Starting phenix.real_space_refine on Tue Jul 29 02:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xsy_6770/07_2025/5xsy_6770.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xsy_6770/07_2025/5xsy_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_6770/07_2025/5xsy_6770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xsy_6770/07_2025/5xsy_6770.map" model { file = "/net/cci-nas-00/data/ceres_data/5xsy_6770/07_2025/5xsy_6770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xsy_6770/07_2025/5xsy_6770.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.61, per 1000 atoms: 0.62 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.03 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: 3.47 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1903 1.32 - 1.45: 2916 1.45 - 1.57: 5904 1.57 - 1.69: 1 1.69 - 1.81: 150 Bond restraints: 10874 Sorted by residual: bond pdb=" CA GLU B 136 " pdb=" C GLU B 136 " ideal model delta sigma weight residual 1.523 1.681 -0.159 1.28e-02 6.10e+03 1.54e+02 bond pdb=" C GLY A1518 " pdb=" N PRO A1519 " ideal model delta sigma weight residual 1.329 1.403 -0.073 1.18e-02 7.18e+03 3.87e+01 bond pdb=" N PRO A1520 " pdb=" CD PRO A1520 " ideal model delta sigma weight residual 1.474 1.554 -0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 1.473 1.550 -0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" N PRO A1519 " pdb=" CD PRO A1519 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.63: 14585 5.63 - 11.26: 134 11.26 - 16.90: 19 16.90 - 22.53: 3 22.53 - 28.16: 4 Bond angle restraints: 14745 Sorted by residual: angle pdb=" N LEU B 130 " pdb=" CA LEU B 130 " pdb=" C LEU B 130 " ideal model delta sigma weight residual 109.46 81.30 28.16 1.66e+00 3.63e-01 2.88e+02 angle pdb=" C TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta sigma weight residual 109.48 83.04 26.44 1.68e+00 3.54e-01 2.48e+02 angle pdb=" C LEU B 130 " pdb=" CA LEU B 130 " pdb=" CB LEU B 130 " ideal model delta sigma weight residual 109.80 134.63 -24.83 1.64e+00 3.72e-01 2.29e+02 angle pdb=" C SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta sigma weight residual 109.38 82.35 27.03 2.03e+00 2.43e-01 1.77e+02 angle pdb=" C MET B 83 " pdb=" CA MET B 83 " pdb=" CB MET B 83 " ideal model delta sigma weight residual 110.19 92.25 17.94 1.62e+00 3.81e-01 1.23e+02 ... (remaining 14740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 6041 23.10 - 46.21: 355 46.21 - 69.31: 100 69.31 - 92.41: 35 92.41 - 115.52: 29 Dihedral angle restraints: 6560 sinusoidal: 2729 harmonic: 3831 Sorted by residual: dihedral pdb=" C SER B 76 " pdb=" N SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta harmonic sigma weight residual -122.60 -94.64 -27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR B 110 " pdb=" N TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta harmonic sigma weight residual -122.60 -95.89 -26.71 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -168.70 82.70 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1482 0.095 - 0.190: 217 0.190 - 0.285: 39 0.285 - 0.380: 8 0.380 - 0.475: 5 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA ALA A1573 " pdb=" N ALA A1573 " pdb=" C ALA A1573 " pdb=" CB ALA A1573 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA GLU B 136 " pdb=" N GLU B 136 " pdb=" C GLU B 136 " pdb=" CB GLU B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA GLU A 586 " pdb=" N GLU A 586 " pdb=" C GLU A 586 " pdb=" CB GLU A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 1748 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 213 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 268 " -1.014 9.50e-02 1.11e+02 4.55e-01 1.25e+02 pdb=" NE ARG A 268 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 268 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 268 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 268 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 336 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO A 337 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.064 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 27 2.37 - 3.00: 6081 3.00 - 3.63: 15491 3.63 - 4.27: 22949 4.27 - 4.90: 36672 Nonbonded interactions: 81220 Sorted by model distance: nonbonded pdb=" CG1 VAL A1016 " pdb=" CD1 LEU A1034 " model vdw 1.735 3.880 nonbonded pdb=" O GLN A1346 " pdb=" OG SER A1347 " model vdw 1.915 3.040 nonbonded pdb=" O LEU A 620 " pdb=" O ASP A 621 " model vdw 1.993 3.040 nonbonded pdb=" O THR A 629 " pdb=" CG2 ILE A 632 " model vdw 2.137 3.460 nonbonded pdb=" O ASP A1483 " pdb=" OD1 ASP A1484 " model vdw 2.176 3.040 ... (remaining 81215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.354 10898 Z= 0.594 Angle : 1.790 55.668 14809 Z= 1.024 Chirality : 0.077 0.475 1751 Planarity : 0.017 0.482 1789 Dihedral : 18.877 115.517 4062 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 1.54 % Allowed : 6.64 % Favored : 91.82 % Rotamer: Outliers : 7.45 % Allowed : 8.35 % Favored : 84.20 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (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 TRP 0.055 0.003 TRP A1215 HIS 0.022 0.004 HIS A 588 PHE 0.031 0.003 PHE B 63 TYR 0.035 0.004 TYR A 714 ARG 0.011 0.001 ARG A1027 Details of bonding type rmsd link_NAG-ASN : bond 0.01304 ( 5) link_NAG-ASN : angle 4.65672 ( 15) link_BETA1-4 : bond 0.01626 ( 9) link_BETA1-4 : angle 3.71734 ( 27) hydrogen bonds : bond 0.30611 ( 552) hydrogen bonds : angle 9.92518 ( 1593) link_BETA1-6 : bond 0.00583 ( 1) link_BETA1-6 : angle 1.04308 ( 3) SS BOND : bond 0.15513 ( 8) SS BOND : angle 26.36939 ( 16) link_BETA1-3 : bond 0.00488 ( 1) link_BETA1-3 : angle 1.61106 ( 3) covalent geometry : bond 0.01094 (10874) covalent geometry : angle 1.55406 (14745) *********************** 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 : 1.063 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: 0.5324 (ptt180) REVERT: A 129 MET cc_start: 0.8068 (ttm) cc_final: 0.7513 (tmm) REVERT: A 133 PHE cc_start: 0.7602 (t80) cc_final: 0.7376 (t80) REVERT: A 139 MET cc_start: 0.8688 (tpp) cc_final: 0.8260 (mtt) REVERT: A 194 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6163 (mmp) REVERT: A 232 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6818 (tpt170) REVERT: A 250 PHE cc_start: 0.8270 (t80) cc_final: 0.7236 (m-10) REVERT: A 255 PHE cc_start: 0.9090 (m-80) cc_final: 0.8887 (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: 0.7644 (ttm170) REVERT: A 298 GLU cc_start: 0.9374 (tt0) cc_final: 0.8654 (pt0) REVERT: A 372 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7373 (ttm170) REVERT: A 405 TYR cc_start: 0.6925 (m-10) cc_final: 0.6694 (m-10) REVERT: A 590 MET cc_start: 0.7093 (mtp) cc_final: 0.6790 (mmm) REVERT: A 647 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2826 (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: 0.8169 (m-10) REVERT: A 725 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6974 (t) REVERT: A 726 GLU cc_start: 0.8725 (tt0) cc_final: 0.7514 (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: 0.7011 (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: 0.8115 (t80) REVERT: A 1059 LYS cc_start: 0.7619 (tttp) cc_final: 0.7181 (mptt) REVERT: A 1064 ASP cc_start: 0.7845 (m-30) cc_final: 0.7551 (t0) REVERT: A 1067 CYS cc_start: 0.8568 (m) cc_final: 0.8228 (m) REVERT: A 1071 PHE cc_start: 0.8683 (t80) cc_final: 0.8460 (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: 0.7895 (ttm110) REVERT: A 1165 GLU cc_start: 0.8720 (tt0) cc_final: 0.8119 (mm-30) REVERT: A 1192 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8023 (tm) REVERT: A 1231 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 1240 MET cc_start: 0.9257 (mmp) cc_final: 0.8767 (tpp) REVERT: A 1288 TYR cc_start: 0.8283 (m-10) cc_final: 0.7850 (m-10) REVERT: A 1294 LYS cc_start: 0.6906 (mttt) cc_final: 0.6474 (mmmt) REVERT: A 1325 ASP cc_start: 0.8607 (m-30) cc_final: 0.8368 (t0) REVERT: A 1326 ILE cc_start: 0.8148 (mt) cc_final: 0.7773 (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: 0.8600 (ttt) REVERT: A 1377 ARG cc_start: 0.3999 (tpt170) cc_final: 0.3646 (mmt-90) 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: 0.7973 (ttm) REVERT: A 1468 PHE cc_start: 0.8617 (t80) cc_final: 0.8346 (t80) REVERT: A 1523 ASP cc_start: 0.7661 (m-30) cc_final: 0.7190 (t70) REVERT: B 27 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: B 28 VAL cc_start: 0.8886 (p) cc_final: 0.8597 (p) REVERT: B 38 HIS cc_start: 0.8160 (t-90) cc_final: 0.7835 (t-90) REVERT: B 62 TRP cc_start: 0.8178 (m100) cc_final: 0.7404 (m-10) REVERT: B 72 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (t) REVERT: B 75 TYR cc_start: 0.8686 (t80) cc_final: 0.8181 (t80) REVERT: B 81 THR cc_start: 0.9063 (m) cc_final: 0.8846 (m) REVERT: B 94 ASN cc_start: 0.8316 (t0) cc_final: 0.7842 (t0) REVERT: B 114 VAL cc_start: 0.9382 (t) cc_final: 0.8998 (p) REVERT: B 121 THR cc_start: 0.7770 (m) cc_final: 0.7525 (m) REVERT: B 125 TYR cc_start: 0.7672 (t80) cc_final: 0.6948 (t80) REVERT: B 155 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8156 (mtt180) REVERT: B 163 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: B 165 MET cc_start: 0.8112 (mmm) cc_final: 0.7348 (tmm) REVERT: B 177 LEU cc_start: 0.8981 (mt) cc_final: 0.8747 (mt) REVERT: B 183 TYR cc_start: 0.8035 (t80) cc_final: 0.7561 (t80) REVERT: B 194 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7273 (mp0) outliers start: 83 outliers final: 27 residues processed: 477 average time/residue: 0.2248 time to fit residues: 149.5017 Evaluate side-chains 350 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 110 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 346 ASN A 560 HIS A 628 GLN A 631 ASN A 690 ASN A1270 GLN B 73 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112133 restraints weight = 21724.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114787 restraints weight = 11912.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116498 restraints weight = 7904.838| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10898 Z= 0.193 Angle : 0.878 11.658 14809 Z= 0.454 Chirality : 0.048 0.252 1751 Planarity : 0.006 0.087 1789 Dihedral : 15.234 89.195 1824 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.63 % Favored : 93.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.21), residues: 1296 helix: -1.25 (0.16), residues: 841 sheet: -2.51 (0.57), residues: 66 loop : -2.71 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1215 HIS 0.008 0.002 HIS A 588 PHE 0.023 0.002 PHE A 177 TYR 0.025 0.002 TYR B 110 ARG 0.006 0.001 ARG A 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 5) link_NAG-ASN : angle 3.05102 ( 15) link_BETA1-4 : bond 0.00846 ( 9) link_BETA1-4 : angle 2.64330 ( 27) hydrogen bonds : bond 0.05823 ( 552) hydrogen bonds : angle 5.50197 ( 1593) link_BETA1-6 : bond 0.00671 ( 1) link_BETA1-6 : angle 3.07325 ( 3) SS BOND : bond 0.01757 ( 8) SS BOND : angle 4.18463 ( 16) link_BETA1-3 : bond 0.01711 ( 1) link_BETA1-3 : angle 2.29383 ( 3) covalent geometry : bond 0.00408 (10874) covalent geometry : angle 0.85433 (14745) *********************** 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 437 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 364 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6888 (mtt90) cc_final: 0.5536 (ptt180) REVERT: A 129 MET cc_start: 0.7751 (ttm) cc_final: 0.7199 (tmm) REVERT: A 133 PHE cc_start: 0.7262 (t80) cc_final: 0.7031 (t80) REVERT: A 139 MET cc_start: 0.8351 (tpp) cc_final: 0.8087 (mtt) REVERT: A 228 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8249 (ttmt) REVERT: A 232 ARG cc_start: 0.7205 (ttt180) cc_final: 0.6635 (tpt90) REVERT: A 250 PHE cc_start: 0.8093 (t80) cc_final: 0.7401 (m-10) REVERT: A 266 ASN cc_start: 0.8914 (m-40) cc_final: 0.8180 (m110) REVERT: A 300 GLU cc_start: 0.8478 (tt0) cc_final: 0.8236 (tt0) REVERT: A 324 CYS cc_start: 0.5536 (t) cc_final: 0.5317 (t) REVERT: A 335 ARG cc_start: 0.9115 (tmm-80) cc_final: 0.8819 (ptm160) REVERT: A 382 PHE cc_start: 0.8746 (m-10) cc_final: 0.8542 (m-80) REVERT: A 384 MET cc_start: 0.8290 (mmp) cc_final: 0.8036 (mmm) REVERT: A 407 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7283 (tt0) REVERT: A 690 ASN cc_start: 0.8590 (t0) cc_final: 0.8274 (t0) REVERT: A 771 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6065 (ttt) REVERT: A 1059 LYS cc_start: 0.7557 (tttp) cc_final: 0.7351 (mptt) REVERT: A 1061 TYR cc_start: 0.8091 (t80) cc_final: 0.7582 (t80) REVERT: A 1071 PHE cc_start: 0.8606 (t80) cc_final: 0.8311 (t80) REVERT: A 1120 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7984 (ttm110) REVERT: A 1156 TYR cc_start: 0.7974 (m-80) cc_final: 0.7736 (m-80) REVERT: A 1191 ASN cc_start: 0.8801 (t0) cc_final: 0.8428 (t0) REVERT: A 1203 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8674 (t80) REVERT: A 1240 MET cc_start: 0.8209 (mmp) cc_final: 0.7935 (tpp) REVERT: A 1294 LYS cc_start: 0.7323 (mttt) cc_final: 0.7120 (mmmt) REVERT: A 1316 TYR cc_start: 0.7290 (t80) cc_final: 0.7074 (t80) REVERT: A 1325 ASP cc_start: 0.8355 (m-30) cc_final: 0.7855 (t0) REVERT: A 1377 ARG cc_start: 0.4890 (tpt170) cc_final: 0.4547 (mmt-90) REVERT: A 1394 VAL cc_start: 0.9444 (m) cc_final: 0.9201 (p) REVERT: A 1566 ILE cc_start: 0.8396 (mt) cc_final: 0.8135 (tt) REVERT: B 27 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: B 164 VAL cc_start: 0.9235 (t) cc_final: 0.9014 (p) REVERT: B 165 MET cc_start: 0.7891 (mmm) cc_final: 0.7681 (tmm) REVERT: B 166 MET cc_start: 0.8778 (tmm) cc_final: 0.8575 (tmm) REVERT: B 167 TYR cc_start: 0.8513 (m-80) cc_final: 0.8281 (m-80) REVERT: B 183 TYR cc_start: 0.7686 (t80) cc_final: 0.7301 (t80) outliers start: 73 outliers final: 31 residues processed: 402 average time/residue: 0.2107 time to fit residues: 121.6775 Evaluate side-chains 329 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 134 SER 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 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 781 MET Chi-restraints excluded: chain A residue 782 LEU 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 1359 VAL Chi-restraints excluded: chain A residue 1380 PHE 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 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 130 LEU 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 11 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN B 105 GLN B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110177 restraints weight = 22276.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112826 restraints weight = 11998.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114509 restraints weight = 7858.336| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10898 Z= 0.167 Angle : 0.774 9.826 14809 Z= 0.397 Chirality : 0.045 0.237 1751 Planarity : 0.005 0.099 1789 Dihedral : 11.856 89.718 1777 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.25 % Favored : 93.21 % Rotamer: Outliers : 6.73 % Allowed : 20.65 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1296 helix: -0.79 (0.17), residues: 845 sheet: -1.89 (0.62), residues: 56 loop : -2.51 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1507 HIS 0.007 0.002 HIS B 38 PHE 0.021 0.002 PHE B 102 TYR 0.026 0.002 TYR B 110 ARG 0.008 0.000 ARG A 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 5) link_NAG-ASN : angle 2.68620 ( 15) link_BETA1-4 : bond 0.00495 ( 9) link_BETA1-4 : angle 2.73317 ( 27) hydrogen bonds : bond 0.04783 ( 552) hydrogen bonds : angle 4.96249 ( 1593) link_BETA1-6 : bond 0.00369 ( 1) link_BETA1-6 : angle 2.92800 ( 3) SS BOND : bond 0.00533 ( 8) SS BOND : angle 2.00908 ( 16) link_BETA1-3 : bond 0.01341 ( 1) link_BETA1-3 : angle 2.37004 ( 3) covalent geometry : bond 0.00368 (10874) covalent geometry : angle 0.75745 (14745) *********************** 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 389 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 314 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6807 (mtt90) cc_final: 0.5552 (ptt180) REVERT: A 129 MET cc_start: 0.7939 (ttm) cc_final: 0.7354 (tmm) REVERT: A 139 MET cc_start: 0.8374 (tpp) cc_final: 0.8123 (mtt) REVERT: A 166 LYS cc_start: 0.8957 (mttt) cc_final: 0.8378 (mtpt) REVERT: A 184 TRP cc_start: 0.7894 (m100) cc_final: 0.7672 (m100) REVERT: A 228 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8213 (mtmm) REVERT: A 250 PHE cc_start: 0.8146 (t80) cc_final: 0.7488 (m-10) REVERT: A 266 ASN cc_start: 0.8959 (m-40) cc_final: 0.8396 (m-40) REVERT: A 305 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8175 (p90) REVERT: A 324 CYS cc_start: 0.5668 (t) cc_final: 0.5325 (t) REVERT: A 335 ARG cc_start: 0.9126 (tmm-80) cc_final: 0.8867 (ptm160) REVERT: A 382 PHE cc_start: 0.8786 (m-10) cc_final: 0.8253 (m-80) REVERT: A 391 PHE cc_start: 0.8743 (t80) cc_final: 0.8532 (t80) REVERT: A 625 TYR cc_start: 0.4955 (t80) cc_final: 0.4622 (t80) REVERT: A 771 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.5975 (ttt) REVERT: A 1061 TYR cc_start: 0.7881 (t80) cc_final: 0.7545 (t80) REVERT: A 1063 THR cc_start: 0.9043 (p) cc_final: 0.8830 (t) REVERT: A 1120 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: A 1203 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (t80) REVERT: A 1258 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 1292 MET cc_start: 0.6577 (mmp) cc_final: 0.5280 (mtt) REVERT: A 1325 ASP cc_start: 0.8325 (m-30) cc_final: 0.7852 (t0) REVERT: A 1335 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8534 (t0) REVERT: A 1336 MET cc_start: 0.8348 (ttt) cc_final: 0.8095 (tmm) REVERT: A 1377 ARG cc_start: 0.4742 (tpt170) cc_final: 0.4370 (mmt-90) REVERT: A 1448 LEU cc_start: 0.9317 (tt) cc_final: 0.9094 (tp) REVERT: A 1515 