Starting phenix.real_space_refine on Sun Sep 13 09:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xez_22160/09_2026/6xez_22160.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 76 5.49 5 Mg 3 5.21 5 S 148 5.16 5 C 13519 2.51 5 N 3671 2.21 5 O 4309 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21742 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7459 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1383 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNAv2': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 88.721 102.304 119.424 1.00 68.21 S ATOM 2487 SG CYS A 306 88.421 100.924 122.609 1.00 63.53 S ATOM 2519 SG CYS A 310 86.803 104.423 121.909 1.00 60.93 S ATOM 3927 SG CYS A 487 86.518 86.967 105.077 1.00 80.68 S ATOM 5180 SG CYS A 645 87.725 84.546 108.337 1.00 88.48 S ATOM 5186 SG CYS A 646 88.285 87.912 107.513 1.00 83.87 S ATOM 10836 SG CYS E 5 35.198 82.097 55.078 1.00166.51 S ATOM 10857 SG CYS E 8 31.322 80.782 54.935 1.00172.10 S ATOM 10995 SG CYS E 26 34.582 78.680 55.069 1.00168.19 S ATOM 11016 SG CYS E 29 33.664 79.940 52.226 1.00172.63 S ATOM 11181 SG CYS E 50 56.471 65.217 50.133 1.00219.44 S ATOM 11211 SG CYS E 55 56.897 64.867 46.869 1.00232.67 S ATOM 11344 SG CYS E 72 55.192 62.162 47.361 1.00223.45 S ATOM 10918 SG CYS E 16 44.259 80.491 46.350 1.00182.34 S ATOM 10933 SG CYS E 19 42.754 82.711 44.924 1.00184.86 S ATOM 15454 SG CYS F 5 88.579 86.061 55.194 1.00180.72 S ATOM 15475 SG CYS F 8 85.587 84.904 54.927 1.00185.31 S ATOM 15613 SG CYS F 26 87.698 81.703 54.852 1.00198.76 S ATOM 15634 SG CYS F 29 89.784 82.795 52.868 1.00206.02 S ATOM 15799 SG CYS F 50 98.078 68.991 74.102 1.00227.89 S ATOM 15829 SG CYS F 55 101.194 68.363 74.238 1.00239.77 S ATOM 15962 SG CYS F 72 100.061 65.848 72.923 1.00235.51 S ATOM 15536 SG CYS F 16 98.784 82.792 61.307 1.00188.21 S ATOM 15551 SG CYS F 19 100.099 86.280 59.520 1.00196.10 S Time building chain proxies: 4.24, per 1000 atoms: 0.20 Number of scatterers: 21742 At special positions: 0 Unit cell: (152.9, 149.6, 185.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 148 16.00 P 76 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4309 8.00 N 3671 7.00 C 13519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " Number of angles added : 28 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 31 sheets defined 41.7% alpha, 8.4% beta 32 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.970A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.655A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 removed outlier: 4.704A pdb=" N GLN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.698A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.587A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.533A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.524A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 318 removed outlier: 4.060A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.994A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.529A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 455 removed outlier: 3.881A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 467 through 480 removed outlier: 4.336A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.154A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 4.192A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.544A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.871A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.558A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 4.041A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 767 through 774 removed outlier: 3.794A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.687A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 854 through 867 removed outlier: 4.624A pdb=" N VAL A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.729A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.668A pdb=" N GLU A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.227A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 96 removed outlier: 4.130A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.553A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 173 through 177 removed outlier: 4.026A pdb=" N SER B 177 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.634A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'D' and resid 9 through 28 removed outlier: 4.389A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.909A pdb=" N GLN D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.094A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.622A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 4.067A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.590A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 265 through 275 removed outlier: 3.835A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.551A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 391 removed outlier: 4.109A pdb=" N LEU E 391 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 430 Processing helix chain 'E' and resid 445 through 455 Processing helix chain 'E' and resid 489 through 497 removed outlier: 3.546A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 515 through 523 removed outlier: 3.850A pdb=" N ALA E 522 " --> pdb=" O GLN E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.698A pdb=" N LYS E 584 " --> pdb=" O ASP E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.590A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.813A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.736A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 275 removed outlier: 3.709A pdb=" N ALA F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 299 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.716A pdb=" N LEU F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.922A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 580 through 585 removed outlier: 3.748A pdb=" N LYS F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.814A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.533A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.513A