Starting phenix.real_space_refine on Sat Jul 4 16:18:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.map" model { file = "/net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uht_64175/07_2026/9uht_64175.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 59 5.49 5 S 158 5.16 5 C 13791 2.51 5 N 3715 2.21 5 O 4337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22068 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7496 Classifications: {'peptide': 931} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1417 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 183} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 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': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1426 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 71.777 48.241 121.819 1.00 86.97 S ATOM 2506 SG CYS A 306 71.497 49.666 125.363 1.00 84.94 S ATOM 2538 SG CYS A 310 73.251 46.304 124.731 1.00 84.77 S ATOM 3946 SG CYS A 487 72.911 62.993 106.471 1.00 95.87 S ATOM 5199 SG CYS A 645 71.796 64.847 109.643 1.00 97.77 S ATOM 5205 SG CYS A 646 70.959 61.099 109.183 1.00 89.00 S ATOM 11048 SG CYS E 16 56.315 66.631 65.698 1.00165.58 S ATOM 11063 SG CYS E 19 54.096 63.852 64.267 1.00179.24 S ATOM 10966 SG CYS E 5 65.807 63.922 58.148 1.00188.71 S ATOM 10987 SG CYS E 8 66.336 66.043 55.123 1.00197.10 S ATOM 11125 SG CYS E 26 67.502 67.539 58.508 1.00186.39 S ATOM 11142 SG CYS E 29 63.923 67.276 57.299 1.00167.57 S ATOM 11307 SG CYS E 50 59.222 79.574 80.120 1.00176.08 S ATOM 11337 SG CYS E 55 55.801 80.590 81.514 1.00192.48 S ATOM 11470 SG CYS E 72 57.633 82.939 79.098 1.00187.74 S ATOM 15561 SG CYS F 16 98.612 63.021 51.372 1.00183.45 S ATOM 15576 SG CYS F 19 99.742 60.534 48.658 1.00198.14 S ATOM 15479 SG CYS F 5 110.802 65.793 51.495 1.00183.01 S ATOM 15500 SG CYS F 8 111.353 68.799 49.213 1.00185.13 S ATOM 15638 SG CYS F 26 109.986 69.468 52.406 1.00172.26 S ATOM 15655 SG CYS F 29 107.772 67.375 49.913 1.00175.19 S ATOM 15820 SG CYS F 50 87.556 72.946 66.563 1.00158.72 S ATOM 15850 SG CYS F 55 84.319 71.754 65.008 1.00164.97 S ATOM 15983 SG CYS F 72 86.199 74.409 63.343 1.00168.17 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 Time building chain proxies: 5.32, per 1000 atoms: 0.24 Number of scatterers: 22068 At special positions: 0 Unit cell: (157.44, 135.36, 187.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 59 15.00 O 4337 8.00 N 3715 7.00 C 13791 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=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 931.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " 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 ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5100 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 30 sheets defined 40.1% alpha, 10.4% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.972A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.691A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.649A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.622A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.816A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.629A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.527A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.864A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.570A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.555A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.614A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.644A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.553A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.035A 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 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.504A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.621A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.866A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.587A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.572A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.585A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.527A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.504A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.792A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 850 removed outlier: 3.791A pdb=" N LYS