LEU cc_start: 0.8951 (mt) cc_final: 0.8714 (mm) REVERT: A 1566 ILE cc_start: 0.8463 (mt) cc_final: 0.8212 (tt) REVERT: B 164 VAL cc_start: 0.9313 (t) cc_final: 0.9005 (p) REVERT: B 165 MET cc_start: 0.7889 (mmm) cc_final: 0.7665 (tmm) REVERT: B 166 MET cc_start: 0.8949 (tmm) cc_final: 0.8546 (tmm) REVERT: B 183 TYR cc_start: 0.7721 (t80) cc_final: 0.7475 (t80) outliers start: 75 outliers final: 44 residues processed: 357 average time/residue: 0.2004 time to fit residues: 104.9128 Evaluate side-chains 327 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR 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 694 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 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 1335 ASN Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 ILE 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 50 ARG 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 150 VAL 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 118 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 127 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 HIS A1335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111757 restraints weight = 22002.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114351 restraints weight = 11756.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116043 restraints weight = 7659.989| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10898 Z= 0.144 Angle : 0.732 11.347 14809 Z= 0.373 Chirality : 0.044 0.249 1751 Planarity : 0.005 0.114 1789 Dihedral : 10.142 87.243 1768 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.94 % Favored : 93.52 % Rotamer: Outliers : 5.39 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1296 helix: -0.45 (0.17), residues: 846 sheet: -1.70 (0.62), residues: 56 loop : -2.46 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1507 HIS 0.006 0.001 HIS A 588 PHE 0.021 0.001 PHE B 102 TYR 0.020 0.001 TYR B 110 ARG 0.006 0.000 ARG A 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 2.46557 ( 15) link_BETA1-4 : bond 0.00636 ( 9) link_BETA1-4 : angle 2.48705 ( 27) hydrogen bonds : bond 0.04255 ( 552) hydrogen bonds : angle 4.67617 ( 1593) link_BETA1-6 : bond 0.00062 ( 1) link_BETA1-6 : angle 2.75006 ( 3) SS BOND : bond 0.00497 ( 8) SS BOND : angle 2.91133 ( 16) link_BETA1-3 : bond 0.01396 ( 1) link_BETA1-3 : angle 2.37555 ( 3) covalent geometry : bond 0.00305 (10874) covalent geometry : angle 0.71295 (14745) *********************** 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 375 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 315 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6705 (mtt90) cc_final: 0.5485 (ptt-90) REVERT: A 129 MET cc_start: 0.7777 (ttm) cc_final: 0.7285 (tmm) REVERT: A 184 TRP cc_start: 0.7945 (m100) cc_final: 0.7745 (m100) REVERT: A 250 PHE cc_start: 0.8226 (t80) cc_final: 0.7523 (m-10) REVERT: A 266 ASN cc_start: 0.8903 (m-40) cc_final: 0.8110 (m110) REVERT: A 335 ARG cc_start: 0.9172 (tmm-80) cc_final: 0.8953 (ptm160) REVERT: A 382 PHE cc_start: 0.8592 (m-10) cc_final: 0.8288 (m-80) REVERT: A 605 PHE cc_start: 0.8416 (m-80) cc_final: 0.8156 (m-80) REVERT: A 625 TYR cc_start: 0.4708 (t80) cc_final: 0.4355 (t80) REVERT: A 759 GLU cc_start: 0.8155 (tt0) cc_final: 0.7951 (tt0) REVERT: A 771 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6186 (ttt) REVERT: A 1061 TYR cc_start: 0.7883 (t80) cc_final: 0.7548 (t80) REVERT: A 1203 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8814 (t80) REVERT: A 1258 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8680 (tp) REVERT: A 1281 MET cc_start: 0.8569 (mpp) cc_final: 0.8302 (mpp) REVERT: A 1292 MET cc_start: 0.6570 (mmp) cc_final: 0.5440 (mtt) REVERT: A 1316 TYR cc_start: 0.7255 (t80) cc_final: 0.7018 (t80) REVERT: A 1325 ASP cc_start: 0.8310 (m-30) cc_final: 0.7860 (t0) REVERT: A 1377 ARG cc_start: 0.4048 (tpt170) cc_final: 0.3450 (mmt-90) REVERT: A 1475 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.6376 (p90) REVERT: A 1508 ASP cc_start: 0.7973 (p0) cc_final: 0.7746 (p0) REVERT: A 1515 LEU cc_start: 0.8924 (mt) cc_final: 0.8706 (mt) REVERT: A 1566 ILE cc_start: 0.8494 (mt) cc_final: 0.8249 (tt) REVERT: B 163 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 166 MET cc_start: 0.9048 (tmm) cc_final: 0.8618 (tmm) REVERT: B 183 TYR cc_start: 0.7675 (t80) cc_final: 0.7219 (t80) outliers start: 60 outliers final: 39 residues processed: 357 average time/residue: 0.1892 time to fit residues: 99.5321 Evaluate side-chains 333 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 176 HIS 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 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 TYR 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 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 1016 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 1335 ASN Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1533 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 74 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111944 restraints weight = 22002.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114570 restraints weight = 11774.