pdb=" N VAL A 844 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.731A pdb=" N THR A 540 " --> pdb=" O MET A 666 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 543 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB4, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.629A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.061A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.917A pdb=" N LEU D 128 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.698A pdb=" N TRP D 154 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC1, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC2, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC3, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'E' and resid 208 through 209 removed outlier: 7.116A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 154 " --> pdb=" O ASP E 223 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.491A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 397 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E 373 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 399 " --> pdb=" O PHE E 373 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS E 330 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR E 359 " --> pdb=" O CYS E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AC7, first strand: chain 'E' and resid 510 through 512 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC9, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AD1, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AD2, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.725A pdb=" N VAL F 154 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER F 166 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.568A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 511 through 512 753 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 1.99 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: 3784 1.32 - 1.44: 6140 1.44 - 1.57: 12017 1.57 - 1.69: 202 1.69 - 1.81: 212 Bond restraints: 22355 Sorted by residual: bond pdb=" F1 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" F1 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" F2 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" F2 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" F3 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 22350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 30101 2.92 - 5.83: 543 5.83 - 8.75: 76 8.75 - 11.66: 15 11.66 - 14.58: 7 Bond angle restraints: 30742 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 134.55 -12.85 1.80e+00 3.09e-01 5.10e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 132.81 -11.11 1.80e+00 3.09e-01 3.81e+01 angle pdb=" O1B ADP E 704 " pdb=" PB ADP E 704 " pdb=" O2B ADP E 704 " ideal model delta sigma weight residual 119.90 105.32 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O1B ADP F1003 " pdb=" PB ADP F1003 " pdb=" O2B ADP F1003 " ideal model delta sigma weight residual 119.90 105.35 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C1' ADP F1003 " pdb=" C2' ADP F1003 " pdb=" C3' ADP F1003 " ideal model delta sigma weight residual 111.00 96.73 14.27 3.00e+00 1.11e-01 2.26e+01 ... (remaining 30737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 12616 34.01 - 68.01: 534 68.01 - 102.02: 28 102.02 - 136.03: 3 136.03 - 170.04: 5 Dihedral angle restraints: 13186 sinusoidal: 5600 harmonic: 7586 Sorted by residual: dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -35.62 71.97 1 3.10e+00 1.04e-01 6.90e+02 dihedral pdb=" O4' A P 35 " pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " ideal model delta sinusoidal sigma weight residual -35.15 23.04 -58.18 1 4.00e+00 6.25e-02 2.84e+02 dihedral pdb=" O4' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " pdb=" C3' A P 35 " ideal model delta sinusoidal sigma weight residual -94.41 -36.85 -57.56 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 13183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3416 0.123 - 0.247: 127 0.247 - 0.370: 24 0.370 - 0.493: 6 0.493 - 0.617: 1 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" C6 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" C5 1N7 A1006 " pdb=" C7 1N7 A1006 " both_signs ideal model delta sigma weight residual False -2.43 -2.86 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 1N7 A1005 " pdb=" C1 1N7 A1005 " pdb=" C15 1N7 A1005 " pdb=" C19 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.81 -2.40 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 3571 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 824 " 0.039 2.00e-02 2.50e+03 7.84e-02 6.14e+01 pdb=" CG ASP A 824 " -0.136 2.00e-02 2.50e+03 pdb=" OD1 ASP A 824 " 0.050 2.00e-02 2.50e+03 pdb=" OD2 ASP A 824 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 289 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C SER F 289 " 0.060 2.00e-02 2.50e+03 pdb=" O SER F 289 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS F 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 582 " 0.028 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR F 582 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR F 582 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 582 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 582 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 582 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 582 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 582 " 0.006 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 5 1.90 - 2.65: 693 2.65 - 3.40: 31508 3.40 - 4.15: 51638 4.15 - 4.90: 88232 Nonbonded interactions: 172076 Sorted by model distance: nonbonded pdb=" O LEU E 65 " pdb=" OG SER E 80 " model vdw 1.146 3.040 nonbonded pdb=" O1B ADP E 704 " pdb=" F3 AF3 E 705 " model vdw 1.813 2.990 nonbonded pdb=" O2B ADP F1003 " pdb=" F3 AF3 F1004 " model vdw 1.813 2.990 nonbonded pdb=" O1B ADP F1003 " pdb=" F1 AF3 F1004 " model vdw 1.820 2.990 nonbonded pdb=" O2B ADP E 704 " pdb=" F1 AF3 E 705 " model vdw 1.820 2.990 ... (remaining 172071 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 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 41 or (resid 42 through 4 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 44 through 1 \ 91)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 50 or (resid 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 706)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 1005)) } 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=0.00 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: 2.940 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.800 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.014 0.830 22388 Z= 0.747 Angle : 1.185 57.152 30770 Z= 0.507 Chirality : 0.065 0.617 3574 Planarity : 0.005 0.078 3641 Dihedral : 17.923 170.035 8292 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.01 % Favored : 86.91 % Rotamer: Outliers : 10.77 % Allowed : 22.63 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.14), residues: 2551 helix: -2.11 (0.13), residues: 946 sheet: -3.54 (0.25), residues: 312 loop : -3.60 (0.14), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 533 TYR 0.051 0.002 TYR F 582 PHE 0.020 0.002 PHE A 471 TRP 0.021 0.002 TRP A 916 HIS 0.016 0.002 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01064 / 0.47 (22355) covalent geometry : angle 0.98676 / 0.49 (30742) hydrogen bonds : bond 0.14162 / 9.52 ( 832) hydrogen bonds : angle 6.28838 / 4.34 ( 2227) metal coordination : bond 0.18994 / 11.14 ( 32) metal coordination : angle 21.75890 / 16.63 ( 28) Misc. bond : bond 0.82974 / 43.67 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 131 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 261 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 331 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (ttm-80) REVERT: A 431 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7432 (mm-30) REVERT: A 553 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7272 (ptt180) REVERT: A 668 MET cc_start: 0.8593 (ttp) cc_final: 0.8353 (ttt) REVERT: B 55 MET cc_start: 0.9535 (mmm) cc_final: 0.9279 (mmm) REVERT: B 165 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8340 (pttt) REVERT: B 174 MET cc_start: 0.9046 (tpt) cc_final: 0.8801 (tpp) REVERT: B 189 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8121 (mt) REVERT: C 38 ASP cc_start: 0.8737 (t0) cc_final: 0.8483 (t0) REVERT: E 274 MET cc_start: 0.8360 (mmm) cc_final: 0.8115 (mmp) REVERT: E 448 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8064 (pt) REVERT: F 62 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: F 502 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7649 (ptm160) REVERT: F 585 LEU cc_start: 0.3740 (OUTLIER) cc_final: 0.3531 (pt) outliers start: 237 outliers final: 178 residues processed: 356 average time/residue: 0.1337 time to fit residues: 76.7320 Evaluate side-chains 303 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 117 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 354 GLN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 81 GLN A 99 HIS A 117 GLN A 168 ASN A 184 GLN A 224 GLN A 360 ASN A 381 HIS A 404 ASN A 439 HIS A 489 ASN A 492 GLN A 524 GLN A 534 ASN A 568 ASN A 611 ASN A 810 HIS A 816 HIS A 911 ASN B 108 ASN B 157 GLN B 168 GLN C 34 GLN D 104 ASN E 46 ASN E 245 HIS E 275 GLN E 311 HIS E 354 GLN E 388 ASN E 395 HIS E 464 HIS E 470 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 51 ASN F 164 HIS F 177 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN F 586 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067776 restraints weight = 57142.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068644 restraints weight = 30252.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069583 restraints weight = 17274.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069659 restraints weight = 14414.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069779 restraints weight = 12984.892| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 22388 Z= 0.339 Angle : 0.888 25.499 30770 Z= 0.418 Chirality : 0.050 0.369 3574 Planarity : 0.005 0.055 3641 Dihedral : 13.501 157.307 4005 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.25 % Favored : 88.71 % Rotamer: Outliers : 8.27 % Allowed : 25.40 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.15), residues: 2551 helix: -0.84 (0.16), residues: 953 sheet: -3.27 (0.24), residues: 329 loop : -3.08 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 750 TYR 0.024 0.002 TYR A 748 PHE 0.018 0.002 PHE A 471 TRP 0.017 0.002 TRP A 916 HIS 0.008 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.34 (22355) covalent geometry : angle 0.83757 / 0.41 (30742) hydrogen bonds : bond 0.06207 / 4.02 ( 832) hydrogen bonds : angle 5.36922 / 3.70 ( 2227) metal coordination : bond 0.02160 / 1.20 ( 32) metal coordination : angle 9.82414 / 7.57 ( 28) Misc. bond : bond 0.00190 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 124 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 431 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7479 (mm-30) REVERT: A 668 MET cc_start: 0.8671 (ttp) cc_final: 0.8382 (ttt) REVERT: A 786 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 805 LEU cc_start: 0.8416 (tp) cc_final: 0.8200 (tp) REVERT: A 891 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 55 MET cc_start: 0.9549 (mmm) cc_final: 0.9331 (mmm) REVERT: B 56 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: B 60 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8934 (mp0) REVERT: B 165 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8172 (pttt) REVERT: C 38 ASP cc_start: 0.8855 (t0) cc_final: 0.8384 (t0) REVERT: D 168 GLN cc_start: 0.9177 (mp10) cc_final: 0.8857 (mp10) REVERT: E 274 MET cc_start: 0.8460 (mmm) cc_final: 0.8156 (mmp) REVERT: F 41 LEU cc_start: 0.7243 (tt) cc_final: 0.6894 (pp) REVERT: F 333 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6336 (mt) REVERT: F 429 MET cc_start: 0.6106 (mmm) cc_final: 0.5875 (mmt) REVERT: F 502 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7754 (ptm160) outliers start: 182 outliers final: 128 residues processed: 296 average time/residue: 0.1334 time to fit residues: 64.9158 Evaluate side-chains 252 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 119 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 748 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 575 ILE Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 250 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN E 518 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.121348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.071449 restraints weight = 57202.