A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.386A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.676A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.607A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (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 11 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.644A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.764A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.665A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.680A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 80 removed outlier: 3.886A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.842A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.092A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.747A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.862A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.498A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 505 through 509 removed outlier: 4.423A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 509' Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.016A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.230A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.683A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.631A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.998A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.616A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.911A pdb=" N TRP F 506 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 516 through 523 Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.374A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.688A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.970A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.345A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.433A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB5, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.673A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.960A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.592A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 481 through 482 removed outlier: 3.854A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 511 through 512 removed outlier: 6.087A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AC6, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AC7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 305 removed outlier: 5.091A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 330 through 331 removed outlier: 3.531A pdb=" N SER F 331 " --> pdb=" O TYR F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.739A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.534A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3514 1.31 - 1.44: 6453 1.44 - 1.57: 12338 1.57 - 1.69: 118 1.69 - 1.82: 227 Bond restraints: 22650 Sorted by residual: bond pdb=" C ASN G 1 " pdb=" N ASN G 2 " ideal model delta sigma weight residual 1.331 1.555 -0.225 1.48e-02 4.57e+03 2.31e+02 bond pdb=" O3' A H 1 " pdb=" P U H 2 " ideal model delta sigma weight residual 1.607 1.454 0.153 1.50e-02 4.44e+03 1.05e+02 bond pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 1.526 1.436 0.089 1.28e-02 6.10e+03 4.88e+01 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.266 0.237 3.40e-02 8.65e+02 4.88e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.68e+01 ... (remaining 22645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 30972 5.96 - 11.92: 68 11.92 - 17.88: 13 17.88 - 23.84: 6 23.84 - 29.80: 2 Bond angle restraints: 31061 Sorted by residual: angle pdb=" O ASN G 1 " pdb=" C ASN G 1 " pdb=" N ASN G 2 " ideal model delta sigma weight residual 123.00 93.20 29.80 1.60e+00 3.91e-01 3.47e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.96 22.04 1.40e+00 5.10e-01 2.48e+02 angle pdb=" C3' A H 1 " pdb=" O3' A H 1 " pdb=" P U H 2 " ideal model delta sigma weight residual 120.20 140.56 -20.36 1.50e+00 4.44e-01 1.84e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.71 -27.91 2.13e+00 2.20e-01 1.72e+02 angle pdb=" C THR A 850 " pdb=" N ASP A 851 " pdb=" CA ASP A 851 " ideal model delta sigma weight residual 122.76 142.70 -19.94 1.63e+00 3.76e-01 1.50e+02 ... (remaining 31056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 11654 19.40 - 38.79: 1459 38.79 - 58.19: 451 58.19 - 77.58: 80 77.58 - 96.98: 15 Dihedral angle restraints: 13659 sinusoidal: 5755 harmonic: 