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116218 restraints weight = 7646.215| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10898 Z= 0.140 Angle : 0.715 11.632 14809 Z= 0.362 Chirality : 0.043 0.239 1751 Planarity : 0.005 0.099 1789 Dihedral : 8.935 86.776 1762 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.17 % Favored : 93.29 % Rotamer: Outliers : 5.92 % Allowed : 24.15 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1296 helix: -0.17 (0.17), residues: 846 sheet: -1.72 (0.58), residues: 62 loop : -2.53 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 176 HIS 0.006 0.001 HIS A 588 PHE 0.021 0.001 PHE B 102 TYR 0.016 0.001 TYR B 110 ARG 0.012 0.001 ARG A1120 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 5) link_NAG-ASN : angle 2.41327 ( 15) link_BETA1-4 : bond 0.00553 ( 9) link_BETA1-4 : angle 2.26109 ( 27) hydrogen bonds : bond 0.03920 ( 552) hydrogen bonds : angle 4.53567 ( 1593) link_BETA1-6 : bond 0.00257 ( 1) link_BETA1-6 : angle 2.61871 ( 3) SS BOND : bond 0.00668 ( 8) SS BOND : angle 1.98280 ( 16) link_BETA1-3 : bond 0.01378 ( 1) link_BETA1-3 : angle 2.30012 ( 3) covalent geometry : bond 0.00307 (10874) covalent geometry : angle 0.70052 (14745) *********************** 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 368 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 302 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6714 (mtt90) cc_final: 0.5467 (ptt180) REVERT: A 129 MET cc_start: 0.7800 (ttm) cc_final: 0.7330 (tmm) REVERT: A 266 ASN cc_start: 0.8912 (m-40) cc_final: 0.8286 (m-40) REVERT: A 335 ARG cc_start: 0.9156 (tmm-80) cc_final: 0.8734 (ptm160) REVERT: A 563 MET cc_start: 0.7046 (tmm) cc_final: 0.6832 (tmm) REVERT: A 605 PHE cc_start: 0.8425 (m-80) cc_final: 0.8058 (m-80) REVERT: A 608 ILE cc_start: 0.8874 (mm) cc_final: 0.8614 (mt) REVERT: A 625 TYR cc_start: 0.4547 (t80) cc_final: 0.4133 (t80) REVERT: A 754 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: A 759 GLU cc_start: 0.8275 (tt0) cc_final: 0.7999 (tt0) REVERT: A 771 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6149 (ttt) REVERT: A 1203 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8780 (t80) REVERT: A 1258 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 1292 MET cc_start: 0.6649 (mmp) cc_final: 0.5523 (mtt) REVERT: A 1325 ASP cc_start: 0.8303 (m-30) cc_final: 0.7884 (t0) REVERT: A 1475 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.6351 (p90) REVERT: A 1485 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8920 (mp) REVERT: A 1515 LEU cc_start: 0.8954 (mt) cc_final: 0.8725 (mt) REVERT: B 81 THR cc_start: 0.8697 (m) cc_final: 0.8427 (t) REVERT: B 166 MET cc_start: 0.9096 (tmm) cc_final: 0.8597 (tmm) REVERT: B 176 TRP cc_start: 0.7180 (OUTLIER) cc_final: 0.6944 (t60) outliers start: 66 outliers final: 47 residues processed: 345 average time/residue: 0.1810 time to fit residues: 93.1239 Evaluate side-chains 337 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 176 HIS 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 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 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 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU 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 1149 ASN 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 1335 ASN Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS 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 150 VAL 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 39 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113785 restraints weight = 22441.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116292 restraints weight = 12309.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117939 restraints weight = 8240.108| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10898 Z= 0.137 Angle : 0.723 14.975 14809 Z= 0.363 Chirality : 0.043 0.227 1751 Planarity : 0.005 0.093 1789 Dihedral : 8.063 85.224 1755 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.71 % Favored : 93.75 % Rotamer: Outliers : 6.55 % Allowed : 23.61 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1296 helix: 0.08 (0.18), residues: 839 sheet: -1.55 (0.59), residues: 62 loop : -2.46 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 PHE 0.023 0.001 PHE A1499 TYR 0.018 0.001 TYR B 183 ARG 0.009 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 5) link_NAG-ASN : angle 2.38227 ( 15) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 2.12213 ( 27) hydrogen bonds : bond 0.03818 ( 552) hydrogen bonds : angle 4.46198 ( 1593) link_BETA1-6 : bond 0.00266 ( 1) link_BETA1-6 : angle 2.57533 ( 3) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.57058 ( 16) link_BETA1-3 : bond 0.01150 ( 1) link_BETA1-3 : angle 2.11912 ( 3) covalent geometry : bond 0.00303 (10874) covalent geometry : angle 0.71123 (14745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6731 (mtt90) cc_final: 0.5412 (ptt180) REVERT: A 129 MET cc_start: 0.7782 (ttm) cc_final: 0.7295 (tmm) REVERT: A 250 PHE cc_start: 0.8291 (t80) cc_final: 0.7562 (m-10) REVERT: A 266 ASN cc_start: 0.8884 (m-40) cc_final: 0.8254 (m-40) REVERT: A 335 ARG cc_start: 0.9147 (tmm-80) cc_final: 0.8708 (ptm160) REVERT: A 343 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7568 (p0) REVERT: A 383 ILE cc_start: 0.8888 (mm) cc_final: 0.8656 (mm) REVERT: A 563 MET cc_start: 0.6856 (tmm) cc_final: 0.6616 (tmm) REVERT: A 605 PHE cc_start: 0.8439 (m-80) cc_final: 0.8154 (m-80) REVERT: A 625 TYR cc_start: 0.4469 (t80) cc_final: 0.3808 (t80) REVERT: A 656 LEU cc_start: 0.8983 (mt) cc_final: 0.8717 (mm) REVERT: A 759 GLU cc_start: 0.8230 (tt0) cc_final: 0.7915 (tt0) REVERT: A 771 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6322 (ttt) REVERT: A 993 CYS cc_start: 0.8460 (m) cc_final: 0.8142 (m) REVERT: A 1009 MET cc_start: 0.8318 (mmp) cc_final: 0.8013 (mmp) REVERT: A 1024 ILE cc_start: 0.8633 (tp) cc_final: 0.8433 (tp) REVERT: A 1203 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8787 (t80) REVERT: A 1240 MET cc_start: 0.8550 (mmp) cc_final: 0.8213 (tpp) REVERT: A 1258 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (tp) REVERT: A 1292 MET cc_start: 0.6694 (mmp) cc_final: 0.5559 (mtt) REVERT: A 1325 ASP cc_start: 0.8474 (m-30) cc_final: 0.7896 (t0) REVERT: A 1451 LEU cc_start: 0.9344 (tp) cc_final: 0.9117 (tt) REVERT: A 1456 LEU cc_start: 0.9259 (tp) cc_final: 0.8844 (tp) REVERT: A 1475 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.6241 (p90) REVERT: A 1508 ASP cc_start: 0.7926 (p0) cc_final: 0.7718 (p0) REVERT: A 1515 LEU cc_start: 0.9170 (mt) cc_final: 0.8966 (mt) REVERT: A 1566 ILE cc_start: 0.8582 (mt) cc_final: 0.8362 (tt) REVERT: B 125 TYR cc_start: 0.6733 (t80) cc_final: 0.5882 (t80) REVERT: B 128 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8357 (mtm180) REVERT: B 148 ASN cc_start: 0.8577 (p0) cc_final: 0.8258 (p0) REVERT: B 163 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 166 MET cc_start: 0.9085 (tmm) cc_final: 0.8626 (tmm) outliers start: 73 outliers final: 49 residues processed: 342 average time/residue: 0.1865 time to fit residues: 95.2242 Evaluate side-chains 339 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 176 HIS 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 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN 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 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 781 MET Chi-restraints excluded: chain A residue 782 LEU 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 1149 ASN 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 1335 ASN Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 74 ILE 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 170 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114414 restraints weight = 22744.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117011 restraints weight = 12407.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118637 restraints weight = 8237.840| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10898 Z= 0.135 Angle : 0.711 11.430 14809 Z= 0.358 Chirality : 0.042 0.185 1751 Planarity : 0.004 0.091 1789 Dihedral : 7.447 82.968 1753 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.79 % Favored : 93.67 % Rotamer: Outliers : 5.03 % Allowed : 25.13 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1296 helix: 0.22 (0.18), residues: 843 sheet: -0.84 (0.70), residues: 49 loop : -2.35 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS A 588 PHE 0.022 0.001 PHE B 102 TYR 0.017 0.001 TYR B 183 ARG 0.007 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 2.31599 ( 15) link_BETA1-4 : bond 0.00527 ( 9) link_BETA1-4 : angle 2.03062 ( 27) hydrogen bonds : bond 0.03721 ( 552) hydrogen bonds : angle 4.42830 ( 1593) link_BETA1-6 : bond 0.00425 ( 1) link_BETA1-6 : angle 2.46825 ( 3) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.67398 ( 16) link_BETA1-3 : bond 0.01001 ( 1) link_BETA1-3 : angle 2.00065 ( 3) covalent geometry : bond 0.00295 (10874) covalent geometry : angle 0.69965 (14745) *********************** 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 353 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6752 (mtt90) cc_final: 0.5421 (ptt180) REVERT: A 129 MET cc_start: 0.7741 (ttm) cc_final: 0.7367 (tmm) REVERT: A 266 ASN cc_start: 0.8825 (m-40) cc_final: 0.8264 (m-40) REVERT: A 305 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7921 (p90) REVERT: A 335 ARG cc_start: 0.8974 (tmm-80) cc_final: 0.8690 (ptm160) REVERT: A 343 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7624 (p0) REVERT: A 563 MET cc_start: 0.6797 (tmm) cc_final: 0.6580 (tmm) REVERT: A 625 TYR cc_start: 0.4107 (t80) cc_final: 0.3785 (t80) REVERT: A 656 LEU cc_start: 0.9044 (mt) cc_final: 0.8769 (mm) REVERT: A 771 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6493 (ttt) REVERT: A 993 CYS cc_start: 0.8343 (m) cc_final: 0.8076 (m) REVERT: A 1009 MET cc_start: 0.8207 (mmp) cc_final: 0.7882 (mmp) REVERT: A 1203 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8647 (t80) REVERT: A 1240 MET cc_start: 0.8528 (mmp) cc_final: 0.8219 (tpp) REVERT: A 1258 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 1292 MET cc_start: 0.6711 (mmp) cc_final: 0.5644 (mtt) REVERT: A 1325 ASP cc_start: 0.8436 (m-30) cc_final: 0.7864 (t0) REVERT: A 1335 ASN cc_start: 0.8311 (t0) cc_final: 0.7756 (t0) REVERT: A 1451 LEU cc_start: 0.9321 (tp) cc_final: 0.9082 (tt) REVERT: A 1456 LEU cc_start: 0.9248 (tp) cc_final: 0.8828 (tp) REVERT: A 1475 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.6118 (p90) REVERT: A 1515 LEU cc_start: 0.9194 (mt) cc_final: 0.8979 (mt) REVERT: B 125 TYR cc_start: 0.6681 (t80) cc_final: 0.5915 (t80) REVERT: B 148 ASN cc_start: 0.8620 (p0) cc_final: 0.8292 (p0) REVERT: B 166 MET cc_start: 0.9006 (tmm) cc_final: 0.8571 (tmm) outliers start: 56 outliers final: 39 residues processed: 333 average time/residue: 0.1858 time to fit residues: 92.2229 Evaluate side-chains 329 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 176 HIS 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 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 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 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 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 1149 ASN 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 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 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS 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 150 VAL 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 32 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN A1335 ASN A1472 ASN A1528 ASN B 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107929 restraints weight = 22657.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110357 restraints weight = 12738.