80) REVERT: B 148 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8508 (p0) REVERT: B 164 VAL cc_start: 0.9279 (t) cc_final: 0.8927 (p) REVERT: B 166 MET cc_start: 0.9025 (tmm) cc_final: 0.8601 (tmm) REVERT: B 167 TYR cc_start: 0.8236 (m-80) cc_final: 0.7463 (m-80) outliers start: 63 outliers final: 43 residues processed: 333 average time/residue: 0.0827 time to fit residues: 41.8564 Evaluate side-chains 350 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ILE 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 357 LEU 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 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 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 1064 ASP Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110214 restraints weight = 22536.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112827 restraints weight = 12132.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114522 restraints weight = 8028.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115432 restraints weight = 6174.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116155 restraints weight = 5337.401| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10898 Z= 0.186 Angle : 0.768 12.269 14809 Z= 0.390 Chirality : 0.046 0.291 1751 Planarity : 0.005 0.100 1789 Dihedral : 6.816 80.550 1429 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.40 % Favored : 93.06 % Rotamer: Outliers : 5.66 % Allowed : 27.38 % Favored : 66.97 % 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: -0.63 (0.23), residues: 1296 helix: 0.43 (0.18), residues: 840 sheet: -1.20 (0.64), residues: 62 loop : -2.04 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 138 TYR 0.017 0.002 TYR A 625 PHE 0.028 0.002 PHE A1499 TRP 0.013 0.001 TRP B 176 HIS 0.007 0.002 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (10874) covalent geometry : angle 0.75886 / 0.39 (14745) SS BOND : bond 0.00486 / 0.25 ( 8) SS BOND : angle 1.64605 / 1.05 ( 16) hydrogen bonds : bond 0.03817 / 2.47 ( 552) hydrogen bonds : angle 4.62916 / 3.22 ( 1593) link_BETA1-3 : bond 0.00702 / 0.47 ( 1) link_BETA1-3 : angle 2.02342 / 1.67 ( 3) link_BETA1-4 : bond 0.00395 / 0.19 ( 9) link_BETA1-4 : angle 1.84899 / 1.14 ( 27) link_BETA1-6 : bond 0.00121 / 0.08 ( 1) link_BETA1-6 : angle 1.73706 / 1.35 ( 3) link_NAG-ASN : bond 0.00432 / 0.25 ( 5) link_NAG-ASN : angle 2.38404 / 1.44 ( 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 349 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6908 (mtt90) cc_final: 0.5285 (ptt180) REVERT: A 129 MET cc_start: 0.7976 (ttm) cc_final: 0.7382 (tmm) REVERT: A 166 LYS cc_start: 0.9144 (mttt) cc_final: 0.8911 (mmmt) REVERT: A 250 PHE cc_start: 0.8431 (t80) cc_final: 0.7530 (m-10) REVERT: A 305 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7970 (p90) REVERT: A 357 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9292 (tp) REVERT: A 369 MET cc_start: 0.9105 (mtp) cc_final: 0.8808 (mtm) REVERT: A 391 PHE cc_start: 0.9069 (t80) cc_final: 0.8679 (t80) REVERT: A 393 LEU cc_start: 0.8740 (mt) cc_final: 0.8040 (tp) REVERT: A 563 MET cc_start: 0.6842 (tmm) cc_final: 0.6585 (tmm) REVERT: A 771 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6282 (ttt) REVERT: A 779 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8363 (tm) REVERT: A 993 CYS cc_start: 0.8353 (m) cc_final: 0.8063 (m) REVERT: A 1203 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8811 (t80) REVERT: A 1240 MET cc_start: 0.8598 (mmp) cc_final: 0.8386 (tpp) REVERT: A 1258 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8735 (tp) REVERT: A 1292 MET cc_start: 0.6778 (mmp) cc_final: 0.5736 (mtt) REVERT: A 1325 ASP cc_start: 0.8296 (m-30) cc_final: 0.7969 (t0) REVERT: A 1368 GLU cc_start: 0.8947 (tt0) cc_final: 0.8707 (mm-30) REVERT: A 1377 ARG cc_start: 0.4149 (tpt170) cc_final: 0.3420 (mmt-90) REVERT: A 1438 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7509 (ptm-80) REVERT: A 1456 LEU cc_start: 0.9314 (tp) cc_final: 0.8941 (tp) REVERT: A 1475 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.6341 (p90) REVERT: A 1539 ASN cc_start: 0.7729 (t0) cc_final: 0.7503 (m-40) REVERT: A 1548 CYS cc_start: 0.8356 (m) cc_final: 0.7895 (m) REVERT: B 125 TYR cc_start: 0.6760 (t80) cc_final: 0.5793 (t80) REVERT: B 164 VAL cc_start: 0.9304 (t) cc_final: 0.8961 (p) REVERT: B 166 MET cc_start: 0.9026 (tmm) cc_final: 0.8613 (tmm) outliers start: 63 outliers final: 50 residues processed: 325 average time/residue: 0.0833 time to fit residues: 41.1652 Evaluate side-chains 337 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 357 LEU 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 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 763 VAL Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 1009 MET 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 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 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 1424 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE 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 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 130 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112904 restraints weight = 22461.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115638 restraints weight = 11991.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117354 restraints weight = 7847.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118454 restraints weight = 6020.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118840 restraints weight = 5116.016| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10898 Z= 0.143 Angle : 0.766 13.811 14809 Z= 0.385 Chirality : 0.045 0.231 1751 Planarity : 0.004 0.098 1789 Dihedral : 6.753 79.270 1429 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.86 % Favored : 93.60 % Rotamer: Outliers : 5.30 % Allowed : 27.47 % Favored : 67.24 % 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: -0.49 (0.24), residues: 1296 helix: 0.51 (0.18), residues: 841 sheet: -1.03 (0.63), residues: 62 loop : -1.95 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1120 TYR 0.028 0.001 TYR B 125 PHE 0.033 0.001 PHE A1499 TRP 0.022 0.001 TRP A 987 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10874) covalent geometry : angle 0.75890 / 0.38 (14745) SS BOND : bond 0.00344 / 0.18 ( 8) SS BOND : angle 1.35528 / 0.86 ( 16) hydrogen bonds : bond 0.03734 / 2.41 ( 552) hydrogen bonds : angle 4.60688 / 3.21 ( 1593) link_BETA1-3 : bond 0.00851 / 0.57 ( 1) link_BETA1-3 : angle 1.94530 / 1.58 ( 3) link_BETA1-4 : bond 0.00521 / 0.28 ( 9) link_BETA1-4 : angle 1.75704 / 1.06 ( 27) link_BETA1-6 : bond 0.00452 / 0.30 ( 1) link_BETA1-6 : angle 1.56971 / 1.21 ( 3) link_NAG-ASN : bond 0.00294 / 0.15 ( 5) link_NAG-ASN : angle 2.25760 / 1.37 ( 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: 59 poor density : 288 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6893 (mtt90) cc_final: 0.5244 (ptt180) REVERT: A 129 MET cc_start: 0.7914 (ttm) cc_final: 0.7359 (tmm) REVERT: A 166 LYS cc_start: 0.9091 (mttt) cc_final: 0.8884 (mmmt) REVERT: A 305 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8020 (p90) REVERT: A 357 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9256 (tp) REVERT: A 358 MET cc_start: 0.9153 (tmm) cc_final: 0.8872 (tmm) REVERT: A 369 MET cc_start: 0.9001 (mtp) cc_final: 0.8654 (mtm) REVERT: A 391 PHE cc_start: 0.9006 (t80) cc_final: 0.8716 (t80) REVERT: A 393 LEU cc_start: 0.8744 (mt) cc_final: 0.8047 (tp) REVERT: A 563 MET cc_start: 0.6764 (tmm) cc_final: 0.6541 (tmm) REVERT: A 582 PHE cc_start: 0.8655 (t80) cc_final: 0.8164 (t80) REVERT: A 634 ASP cc_start: 0.8699 (m-30) cc_final: 0.8125 (p0) REVERT: A 656 LEU cc_start: 0.8963 (mt) cc_final: 0.8697 (mm) REVERT: A 771 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6327 (ttt) REVERT: A 779 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8350 (tm) REVERT: A 993 CYS cc_start: 0.8255 (m) cc_final: 0.7938 (m) REVERT: A 1112 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: A 1144 SER cc_start: 0.9451 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 1201 MET cc_start: 0.8285 (tpp) cc_final: 0.7997 (tpp) REVERT: A 1203 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (t80) REVERT: A 1240 MET cc_start: 0.8548 (mmp) cc_final: 0.8293 (tpp) REVERT: A 1258 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 1292 MET cc_start: 0.6772 (mmp) cc_final: 0.5760 (mtt) REVERT: A 1325 ASP cc_start: 0.8307 (m-30) cc_final: 0.7976 (t0) REVERT: A 1368 GLU cc_start: 0.8942 (tt0) cc_final: 0.8671 (mm-30) REVERT: A 1438 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7416 (ptm-80) REVERT: A 1456 LEU cc_start: 0.9287 (tp) cc_final: 0.8954 (tp) REVERT: A 1475 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.6554 (p90) REVERT: A 1495 MET cc_start: 0.8473 (mmm) cc_final: 0.8157 (mmm) REVERT: A 1534 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.7574 (mtm180) REVERT: A 1539 ASN cc_start: 0.7733 (t0) cc_final: 0.7511 (m-40) REVERT: A 1548 CYS cc_start: 0.8260 (m) cc_final: 0.7808 (m) REVERT: B 125 TYR cc_start: 0.6674 (t80) cc_final: 0.6243 (t80) REVERT: B 127 ASP cc_start: 0.6347 (m-30) cc_final: 0.5010 (m-30) REVERT: B 164 VAL cc_start: 0.9287 (t) cc_final: 0.8939 (p) REVERT: B 166 MET cc_start: 0.9011 (tmm) cc_final: 0.8609 (tmm) outliers start: 59 outliers final: 47 residues processed: 322 average time/residue: 0.0824 time to fit residues: 40.5236 Evaluate side-chains 337 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 186 TRP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 357 LEU 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 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 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 1112 PHE 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 1332 ILE 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 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 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 101 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114092 restraints weight = 22696.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116835 restraints weight = 11952.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118553 restraints weight = 7773.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119470 restraints weight = 5957.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120002 restraints weight = 5140.397| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10898 Z= 0.138 Angle : 0.754 12.758 14809 Z= 0.377 Chirality : 0.045 0.295 1751 Planarity : 0.004 0.097 1789 Dihedral : 6.636 76.909 1429 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 4.94 % Allowed : 28.28 % Favored : 66.79 % 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: -0.36 (0.24), residues: 1296 helix: 0.60 (0.18), residues: 841 sheet: -0.93 (0.63), residues: 61 loop : -1.88 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.024 0.001 TYR A 625 PHE 0.029 0.001 PHE A1499 TRP 0.017 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10874) covalent geometry : angle 0.74646 / 0.38 (14745) SS BOND : bond 0.00309 / 0.16 ( 8) SS BOND : angle 1.29000 / 0.82 ( 16) hydrogen bonds : bond 0.03623 / 2.34 ( 552) hydrogen bonds : angle 4.53511 / 3.18 ( 1593) link_BETA1-3 : bond 0.00823 / 0.55 ( 1) link_BETA1-3 : angle 1.99650 / 1.63 ( 3) link_BETA1-4 : bond 0.00451 / 0.23 ( 9) link_BETA1-4 : angle 1.69380 / 1.03 ( 27) link_BETA1-6 : bond 0.00306 / 0.20 ( 1) link_BETA1-6 : angle 1.49081 / 1.14 ( 3) link_NAG-ASN : bond 0.00357 / 0.18 ( 5) link_NAG-ASN : angle 2.17414 / 1.31 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.86 seconds wall clock time: 36 minutes 40.30 seconds (2200.30 seconds total)