7904 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.44 -36.64 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.52 35.92 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.39 -24.59 0 2.50e+00 1.60e-01 9.68e+01 ... (remaining 13656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3596 0.321 - 0.642: 4 0.642 - 0.963: 1 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3605 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.60 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.41e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 3602 not shown) Planarity restraints: 3757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " -0.089 2.00e-02 2.50e+03 1.37e-01 1.87e+02 pdb=" C ASN G 1 " 0.236 2.00e-02 2.50e+03 pdb=" O ASN G 1 " -0.079 2.00e-02 2.50e+03 pdb=" N ASN G 2 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PRO E 364 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 364 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PRO E 364 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO E 364 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU E 365 " 0.018 2.00e-02 2.50e+03 ... (remaining 3754 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 20 2.25 - 2.91: 9143 2.91 - 3.57: 30968 3.57 - 4.24: 50526 4.24 - 4.90: 84249 Nonbonded interactions: 174906 Sorted by model distance: nonbonded pdb=" N ASN G 1 " pdb=" P A H 1 " model vdw 1.587 3.480 nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.142 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.147 2.496 ... (remaining 174901 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 192)) 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 46 or (resid 47 and (name N or name CA or name C or na \ me O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } 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=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 23.390 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.005 0.237 22682 Z= 0.310 Angle : 0.984 29.798 31088 Z= 0.562 Chirality : 0.065 1.605 3605 Planarity : 0.006 0.141 3757 Dihedral : 18.702 96.981 8559 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.46 % Favored : 91.17 % Rotamer: Outliers : 5.21 % Allowed : 33.51 % Favored : 61.28 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.94 (0.16), residues: 2655 helix: 0.30 (0.18), residues: 953 sheet: -1.49 (0.35), residues: 217 loop : -2.46 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.021 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.038 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.31 (22650) covalent geometry : angle 0.97254 / 0.56 (31061) hydrogen bonds : bond 0.18475 / 12.31 ( 843) hydrogen bonds : angle 6.40981 / 4.49 ( 2324) metal coordination : bond 0.01950 / 1.24 ( 32) metal coordination : angle 5.20166 / 2.77 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 242 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: A 20 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 197 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.6972 (tpt170) REVERT: A 520 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 523 ASP cc_start: 0.8773 (m-30) cc_final: 0.8503 (m-30) REVERT: B 62 MET cc_start: 0.8175 (ttp) cc_final: 0.7922 (tmt) REVERT: E 230 HIS cc_start: 0.5137 (p-80) cc_final: 0.4756 (p90) REVERT: E 245 HIS cc_start: 0.4882 (m-70) cc_final: 0.4401 (t70) REVERT: E 462 LYS cc_start: 0.7923 (mptt) cc_final: 0.7632 (tptp) REVERT: E 543 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.4094 (t80) REVERT: E 576 MET cc_start: 0.0399 (tmm) cc_final: -0.0180 (ppp) REVERT: F 7 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4284 (pt) REVERT: F 344 ASP cc_start: 0.5692 (m-30) cc_final: 0.5427 (m-30) REVERT: F 378 MET cc_start: 0.0157 (ptt) cc_final: -0.1726 (mtt) REVERT: G 33 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6440 (t0) REVERT: G 66 TYR cc_start: 0.5029 (m-10) cc_final: 0.4670 (m-10) REVERT: G 87 TYR cc_start: 0.7469 (m-80) cc_final: 0.7190 (m-80) outliers start: 118 outliers final: 32 residues processed: 345 average time/residue: 0.5462 time to fit residues: 217.1206 Evaluate side-chains 177 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 543 TYR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 2.