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111866 restraints weight = 8642.020| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 10898 Z= 0.240 Angle : 0.793 9.316 14809 Z= 0.409 Chirality : 0.046 0.257 1751 Planarity : 0.005 0.100 1789 Dihedral : 7.639 82.648 1751 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.94 % Favored : 92.59 % Rotamer: Outliers : 5.92 % Allowed : 25.13 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1296 helix: 0.10 (0.17), residues: 857 sheet: -0.60 (0.70), residues: 52 loop : -2.53 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 61 HIS 0.008 0.003 HIS A 588 PHE 0.031 0.002 PHE A1499 TYR 0.023 0.002 TYR B 110 ARG 0.006 0.001 ARG A1429 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 5) link_NAG-ASN : angle 2.56873 ( 15) link_BETA1-4 : bond 0.00529 ( 9) link_BETA1-4 : angle 2.22556 ( 27) hydrogen bonds : bond 0.04214 ( 552) hydrogen bonds : angle 4.74591 ( 1593) link_BETA1-6 : bond 0.00322 ( 1) link_BETA1-6 : angle 1.94971 ( 3) SS BOND : bond 0.00647 ( 8) SS BOND : angle 1.87014 ( 16) link_BETA1-3 : bond 0.00726 ( 1) link_BETA1-3 : angle 2.15626 ( 3) covalent geometry : bond 0.00556 (10874) covalent geometry : angle 0.78145 (14745) *********************** 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 348 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6919 (mtt90) cc_final: 0.5331 (ptt180) REVERT: A 129 MET cc_start: 0.7980 (ttm) cc_final: 0.7471 (tmm) REVERT: A 305 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8187 (p90) REVERT: A 343 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7959 (p0) REVERT: A 393 LEU cc_start: 0.8676 (mt) cc_final: 0.8326 (mt) REVERT: A 563 MET cc_start: 0.6799 (tmm) cc_final: 0.6547 (tmm) REVERT: A 771 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6459 (ttt) REVERT: A 988 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7788 (t0) REVERT: A 993 CYS cc_start: 0.8415 (m) cc_final: 0.8204 (m) REVERT: A 1203 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8894 (t80) REVERT: A 1240 MET cc_start: 0.8615 (mmp) cc_final: 0.8401 (tpp) REVERT: A 1258 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (tp) REVERT: A 1281 MET cc_start: 0.8506 (mpp) cc_final: 0.8005 (mpp) REVERT: A 1325 ASP cc_start: 0.8465 (m-30) cc_final: 0.8037 (t0) REVERT: A 1377 ARG cc_start: 0.4191 (tpt170) cc_final: 0.3393 (mmt-90) REVERT: A 1419 ILE cc_start: 0.8721 (mm) cc_final: 0.8519 (mm) REVERT: A 1456 LEU cc_start: 0.9315 (tp) cc_final: 0.9003 (tp) REVERT: A 1475 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.6465 (p90) REVERT: A 1548 CYS cc_start: 0.8366 (m) cc_final: 0.7825 (m) REVERT: B 49 MET cc_start: 0.8187 (ptm) cc_final: 0.7867 (ptp) REVERT: B 166 MET cc_start: 0.9035 (tmm) cc_final: 0.8618 (tmm) outliers start: 66 outliers final: 48 residues processed: 324 average time/residue: 0.1893 time to fit residues: 92.3074 Evaluate side-chains 328 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 156 THR 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 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 409 ASN 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 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 988 ASN 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 1260 ILE 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 1335 ASN 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 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS 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 150 VAL Chi-restraints excluded: chain B residue 162 SER 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 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111342 restraints weight = 22840.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113848 restraints weight = 12486.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115487 restraints weight = 8376.165| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10898 Z= 0.152 Angle : 0.736 9.963 14809 Z= 0.375 Chirality : 0.043 0.197 1751 Planarity : 0.005 0.093 1789 Dihedral : 7.333 80.724 1751 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 4.94 % Allowed : 27.20 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1296 helix: 0.40 (0.18), residues: 847 sheet: -1.04 (0.63), residues: 62 loop : -2.21 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1507 HIS 0.004 0.001 HIS A 588 PHE 0.026 0.002 PHE A1499 TYR 0.017 0.001 TYR B 125 ARG 0.005 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 5) link_NAG-ASN : angle 2.35501 ( 15) link_BETA1-4 : bond 0.00548 ( 9) link_BETA1-4 : angle 2.02565 ( 27) hydrogen bonds : bond 0.03791 ( 552) hydrogen bonds : angle 4.57329 ( 1593) link_BETA1-6 : bond 0.00422 ( 1) link_BETA1-6 : angle 1.92350 ( 3) SS BOND : bond 0.00378 ( 8) SS BOND : angle 1.37089 ( 16) link_BETA1-3 : bond 0.00907 ( 1) link_BETA1-3 : angle 1.58084 ( 3) covalent geometry : bond 0.00348 (10874) covalent geometry : angle 0.72673 (14745) *********************** 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 339 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6894 (mtt90) cc_final: 0.5303 (ptt180) REVERT: A 129 MET cc_start: 0.7922 (ttm) cc_final: 0.7376 (tmm) REVERT: A 305 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8051 (p90) REVERT: A 343 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7803 (p0) REVERT: A 344 TYR cc_start: 0.8833 (m-80) cc_final: 0.8484 (m-80) REVERT: A 369 MET cc_start: 0.9011 (mtp) cc_final: 0.8669 (mtm) REVERT: A 393 LEU cc_start: 0.8525 (mt) cc_final: 0.8278 (mt) REVERT: A 563 MET cc_start: 0.6771 (tmm) cc_final: 0.6566 (tmm) REVERT: A 656 LEU cc_start: 0.9039 (mt) cc_final: 0.8808 (mm) REVERT: A 771 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6180 (ttt) REVERT: A 993 CYS cc_start: 0.8486 (m) cc_final: 0.8232 (m) REVERT: A 1203 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8760 (t80) REVERT: A 1240 MET cc_start: 0.8586 (mmp) cc_final: 0.8348 (tpp) REVERT: A 1258 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 1281 MET cc_start: 0.8392 (mpp) cc_final: 0.7987 (mpp) REVERT: A 1292 MET cc_start: 0.6781 (mmp) cc_final: 0.5626 (mtt) REVERT: A 1325 ASP cc_start: 0.8499 (m-30) cc_final: 0.8051 (t0) REVERT: A 1438 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7517 (ptm-80) REVERT: A 1475 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.6349 (p90) REVERT: A 1487 ASN cc_start: 0.9456 (p0) cc_final: 0.9234 (p0) REVERT: A 1548 CYS cc_start: 0.8307 (m) cc_final: 0.7822 (m) REVERT: A 1566 ILE cc_start: 0.8710 (mt) cc_final: 0.8502 (tt) REVERT: B 49 MET cc_start: 0.8119 (ptm) cc_final: 0.7830 (ptm) REVERT: B 166 MET cc_start: 0.8971 (tmm) cc_final: 0.8539 (tmm) outliers start: 55 outliers final: 44 residues processed: 317 average time/residue: 0.1852 time to fit residues: 87.8624 Evaluate side-chains 333 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 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 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 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 1335 ASN Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE 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 1475 TYR 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 73 HIS Chi-restraints excluded: chain B residue 75 TYR 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 12 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 9.