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072972 restraints weight = 27663.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073275 restraints weight = 15541.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073448 restraints weight = 14033.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073564 restraints weight = 12560.522| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22388 Z= 0.145 Angle : 0.719 19.787 30770 Z= 0.339 Chirality : 0.045 0.335 3574 Planarity : 0.004 0.044 3641 Dihedral : 11.759 153.531 3861 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 6.41 % Allowed : 25.67 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.16), residues: 2551 helix: 0.12 (0.17), residues: 953 sheet: -2.85 (0.25), residues: 326 loop : -2.63 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.019 0.001 TYR F 582 PHE 0.015 0.001 PHE F 422 TRP 0.020 0.001 TRP F 506 HIS 0.017 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (22355) covalent geometry : angle 0.68258 / 0.34 (30742) hydrogen bonds : bond 0.04707 / 2.96 ( 832) hydrogen bonds : angle 4.66173 / 3.19 ( 2227) metal coordination : bond 0.01401 / 0.71 ( 32) metal coordination : angle 7.52248 / 5.77 ( 28) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 134 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8431 (m-80) cc_final: 0.7963 (m-80) REVERT: A 370 GLU cc_start: 0.8644 (tp30) cc_final: 0.8259 (tp30) REVERT: A 431 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7343 (mm-30) REVERT: A 548 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 633 MET cc_start: 0.8813 (tmm) cc_final: 0.8505 (tmm) REVERT: A 648 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 668 MET cc_start: 0.8538 (ttp) cc_final: 0.8261 (ttt) REVERT: A 779 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 786 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 891 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 56 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 80 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8284 (ttt-90) REVERT: B 155 GLU cc_start: 0.7974 (pm20) cc_final: 0.7706 (pm20) REVERT: B 165 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8212 (pttt) REVERT: C 38 ASP cc_start: 0.8705 (t0) cc_final: 0.8182 (t0) REVERT: C 50 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8236 (mt-10) REVERT: D 94 MET cc_start: 0.8459 (mtp) cc_final: 0.8234 (mtp) REVERT: D 168 GLN cc_start: 0.9129 (mp10) cc_final: 0.8820 (mp10) REVERT: F 41 LEU cc_start: 0.7023 (tt) cc_final: 0.6764 (pp) REVERT: F 202 LYS cc_start: 0.1896 (OUTLIER) cc_final: 0.1617 (tptp) REVERT: F 383 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8507 (p0) REVERT: F 399 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8415 (pt) REVERT: F 429 MET cc_start: 0.6121 (mmm) cc_final: 0.5915 (mmt) REVERT: F 474 MET cc_start: 0.6189 (mmm) cc_final: 0.5979 (mmm) REVERT: F 502 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7836 (ptm160) REVERT: F 506 TRP cc_start: 0.2175 (OUTLIER) cc_final: 0.1819 (m100) outliers start: 141 outliers final: 94 residues processed: 264 average time/residue: 0.1447 time to fit residues: 60.7209 Evaluate side-chains 228 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 123 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 5 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 219 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 237 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 ASN A 492 GLN D 158 GLN E 62 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072046 restraints weight = 56750.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072112 restraints weight = 30660.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073345 restraints weight = 17399.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073459 restraints weight = 13526.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073586 restraints weight = 12255.910| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22388 Z= 0.135 Angle : 0.680 16.157 30770 Z= 0.322 Chirality : 0.044 0.316 3574 Planarity : 0.004 0.042 3641 Dihedral : 10.872 147.297 3810 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.91 % Allowed : 26.17 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2551 helix: 0.56 (0.17), residues: 953 sheet: -2.42 (0.28), residues: 306 loop : -2.41 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 750 TYR 0.017 0.001 TYR F 582 PHE 0.015 0.001 PHE F 346 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (22355) covalent geometry : angle 0.65430 / 0.32 (30742) hydrogen bonds : bond 0.04361 / 2.73 ( 832) hydrogen bonds : angle 4.41445 / 3.03 ( 2227) metal coordination : bond 0.01003 / 0.52 ( 32) metal coordination : angle 6.11596 / 4.54 ( 28) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 128 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8325 (m-80) cc_final: 0.7883 (m-80) REVERT: A 340 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: A 370 GLU cc_start: 0.8634 (tp30) cc_final: 0.8304 (tp30) REVERT: A 431 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7332 (mm-30) REVERT: A 477 ASP cc_start: 0.8891 (t70) cc_final: 0.8637 (t0) REVERT: A 548 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 615 MET cc_start: 0.8591 (tmm) cc_final: 0.8360 (tmm) REVERT: A 633 MET cc_start: 0.8956 (tmm) cc_final: 0.8735 (tmm) REVERT: A 668 MET cc_start: 0.8580 (ttp) cc_final: 0.8304 (ttt) REVERT: A 786 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 891 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 56 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: B 58 LYS cc_start: 0.9406 (mtpt) cc_final: 0.9031 (mtmm) REVERT: B 80 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (ttt-90) REVERT: B 165 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8468 (mmmt) REVERT: D 94 MET cc_start: 0.8539 (mtp) cc_final: 0.8278 (mtp) REVERT: D 168 GLN cc_start: 0.9103 (mp10) cc_final: 0.8804 (mp10) REVERT: E 235 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6840 (mm) REVERT: E 274 MET cc_start: 0.8302 (mmp) cc_final: 0.8071 (mmm) REVERT: E 448 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7713 (pt) REVERT: F 41 LEU cc_start: 0.7133 (tt) cc_final: 0.6916 (pp) REVERT: F 63 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7716 (tp) REVERT: F 274 MET cc_start: 0.7879 (mmm) cc_final: 0.7669 (mmm) REVERT: F 289 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.6367 (p) REVERT: F 333 ILE cc_start: 0.6466 (OUTLIER) cc_final: 0.6205 (mt) REVERT: F 339 ARG cc_start: 0.2045 (OUTLIER) cc_final: 0.0779 (ptp90) REVERT: F 399 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8457 (pt) REVERT: F 502 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7789 (ttt180) outliers start: 130 outliers final: 88 residues processed: 247 average time/residue: 0.1408 time to fit residues: 56.3428 Evaluate side-chains 224 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 123 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 91 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 519 ASN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071677 restraints weight = 56253.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071958 restraints weight = 29440.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073051 restraints weight = 17649.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073331 restraints weight = 12994.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073362 restraints weight = 11886.296| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22388 Z= 0.150 Angle : 0.680 15.247 30770 Z= 0.321 Chirality : 0.044 0.318 3574 Planarity : 0.004 0.041 3641 Dihedral : 10.606 136.418 3789 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.00 % Allowed : 26.12 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.17), residues: 2551 helix: 0.67 (0.17), residues: 960 sheet: -2.33 (0.28), residues: 306 loop : -2.30 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.016 0.001 TYR A 748 PHE 0.012 0.001 PHE E 291 TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22355) covalent geometry : angle 0.65750 / 0.32 (30742) hydrogen bonds : bond 0.04413 / 2.78 ( 832) hydrogen bonds : angle 4.34599 / 2.98 ( 2227) metal coordination : bond 0.01055 / 0.60 ( 32) metal coordination : angle 5.77187 / 4.32 ( 28) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 123 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8347 (m-80) cc_final: 0.7867 (m-80) REVERT: A 340 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: A 370 GLU cc_start: 0.8626 (tp30) cc_final: 0.8270 (tp30) REVERT: A 431 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7333 (mm-30) REVERT: A 477 ASP cc_start: 0.8912 (t70) cc_final: 0.8671 (t0) REVERT: A 548 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 615 MET cc_start: 0.8539 (tmm) cc_final: 0.8290 (tmm) REVERT: A 668 MET cc_start: 0.8634 (ttp) cc_final: 0.8352 (ttt) REVERT: A 786 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 891 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 902 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8460 (ttm) REVERT: B 56 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: B 58 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9053 (mtmm) REVERT: B 65 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: B 80 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8263 (ttt-90) REVERT: B 165 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8225 (pttt) REVERT: D 94 MET cc_start: 0.8546 (mtp) cc_final: 0.8245 (mtp) REVERT: D 168 GLN cc_start: 0.9108 (mp10) cc_final: 0.8808 (mp10) REVERT: E 235 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6746 (mm) REVERT: E 274 MET cc_start: 0.8301 (mmp) cc_final: 0.8030 (mmm) REVERT: E 448 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7711 (pt) REVERT: F 41 LEU cc_start: 0.7120 (tt) cc_final: 0.6886 (pp) REVERT: F 63 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7805 (tp) REVERT: F 274 MET cc_start: 0.7962 (mmm) cc_final: 0.7693 (mmm) REVERT: F 289 SER cc_start: 0.6771 (OUTLIER) cc_final: 0.6456 (p) REVERT: F 333 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6356 (mt) REVERT: F 339 ARG cc_start: 0.2007 (OUTLIER) cc_final: 0.0794 (ptp90) REVERT: F 397 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7829 (t) REVERT: F 399 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8334 (pt) REVERT: F 502 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7788 (mtm180) outliers start: 132 outliers final: 98 residues processed: 242 average time/residue: 0.1382 time to fit residues: 53.6662 Evaluate side-chains 234 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 120 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 128 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 503 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.119047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068429 restraints weight = 56771.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069248 restraints weight = 29700.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069819 restraints weight = 17181.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070172 restraints weight = 14599.