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN A 713 ASN B 168 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN G 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.124629 restraints weight = 108418.116| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 6.86 r_work: 0.3027 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 22682 Z= 0.257 Angle : 0.805 15.854 31088 Z= 0.415 Chirality : 0.049 0.298 3605 Planarity : 0.006 0.061 3757 Dihedral : 13.154 92.904 3861 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.02 % Favored : 90.71 % Rotamer: Outliers : 6.18 % Allowed : 30.57 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2655 helix: 0.00 (0.17), residues: 980 sheet: -1.39 (0.33), residues: 234 loop : -2.54 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 21 TYR 0.018 0.002 TYR F 299 PHE 0.025 0.002 PHE A 753 TRP 0.024 0.002 TRP D 182 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 (22650) covalent geometry : angle 0.78749 / 0.41 (31061) hydrogen bonds : bond 0.07056 / 4.66 ( 843) hydrogen bonds : angle 5.52177 / 3.94 ( 2324) metal coordination : bond 0.01655 / 1.05 ( 32) metal coordination : angle 5.70623 / 3.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 146 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8983 (mmmm) REVERT: A 523 ASP cc_start: 0.8974 (m-30) cc_final: 0.8736 (m-30) REVERT: A 892 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8463 (m-70) REVERT: B 62 MET cc_start: 0.8029 (ttp) cc_final: 0.7557 (tmt) REVERT: C 70 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8881 (tppt) REVERT: D 42 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4204 (pp) REVERT: D 157 GLN cc_start: 0.8337 (mt0) cc_final: 0.7696 (tm130) REVERT: E 462 LYS cc_start: 0.7736 (mptt) cc_final: 0.7487 (tptp) REVERT: E 480 ILE cc_start: 0.0675 (OUTLIER) cc_final: 0.0446 (mp) REVERT: E 576 MET cc_start: 0.0316 (tmm) cc_final: 0.0005 (pp-130) REVERT: F 344 ASP cc_start: 0.5413 (m-30) cc_final: 0.5159 (m-30) REVERT: F 378 MET cc_start: 0.0520 (ptt) cc_final: -0.1944 (mtt) REVERT: F 497 ARG cc_start: 0.3812 (mtt180) cc_final: 0.3162 (tmm160) REVERT: F 576 MET cc_start: 0.3069 (mmm) cc_final: 0.2804 (mpt) REVERT: G 20 GLN cc_start: 0.6413 (mm-40) cc_final: 0.5615 (mp10) REVERT: G 73 CYS cc_start: 0.6572 (t) cc_final: 0.6347 (m) outliers start: 140 outliers final: 49 residues processed: 270 average time/residue: 0.5184 time to fit residues: 162.4710 Evaluate side-chains 182 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 217 optimal weight: 50.0000 chunk 167 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN C 69 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS F 492 GLN ** F 559 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 = 0.4541 r_free = 0.4541 target = 0.160923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.115753 restraints weight = 82787.149| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 5.80 r_work: 0.2982 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22682 Z= 0.247 Angle : 0.740 14.518 31088 Z= 0.379 Chirality : 0.047 0.292 3605 Planarity : 0.005 0.046 3757 Dihedral : 12.785 96.250 3831 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.10 % Favored : 90.64 % Rotamer: Outliers : 4.51 % Allowed : 31.32 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.01 (0.16), residues: 2655 helix: 0.10 (0.17), residues: 986 sheet: -1.17 (0.35), residues: 216 loop : -2.51 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 57 TYR 0.031 0.002 TYR E 543 PHE 0.020 0.002 PHE E 422 TRP 0.024 0.003 TRP E 506 HIS 0.005 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (22650) covalent geometry : angle 0.72311 / 0.38 (31061) hydrogen bonds : bond 0.06864 / 4.54 ( 843) hydrogen bonds : angle 5.38310 / 3.85 ( 2324) metal coordination : bond 0.01463 / 0.92 ( 32) metal coordination : angle 5.35856 / 2.