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108427 restraints weight = 22808.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110892 restraints weight = 12612.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112396 restraints weight = 8484.890| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10898 Z= 0.215 Angle : 0.788 13.696 14809 Z= 0.402 Chirality : 0.045 0.184 1751 Planarity : 0.005 0.096 1789 Dihedral : 7.467 79.427 1751 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.94 % Favored : 92.52 % Rotamer: Outliers : 5.12 % Allowed : 27.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1296 helix: 0.39 (0.18), residues: 841 sheet: -0.52 (0.69), residues: 52 loop : -2.18 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 671 HIS 0.007 0.002 HIS A 588 PHE 0.040 0.002 PHE A1499 TYR 0.020 0.002 TYR A 625 ARG 0.005 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 5) link_NAG-ASN : angle 2.46093 ( 15) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 2.12401 ( 27) hydrogen bonds : bond 0.03862 ( 552) hydrogen bonds : angle 4.72136 ( 1593) link_BETA1-6 : bond 0.00270 ( 1) link_BETA1-6 : angle 1.78014 ( 3) SS BOND : bond 0.00531 ( 8) SS BOND : angle 1.53361 ( 16) link_BETA1-3 : bond 0.00761 ( 1) link_BETA1-3 : angle 1.80297 ( 3) covalent geometry : bond 0.00503 (10874) covalent geometry : angle 0.77765 (14745) ********************** 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 339 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6969 (mtt90) cc_final: 0.5316 (ptt180) REVERT: A 129 MET cc_start: 0.7965 (ttm) cc_final: 0.7448 (tmm) REVERT: A 305 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8026 (p90) REVERT: A 343 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 391 PHE cc_start: 0.9196 (t80) cc_final: 0.8890 (t80) REVERT: A 771 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6417 (ttt) REVERT: A 993 CYS cc_start: 0.8262 (m) cc_final: 0.7957 (m) REVERT: A 1009 MET cc_start: 0.8260 (mmp) cc_final: 0.7823 (mmp) REVERT: A 1203 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (t80) REVERT: A 1240 MET cc_start: 0.8610 (mmp) cc_final: 0.8401 (tpp) REVERT: A 1258 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8740 (tp) REVERT: A 1281 MET cc_start: 0.8442 (mpp) cc_final: 0.8025 (mpp) REVERT: A 1292 MET cc_start: 0.6826 (mmp) cc_final: 0.5676 (mtt) REVERT: A 1325 ASP cc_start: 0.8463 (m-30) cc_final: 0.8038 (t0) REVERT: A 1377 ARG cc_start: 0.4283 (tpt170) cc_final: 0.3521 (mmt-90) REVERT: A 1445 MET cc_start: 0.8828 (tpp) cc_final: 0.8622 (ttp) REVERT: A 1456 LEU cc_start: 0.9270 (tp) cc_final: 0.8855 (tp) REVERT: A 1475 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.6437 (p90) REVERT: A 1487 ASN cc_start: 0.9438 (p0) cc_final: 0.9209 (p0) REVERT: A 1548 CYS cc_start: 0.8393 (m) cc_final: 0.7999 (m) REVERT: B 49 MET cc_start: 0.7982 (ptm) cc_final: 0.7756 (ptt) REVERT: B 128 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8424 (mtm180) REVERT: B 166 MET cc_start: 0.9064 (tmm) cc_final: 0.8617 (tmm) outliers start: 57 outliers final: 45 residues processed: 316 average time/residue: 0.1808 time to fit residues: 85.9964 Evaluate side-chains 325 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 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 781 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 1335 ASN Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1380 PHE 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 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 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 101 optimal weight: 0.0060 chunk 125 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112907 restraints weight = 22489.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115453 restraints weight = 12297.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117053 restraints weight = 8224.322| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10898 Z= 0.142 Angle : 0.749 14.012 14809 Z= 0.376 Chirality : 0.043 0.220 1751 Planarity : 0.004 0.092 1789 Dihedral : 7.144 78.286 1751 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.71 % Favored : 93.75 % Rotamer: Outliers : 4.31 % Allowed : 28.90 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1296 helix: 0.56 (0.18), residues: 841 sheet: -0.39 (0.70), residues: 49 loop : -2.04 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1507 HIS 0.003 0.001 HIS A 731 PHE 0.030 0.001 PHE A1499 TYR 0.019 0.001 TYR A 625 ARG 0.005 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 5) link_NAG-ASN : angle 2.29252 ( 15) link_BETA1-4 : bond 0.00562 ( 9) link_BETA1-4 : angle 1.96385 ( 27) hydrogen bonds : bond 0.03671 ( 552) hydrogen bonds : angle 4.52165 ( 1593) link_BETA1-6 : bond 0.00470 ( 1) link_BETA1-6 : angle 1.68640 ( 3) SS BOND : bond 0.00314 ( 8) SS BOND : angle 1.29988 ( 16) link_BETA1-3 : bond 0.00920 ( 1) link_BETA1-3 : angle 1.58876 ( 3) covalent geometry : bond 0.00317 (10874) covalent geometry : angle 0.74017 (14745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.88 seconds wall clock time: 68 minutes 11.46 seconds (4091.46 seconds total)