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070191 restraints weight = 12602.312| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 22388 Z= 0.310 Angle : 0.797 16.554 30770 Z= 0.381 Chirality : 0.048 0.345 3574 Planarity : 0.004 0.045 3641 Dihedral : 10.676 118.231 3778 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 7.27 % Allowed : 25.31 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2551 helix: 0.40 (0.17), residues: 959 sheet: -2.47 (0.26), residues: 327 loop : -2.38 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 750 TYR 0.030 0.002 TYR A 748 PHE 0.024 0.002 PHE F 422 TRP 0.011 0.002 TRP A 290 HIS 0.006 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.31 (22355) covalent geometry : angle 0.77356 / 0.38 (30742) hydrogen bonds : bond 0.05650 / 3.65 ( 832) hydrogen bonds : angle 4.76603 / 3.28 ( 2227) metal coordination : bond 0.01129 / 0.70 ( 32) metal coordination : angle 6.45533 / 4.90 ( 28) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 126 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: A 370 GLU cc_start: 0.8682 (tp30) cc_final: 0.8351 (tp30) REVERT: A 431 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7495 (mm-30) REVERT: A 548 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 629 MET cc_start: 0.8503 (mmm) cc_final: 0.8257 (tpp) REVERT: A 668 MET cc_start: 0.8684 (ttp) cc_final: 0.8340 (ttt) REVERT: A 786 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 891 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 56 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: B 58 LYS cc_start: 0.9377 (mtpt) cc_final: 0.9005 (mtmm) REVERT: B 65 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: B 80 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8346 (ttt-90) REVERT: B 165 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8194 (pttt) REVERT: D 22 TYR cc_start: 0.7001 (t80) cc_final: 0.6769 (t80) REVERT: D 94 MET cc_start: 0.8553 (mtp) cc_final: 0.8248 (mtp) REVERT: D 168 GLN cc_start: 0.9197 (mp10) cc_final: 0.8855 (mp10) REVERT: E 235 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6759 (mm) REVERT: F 274 MET cc_start: 0.7980 (mmm) cc_final: 0.7693 (mmm) REVERT: F 333 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6415 (mt) REVERT: F 397 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7975 (t) REVERT: F 399 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8451 (pt) REVERT: F 502 ARG cc_start: 0.8029 (mmt180) cc_final: 0.7734 (mtm110) outliers start: 160 outliers final: 118 residues processed: 274 average time/residue: 0.1426 time to fit residues: 62.8548 Evaluate side-chains 251 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 122 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 228 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 203 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 244 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN B 140 ASN D 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.122444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072631 restraints weight = 56342.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073052 restraints weight = 28755.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073844 restraints weight = 17015.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074426 restraints weight = 13187.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074409 restraints weight = 11438.920| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22388 Z= 0.117 Angle : 0.669 14.229 30770 Z= 0.317 Chirality : 0.044 0.321 3574 Planarity : 0.004 0.040 3641 Dihedral : 10.194 118.265 3776 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.95 % Allowed : 27.53 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2551 helix: 0.87 (0.18), residues: 955 sheet: -2.15 (0.28), residues: 311 loop : -2.05 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 502 TYR 0.013 0.001 TYR F 582 PHE 0.027 0.001 PHE F 499 TRP 0.017 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22355) covalent geometry : angle 0.64948 / 0.32 (30742) hydrogen bonds : bond 0.04153 / 2.59 ( 832) hydrogen bonds : angle 4.23507 / 2.90 ( 2227) metal coordination : bond 0.01171 / 0.62 ( 32) metal coordination : angle 5.39053 / 3.99 ( 28) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 127 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8314 (m-80) cc_final: 0.7832 (m-80) REVERT: A 340 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: A 370 GLU cc_start: 0.8578 (tp30) cc_final: 0.8202 (tp30) REVERT: A 431 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7271 (mm-30) REVERT: A 477 ASP cc_start: 0.8819 (t70) cc_final: 0.8617 (t0) REVERT: A 668 MET cc_start: 0.8557 (ttp) cc_final: 0.8266 (ttt) REVERT: A 786 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 891 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8385 (tt) REVERT: B 56 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: B 62 MET cc_start: 0.8933 (tpp) cc_final: 0.8703 (tpp) REVERT: B 65 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: B 165 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8467 (mmmt) REVERT: D 94 MET cc_start: 0.8483 (mtp) cc_final: 0.8146 (mtp) REVERT: D 168 GLN cc_start: 0.9164 (mp10) cc_final: 0.8864 (mp10) REVERT: E 235 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6830 (mm) REVERT: E 274 MET cc_start: 0.8340 (mmp) cc_final: 0.8036 (mmm) REVERT: E 499 PHE cc_start: 0.4167 (OUTLIER) cc_final: 0.3928 (m-80) REVERT: F 41 LEU cc_start: 0.7059 (tt) cc_final: 0.6789 (pp) REVERT: F 63 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7917 (tp) REVERT: F 205 TYR cc_start: 0.6382 (p90) cc_final: 0.5641 (p90) REVERT: F 274 MET cc_start: 0.8136 (mmm) cc_final: 0.7880 (mmm) REVERT: F 333 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6412 (mt) REVERT: F 339 ARG cc_start: 0.1900 (OUTLIER) cc_final: 0.0767 (ptp90) REVERT: F 397 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7837 (t) REVERT: F 399 ILE cc_start: 0.8707 (mp) cc_final: 0.8434 (pt) REVERT: F 474 MET cc_start: 0.5919 (mmm) cc_final: 0.3921 (mtp) outliers start: 109 outliers final: 83 residues processed: 227 average time/residue: 0.1443 time to fit residues: 52.7682 Evaluate side-chains 214 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 120 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 92 optimal weight: 0.0170 chunk 236 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN D 158 GLN ** E 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.120213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069780 restraints weight = 56154.