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 142 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7872 (t0) cc_final: 0.7491 (t0) REVERT: A 110 MET cc_start: 0.8811 (mtp) cc_final: 0.8396 (mmm) REVERT: A 497 ASN cc_start: 0.8970 (t0) cc_final: 0.8715 (t0) REVERT: A 523 ASP cc_start: 0.8975 (m-30) cc_final: 0.8504 (m-30) REVERT: A 892 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8581 (m-70) REVERT: A 899 MET cc_start: 0.8106 (ttt) cc_final: 0.7697 (tmm) REVERT: B 61 LYS cc_start: 0.8788 (pptt) cc_final: 0.8521 (ptpt) REVERT: B 62 MET cc_start: 0.7717 (ttp) cc_final: 0.6913 (tmt) REVERT: C 70 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9080 (tppt) REVERT: D 42 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4255 (pp) REVERT: D 157 GLN cc_start: 0.8334 (mt0) cc_final: 0.7808 (tm130) REVERT: D 189 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8711 (tt) REVERT: E 462 LYS cc_start: 0.7917 (mptt) cc_final: 0.7708 (tptp) REVERT: E 554 HIS cc_start: 0.4382 (OUTLIER) cc_final: 0.2553 (m170) REVERT: E 576 MET cc_start: 0.0425 (tmm) cc_final: 0.0119 (pp-130) REVERT: F 235 LEU cc_start: 0.3135 (pp) cc_final: 0.2075 (mm) REVERT: F 344 ASP cc_start: 0.5503 (m-30) cc_final: 0.5285 (m-30) REVERT: F 378 MET cc_start: 0.0523 (ptt) cc_final: -0.1274 (mtt) REVERT: F 492 GLN cc_start: -0.2259 (OUTLIER) cc_final: -0.2474 (pt0) REVERT: F 497 ARG cc_start: 0.3742 (mtt180) cc_final: 0.3139 (tmm160) REVERT: F 576 MET cc_start: 0.2813 (mmm) cc_final: 0.2551 (mpt) REVERT: G 20 GLN cc_start: 0.6738 (mm-40) cc_final: 0.6012 (mp10) REVERT: G 73 CYS cc_start: 0.6461 (t) cc_final: 0.6222 (m) REVERT: G 86 LYS cc_start: 0.4965 (OUTLIER) cc_final: 0.4675 (mttt) outliers start: 102 outliers final: 51 residues processed: 229 average time/residue: 0.5474 time to fit residues: 143.1424 Evaluate side-chains 189 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 5 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 32 optimal weight: 0.0050 chunk 95 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.112058 restraints weight = 122607.900| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 7.07 r_work: 0.2947 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22682 Z= 0.142 Angle : 0.666 13.762 31088 Z= 0.339 Chirality : 0.043 0.242 3605 Planarity : 0.004 0.052 3757 Dihedral : 12.646 93.129 3830 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.46 % Favored : 91.28 % Rotamer: Outliers : 3.59 % Allowed : 31.76 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.16), residues: 2655 helix: 0.36 (0.17), residues: 977 sheet: -0.89 (0.35), residues: 218 loop : -2.41 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.014 0.001 TYR E 543 PHE 0.016 0.001 PHE A 652 TRP 0.018 0.002 TRP B 182 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22650) covalent geometry : angle 0.65106 / 0.34 (31061) hydrogen bonds : bond 0.05661 / 3.75 ( 843) hydrogen bonds : angle 5.14917 / 3.69 ( 2324) metal coordination : bond 0.01298 / 0.81 ( 32) metal coordination : angle 4.84281 / 2.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 144 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8026 (t0) cc_final: 0.7497 (t0) REVERT: A 110 MET cc_start: 0.8823 (mtp) cc_final: 0.8453 (mmm) REVERT: A 497 ASN cc_start: 0.8965 (t0) cc_final: 0.8730 (t0) REVERT: A 523 ASP cc_start: 0.8998 (m-30) cc_final: 0.8545 (m-30) REVERT: A 892 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8562 (m-70) REVERT: A 899 MET cc_start: 0.8202 (ttt) cc_final: 0.7760 (tmm) REVERT: B 62 MET cc_start: 0.7736 (ttp) cc_final: 0.7394 (tmt) REVERT: B 71 TYR cc_start: 0.8436 (t80) cc_final: 0.8233 (t80) REVERT: C 70 LYS cc_start: 0.9307 (ttmt) cc_final: 0.9050 (tppt) REVERT: D 42 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4241 (pp) REVERT: D 57 ARG cc_start: 0.9011 (ptp-110) cc_final: 0.8724 (ptp90) REVERT: D 157 GLN cc_start: 0.8334 (mt0) cc_final: 0.7818 (tm130) REVERT: D 189 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8697 (tt) REVERT: E 462 LYS cc_start: 0.7906 (mptt) cc_final: 0.7700 (tptp) REVERT: E 554 HIS cc_start: 0.4371 (OUTLIER) cc_final: 0.2506 (m170) REVERT: E 576 MET cc_start: 0.0280 (tmm) cc_final: 0.0046 (pp-130) REVERT: F 235 LEU cc_start: 0.2935 (pp) cc_final: 0.1937 (mm) REVERT: F 344 ASP cc_start: 0.5597 (m-30) cc_final: 0.5352 (m-30) REVERT: F 378 MET cc_start: 0.0526 (ptt) cc_final: -0.1479 (mtt) REVERT: F 497 ARG cc_start: 0.3661 (mtt180) cc_final: 0.2980 (tmm160) REVERT: F 576 MET cc_start: 0.2901 (mmm) cc_final: 0.2647 (mpt) REVERT: G 20 GLN cc_start: 0.6587 (mm-40) cc_final: 0.5582 (mp10) REVERT: G 73 CYS cc_start: 0.6437 (t) cc_final: 0.6202 (m) REVERT: G 86 LYS cc_start: 0.4931 (OUTLIER) cc_final: 0.4665 (mttt) outliers start: 81 outliers final: 39 residues processed: 210 average time/residue: 0.5744 time to fit residues: 137.3290 Evaluate side-chains 171 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 242 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 0.0770 chunk 41 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 492 GLN A 534 ASN C 69 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.162186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.113001 restraints weight = 126041.774| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 7.18 r_work: 0.2967 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22682 Z= 0.131 Angle : 0.641 12.955 31088 Z= 0.327 Chirality : 0.042 0.265 3605 Planarity : 0.004 0.049 3757 Dihedral : 12.466 89.341 3821 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 4.20 % Allowed : 31.27 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2655 helix: 0.48 (0.17), residues: 984 sheet: -0.81 (0.35), residues: 229 loop : -2.33 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.012 0.001 TYR A 831 PHE 0.016 0.001 PHE E 422 TRP 0.026 0.002 TRP D 182 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22650) covalent geometry : angle 0.62641 / 0.33 (31061) hydrogen bonds : bond 0.05286 / 3.51 ( 843) hydrogen bonds : angle 4.99794 / 3.58 ( 2324) metal coordination : bond 0.01180 / 0.73 ( 32) metal coordination : angle 4.60098 / 2.61 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 142 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7407 (tp-100) REVERT: A 29 ASP cc_start: 0.7975 (t0) cc_final: 0.7489 (t0) REVERT: A 497 ASN cc_start: 0.8962 (t0) cc_final: 0.8664 (t0) REVERT: A 523 ASP cc_start: 0.8993 (m-30) cc_final: 0.8572 (m-30) REVERT: A 553 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8423 (ttp80) REVERT: A 892 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8682 (m-70) REVERT: B 61 LYS cc_start: 0.8771 (pptt) cc_final: 0.8522 (ptpt) REVERT: B 62 MET cc_start: 0.7662 (ttp) cc_final: 0.6868 (tmm) REVERT: C 70 LYS cc_start: 0.9307 (ttmt) cc_final: 0.9061 (tppt) REVERT: D 42 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4269 (pp) REVERT: D 57 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8753 (ptp90) REVERT: D 157 GLN cc_start: 0.8383 (mt0) cc_final: 0.7881 (tm130) REVERT: D 189 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8628 (tm) REVERT: E 436 MET cc_start: 0.0242 (OUTLIER) cc_final: -0.1860 (tpt) REVERT: E 462 LYS cc_start: 0.7848 (mptt) cc_final: 0.7633 (tptp) REVERT: E 554 HIS cc_start: 0.4383 (OUTLIER) cc_final: 0.2462 (m170) REVERT: E 576 MET cc_start: 0.0012 (tmm) cc_final: -0.0201 (pp-130) REVERT: F 235 LEU cc_start: 0.3025 (pp) cc_final: 0.1918 (mm) REVERT: F 344 ASP cc_start: 0.5536 (m-30) cc_final: 0.5251 (m-30) REVERT: F 348 VAL cc_start: 0.3628 (OUTLIER) cc_final: 0.2620 (m) REVERT: F 378 MET cc_start: 0.0583 (ptt) cc_final: -0.1410 (mtt) REVERT: F 429 MET cc_start: -0.4143 (tpp) cc_final: -0.4814 (tpt) REVERT: F 497 ARG cc_start: 0.3593 (mtt180) cc_final: 0.2773 (tmm160) REVERT: F 552 THR cc_start: 0.2187 (OUTLIER) cc_final: 0.1843 (t) REVERT: F 576 MET cc_start: 0.3171 (mmm) cc_final: 0.2888 (mpt) REVERT: G 20 GLN cc_start: 0.6487 (mm-40) cc_final: 0.5725 (mp10) REVERT: G 73 CYS cc_start: 0.6423 (t) cc_final: 0.6205 (m) REVERT: G 86 LYS cc_start: 0.5091 (OUTLIER) cc_final: 0.4739 (mttt) outliers start: 95 outliers final: 41 residues processed: 222 average time/residue: 0.5647 time to fit residues: 143.3908 Evaluate side-chains 179 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 37 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 250 optimal weight: 0.0270 chunk 6 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 172 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 408 GLN B 118 ASN C 69 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.162482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.118487 restraints weight = 111185.877| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 6.65 r_work: 0.3010 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22682 Z= 0.125 Angle : 0.641 12.177 31088 Z= 0.325 Chirality : 0.042 0.223 3605 Planarity : 0.004 0.054 3757 Dihedral : 12.363 84.308 3819 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 3.94 % Allowed : 31.89 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.16), residues: 2655 helix: 0.66 (0.18), residues: 969 sheet: -0.65 (0.37), residues: 211 loop : -2.24 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 21 TYR 0.016 0.001 TYR B 71 PHE 0.014 0.001 PHE E 422 TRP 0.019 0.001 TRP D 182 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22650) covalent geometry : angle 0.62767 / 0.32 (31061) hydrogen bonds : bond 0.05092 / 3.40 ( 843) hydrogen bonds : angle 4.87582 / 3.50 ( 2324) metal coordination : bond 0.01151 / 0.71 ( 32) metal coordination : angle 4.42948 / 2.