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070266 restraints weight = 29001.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071264 restraints weight = 17480.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071352 restraints weight = 14001.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071469 restraints weight = 12339.987| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22388 Z= 0.238 Angle : 0.739 14.631 30770 Z= 0.352 Chirality : 0.046 0.331 3574 Planarity : 0.004 0.041 3641 Dihedral : 10.175 116.823 3765 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.77 % Allowed : 27.03 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2551 helix: 0.73 (0.17), residues: 954 sheet: -2.23 (0.28), residues: 313 loop : -2.13 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 750 TYR 0.026 0.002 TYR A 748 PHE 0.040 0.002 PHE F 422 TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (22355) covalent geometry : angle 0.72011 / 0.35 (30742) hydrogen bonds : bond 0.04985 / 3.19 ( 832) hydrogen bonds : angle 4.49990 / 3.09 ( 2227) metal coordination : bond 0.01012 / 0.60 ( 32) metal coordination : angle 5.61006 / 4.21 ( 28) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 117 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 370 GLU cc_start: 0.8685 (tp30) cc_final: 0.8348 (tp30) REVERT: A 431 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7375 (mm-30) REVERT: A 629 MET cc_start: 0.8363 (mmm) cc_final: 0.8143 (tpp) REVERT: A 668 MET cc_start: 0.8674 (ttp) cc_final: 0.8342 (ttt) REVERT: A 786 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 891 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 56 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: B 62 MET cc_start: 0.8930 (tpp) cc_final: 0.8714 (tpp) REVERT: B 65 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 80 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8297 (ttt-90) REVERT: D 94 MET cc_start: 0.8546 (mtp) cc_final: 0.8225 (mtp) REVERT: D 168 GLN cc_start: 0.9181 (mp10) cc_final: 0.8817 (mp10) REVERT: E 161 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6846 (mmp-170) REVERT: E 233 MET cc_start: 0.8198 (tpp) cc_final: 0.7857 (tpp) REVERT: E 235 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6907 (mm) REVERT: F 63 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7737 (tp) REVERT: F 205 TYR cc_start: 0.6385 (p90) cc_final: 0.5621 (p90) REVERT: F 274 MET cc_start: 0.8154 (mmm) cc_final: 0.7898 (mmm) REVERT: F 333 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6375 (mt) REVERT: F 339 ARG cc_start: 0.1976 (OUTLIER) cc_final: 0.0783 (ptp90) REVERT: F 397 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7849 (t) REVERT: F 399 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8406 (pt) REVERT: F 474 MET cc_start: 0.5877 (mmm) cc_final: 0.3862 (mtp) outliers start: 127 outliers final: 101 residues processed: 235 average time/residue: 0.1444 time to fit residues: 54.5712 Evaluate side-chains 227 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 113 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 145 optimal weight: 5.9990 chunk 92 optimal weight: 0.0570 chunk 210 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN D 158 GLN E 554 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.122276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072132 restraints weight = 56475.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072527 restraints weight = 28852.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073715 restraints weight = 16941.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073938 restraints weight = 12479.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073980 restraints weight = 11171.753| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22388 Z= 0.124 Angle : 0.670 13.725 30770 Z= 0.319 Chirality : 0.044 0.319 3574 Planarity : 0.003 0.039 3641 Dihedral : 9.982 117.053 3765 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.82 % Allowed : 27.99 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2551 helix: 0.92 (0.18), residues: 956 sheet: -2.03 (0.28), residues: 310 loop : -1.93 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 502 TYR 0.013 0.001 TYR D 138 PHE 0.019 0.001 PHE F 499 TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22355) covalent geometry : angle 0.65218 / 0.32 (30742) hydrogen bonds : bond 0.04207 / 2.63 ( 832) hydrogen bonds : angle 4.23439 / 2.90 ( 2227) metal coordination : bond 0.01118 / 0.60 ( 32) metal coordination : angle 5.15322 / 3.81 ( 28) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 122 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 370 GLU cc_start: 0.8608 (tp30) cc_final: 0.8264 (tp30) REVERT: A 431 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7287 (mm-30) REVERT: A 477 ASP cc_start: 0.8830 (t70) cc_final: 0.8623 (t0) REVERT: A 668 MET cc_start: 0.8565 (ttp) cc_final: 0.8278 (ttt) REVERT: A 786 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 891 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8398 (tt) REVERT: B 55 MET cc_start: 0.9367 (mpp) cc_final: 0.9151 (mpp) REVERT: B 56 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: B 65 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: B 80 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8205 (ttt-90) REVERT: B 165 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8197 (pttt) REVERT: D 94 MET cc_start: 0.8492 (mtp) cc_final: 0.8146 (mtp) REVERT: D 168 GLN cc_start: 0.9192 (mp10) cc_final: 0.8901 (mp10) REVERT: E 161 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6855 (mmp-170) REVERT: E 235 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6897 (mm) REVERT: E 299 TYR cc_start: 0.7808 (m-80) cc_final: 0.7589 (m-10) REVERT: F 63 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7728 (tp) REVERT: F 70 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: F 205 TYR cc_start: 0.6504 (p90) cc_final: 0.5792 (p90) REVERT: F 274 MET cc_start: 0.8160 (mmm) cc_final: 0.7886 (mmm) REVERT: F 333 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6348 (mt) REVERT: F 397 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7790 (t) REVERT: F 399 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (pt) REVERT: F 474 MET cc_start: 0.5794 (mmm) cc_final: 0.3638 (mtp) REVERT: F 497 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5047 (mmp-170) REVERT: F 576 MET cc_start: 0.4114 (tpt) cc_final: 0.3216 (tpt) outliers start: 106 outliers final: 84 residues processed: 219 average time/residue: 0.1457 time to fit residues: 50.8363 Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 119 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 497 ARG Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 190 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN E 164 HIS E 562 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 268 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073513 restraints weight = 56274.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074641 restraints weight = 27254.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075299 restraints weight = 15409.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075544 restraints weight = 13263.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075654 restraints weight = 11562.372| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22388 Z= 0.112 Angle : 0.655 13.141 30770 Z= 0.310 Chirality : 0.043 0.302 3574 Planarity : 0.003 0.040 3641 Dihedral : 9.635 115.736 3760 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.04 % Allowed : 28.71 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2551 helix: 1.07 (0.18), residues: 963 sheet: -1.80 (0.29), residues: 297 loop : -1.82 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 502 TYR 0.012 0.001 TYR F 582 PHE 0.047 0.001 PHE F 422 TRP 0.017 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22355) covalent geometry : angle 0.63997 / 0.31 (30742) hydrogen bonds : bond 0.03850 / 2.38 ( 832) hydrogen bonds : angle 4.06495 / 2.78 ( 2227) metal coordination : bond 0.01089 / 0.58 ( 32) metal coordination : angle 4.73141 / 3.46 ( 28) Misc. bond : bond 0.00039 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 128 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8328 (m-80) cc_final: 0.7938 (m-80) REVERT: A 340 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: A 370 GLU cc_start: 0.8528 (tp30) cc_final: 0.8044 (tp30) REVERT: A 431 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7196 (mm-30) REVERT: A 668 MET cc_start: 0.8565 (ttp) cc_final: 0.8286 (ttt) REVERT: A 891 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8386 (tt) REVERT: B 56 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: B 65 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 80 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8213 (ttt-90) REVERT: B 165 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8473 (mmmt) REVERT: D 94 MET cc_start: 0.8514 (mtp) cc_final: 0.8210 (mtp) REVERT: D 168 GLN cc_start: 0.9169 (mp10) cc_final: 0.8901 (mp10) REVERT: E 115 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8108 (p) REVERT: E 235 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6902 (mm) REVERT: E 299 TYR cc_start: 0.7780 (m-80) cc_final: 0.7546 (m-80) REVERT: F 70 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: F 97 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6758 (t) REVERT: F 205 TYR cc_start: 0.6541 (p90) cc_final: 0.6033 (p90) REVERT: F 274 MET cc_start: 0.8175 (mmm) cc_final: 0.7894 (mmm) REVERT: F 333 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6388 (mt) REVERT: F 397 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7829 (t) REVERT: F 399 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (pt) REVERT: F 474 MET cc_start: 0.5867 (mmm) cc_final: 0.3626 (mtp) outliers start: 89 outliers final: 64 residues processed: 210 average time/residue: 0.1467 time to fit residues: 49.1758 Evaluate side-chains 197 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 121 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 137 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 157 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 179 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.120227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068302 restraints weight = 56726.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070763 restraints weight = 25391.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071792 restraints weight = 12470.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071960 restraints weight = 10454.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071954 restraints weight = 9341.840| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22388 Z= 0.182 Angle : 0.695 13.027 30770 Z= 0.332 Chirality : 0.045 0.317 3574 Planarity : 0.004 0.040 3641 Dihedral : 9.549 115.376 3743 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.36 % Allowed : 28.49 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2551 helix: 0.97 (0.17), residues: 964 sheet: -2.01 (0.28), residues: 319 loop : -1.79 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 502 TYR 0.021 0.001 TYR A 748 PHE 0.016 0.001 PHE F 422 TRP 0.014 0.001 TRP F 506 HIS 0.005 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (22355) covalent geometry : angle 0.68001 / 0.33 (30742) hydrogen bonds : bond 0.04477 / 2.83 ( 832) hydrogen bonds : angle 4.22659 / 2.89 ( 2227) metal coordination : bond 0.00944 / 0.54 ( 32) metal coordination : angle 4.84212 / 3.59 ( 28) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3970.17 seconds wall clock time: 69 minutes 30.09 seconds (4170.09 seconds total)