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 135 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7509 (tp-100) REVERT: A 497 ASN cc_start: 0.9002 (t0) cc_final: 0.8685 (t0) REVERT: A 523 ASP cc_start: 0.9005 (m-30) cc_final: 0.8567 (m-30) REVERT: A 553 ARG cc_start: 0.8827 (mtm110) cc_final: 0.8515 (ttp80) REVERT: A 892 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8673 (m-70) REVERT: B 23 GLU cc_start: 0.6210 (pp20) cc_final: 0.5954 (mm-30) REVERT: B 61 LYS cc_start: 0.8668 (pptt) cc_final: 0.8417 (ptpt) REVERT: B 62 MET cc_start: 0.7557 (ttp) cc_final: 0.6791 (tmm) REVERT: B 75 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8226 (tpp80) REVERT: C 52 MET cc_start: 0.9126 (tpp) cc_final: 0.8762 (tpp) REVERT: C 70 LYS cc_start: 0.9292 (ttmt) cc_final: 0.9037 (tppt) REVERT: D 42 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4259 (pp) REVERT: D 57 ARG cc_start: 0.9079 (ptp-110) cc_final: 0.8814 (ptp90) REVERT: D 157 GLN cc_start: 0.8386 (mt0) cc_final: 0.7967 (tm130) REVERT: D 189 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8619 (tm) REVERT: E 554 HIS cc_start: 0.4473 (OUTLIER) cc_final: 0.2566 (m170) REVERT: E 576 MET cc_start: 0.0320 (tmm) cc_final: -0.0057 (pp-130) REVERT: F 235 LEU cc_start: 0.2963 (pp) cc_final: 0.1737 (mm) REVERT: F 344 ASP cc_start: 0.5678 (m-30) cc_final: 0.5330 (m-30) REVERT: F 348 VAL cc_start: 0.3778 (OUTLIER) cc_final: 0.2781 (m) REVERT: F 378 MET cc_start: 0.0948 (ptt) cc_final: -0.1080 (mtt) REVERT: F 429 MET cc_start: -0.4399 (tpp) cc_final: -0.4807 (tpt) REVERT: F 493 ILE cc_start: 0.2319 (OUTLIER) cc_final: 0.1946 (tp) REVERT: F 497 ARG cc_start: 0.3740 (mtt180) cc_final: 0.2889 (tmm160) REVERT: F 552 THR cc_start: 0.2359 (OUTLIER) cc_final: 0.2046 (t) REVERT: F 554 HIS cc_start: 0.1028 (OUTLIER) cc_final: 0.0211 (p-80) REVERT: F 576 MET cc_start: 0.3192 (mmm) cc_final: 0.2903 (mpt) REVERT: G 20 GLN cc_start: 0.6396 (mm-40) cc_final: 0.5951 (mp10) REVERT: G 73 CYS cc_start: 0.6437 (t) cc_final: 0.6206 (m) outliers start: 89 outliers final: 48 residues processed: 214 average time/residue: 0.5263 time to fit residues: 129.3686 Evaluate side-chains 186 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 223 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 0.4980 chunk 226 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.162664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.114657 restraints weight = 101880.515| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 6.63 r_work: 0.2989 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22682 Z= 0.122 Angle : 0.623 11.654 31088 Z= 0.316 Chirality : 0.042 0.224 3605 Planarity : 0.004 0.060 3757 Dihedral : 12.303 78.938 3818 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 3.68 % Allowed : 31.54 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.36 (0.16), residues: 2655 helix: 0.73 (0.18), residues: 972 sheet: -0.81 (0.35), residues: 230 loop : -2.17 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 21 TYR 0.018 0.001 TYR A 903 PHE 0.013 0.001 PHE E 422 TRP 0.018 0.001 TRP D 182 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22650) covalent geometry : angle 0.61098 / 0.32 (31061) hydrogen bonds : bond 0.04930 / 3.29 ( 843) hydrogen bonds : angle 4.79880 / 3.45 ( 2324) metal coordination : bond 0.01076 / 0.66 ( 32) metal coordination : angle 4.24784 / 2.47 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5310 Ramachandran restraints generated. 2655 Oldfield, 0 Emsley, 2655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 137 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7605 (tp-100) REVERT: A 29 ASP cc_start: 0.7757 (t0) cc_final: 0.7263 (t0) REVERT: A 497 ASN cc_start: 0.8924 (t0) cc_final: 0.8634 (t0) REVERT: A 523 ASP cc_start: 0.8986 (m-30) cc_final: 0.8538 (m-30) REVERT: A 553 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8483 (ttp80) REVERT: A 892 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.8727 (m-70) REVERT: B 23 GLU cc_start: 0.6334 (pp20) cc_final: 0.6039 (mm-30) REVERT: B 62 MET cc_start: 0.7535 (ttp) cc_final: 0.7157 (tmm) REVERT: B 71 TYR cc_start: 0.8410 (t80) cc_final: 0.8209 (t80) REVERT: C 44 ASP cc_start: 0.7889 (t0) cc_final: 0.7631 (t0) REVERT: C 70 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9020 (tppt) REVERT: D 42 LEU cc_start: 0.4762 (OUTLIER) cc_final: 0.4312 (pp) REVERT: D 57 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8848 (ptp90) REVERT: D 157 GLN cc_start: 0.8449 (mt0) cc_final: 0.7932 (tm130) REVERT: D 189 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8520 (tm) REVERT: E 554 HIS cc_start: 0.4757 (OUTLIER) cc_final: 0.2639 (m170) REVERT: E 576 MET cc_start: 0.0207 (tmm) cc_final: -0.0079 (pp-130) REVERT: F 9 ASN cc_start: 0.8437 (t0) cc_final: 0.8175 (p0) REVERT: F 181 VAL cc_start: 0.3674 (OUTLIER) cc_final: 0.3286 (p) REVERT: F 235 LEU cc_start: 0.2733 (pp) cc_final: 0.1587 (mm) REVERT: F 329 LYS cc_start: 0.4131 (OUTLIER) cc_final: 0.1788 (mtpm) REVERT: F 344 ASP cc_start: 0.5566 (m-30) cc_final: 0.5276 (m-30) REVERT: F 348 VAL cc_start: 0.3392 (OUTLIER) cc_final: 0.2388 (m) REVERT: F 378 MET cc_start: 0.1408 (ptt) cc_final: -0.0863 (mtt) REVERT: F 429 MET cc_start: -0.4205 (tpp) cc_final: -0.4587 (tpt) REVERT: F 493 ILE cc_start: 0.2397 (OUTLIER) cc_final: 0.2021 (tt) REVERT: F 497 ARG cc_start: 0.3925 (mtt180) cc_final: 0.2936 (tmm160) REVERT: F 552 THR cc_start: 0.2369 (OUTLIER) cc_final: 0.2059 (t) REVERT: F 554 HIS cc_start: 0.0916 (OUTLIER) cc_final: 0.0240 (p-80) REVERT: F 576 MET cc_start: 0.3181 (mmm) cc_final: 0.2870 (mpt) REVERT: F 590 LEU cc_start: 0.4129 (OUTLIER) cc_final: 0.3241 (mt) REVERT: G 20 GLN cc_start: 0.6402 (mm-40) cc_final: 0.5399 (mp10) REVERT: G 73 CYS cc_start: 0.6225 (t) cc_final: 0.6016 (m) outliers start: 83 outliers final: 44 residues processed: 210 average time/residue: 0.5618 time to fit residues: 134.1173 Evaluate side-chains 186 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.9327 > 50: distance: 34 - 58: 20.003 distance: 54 - 58: 17.112 distance: 58 - 59: 10.194 distance: 59 - 60: 28.386 distance: 59 - 62: 12.141 distance: 60 - 61: 20.398 distance: 60 - 66: 20.415 distance: 62 - 63: 28.335 distance: 63 - 64: 32.828 distance: 63 - 65: 15.076 distance: 66 - 67: 22.916 distance: 67 - 68: 7.019 distance: 67 - 70: 3.033 distance: 68 - 69: 5.747 distance: 68 - 77: 10.126 distance: 70 - 71: 9.724 distance: 71 - 72: 20.118 distance: 72 - 73: 4.638 distance: 73 - 74: 5.956 distance: 74 - 75: 13.604 distance: 74 - 76: 6.607 distance: 77 - 78: 13.799 distance: 78 - 79: 8.447 distance: 78 - 81: 7.807 distance: 79 - 80: 10.314 distance: 79 - 84: 25.777 distance: 81 - 82: 19.990 distance: 81 - 83: 18.809 distance: 84 - 85: 40.615 distance: 85 - 86: 42.886 distance: 85 - 88: 40.687 distance: 86 - 87: 43.351 distance: 86 - 93: 47.191 distance: 88 - 89: 38.429 distance: 89 - 90: 26.324 distance: 90 - 91: 28.377 distance: 90 - 92: 32.243 distance: 93 - 94: 37.310 distance: 94 - 95: 13.652 distance: 94 - 97: 40.346 distance: 95 - 96: 53.180 distance: 95 - 99: 14.643 distance: 97 - 98: 30.004 distance: 99 - 100: 22.533 distance: 100 - 101: 15.822 distance: 100 - 103: 23.335 distance: 101 - 102: 31.352 distance: 101 - 105: 19.834 distance: 102 - 128: 14.128 distance: 103 - 104: 42.594 distance: 105 - 106: 20.649 distance: 106 - 107: 15.737 distance: 106 - 109: 33.442 distance: 107 - 108: 37.810 distance: 107 - 111: 27.937 distance: 108 - 142: 25.392 distance: 109 - 110: 49.449 distance: 111 - 112: 23.686 distance: 112 - 113: 24.942 distance: 112 - 115: 16.145 distance: 113 - 114: 26.338 distance: 113 - 120: 5.491 distance: 114 - 147: 29.633 distance: 115 - 116: 49.045 distance: 116 - 117: 23.835 distance: 117 - 118: 36.274 distance: 118 - 119: 32.740 distance: 120 - 121: 33.742 distance: 121 - 122: 24.015 distance: 121 - 124: 8.407 distance: 122 - 123: 13.012 distance: 122 - 128: 11.531 distance: 123 - 155: 22.287 distance: 124 - 125: 15.716 distance: 125 - 126: 25.050 distance: 125 - 127: 34.420 distance: 128 - 129: 23.337 distance: 129 - 130: 14.383 distance: 129 - 132: 23.327 distance: 130 - 131: 13.002 distance: 130 - 142: 15.694 distance: 131 - 161: 23.899 distance: 132 - 133: 28.171 distance: 133 - 134: 13.533 distance: 133 - 135: 8.714 distance: 134 - 136: 5.918 distance: 135 - 137: 7.823 distance: 135 - 138: 5.349 distance: 136 - 137: 10.272 distance: 137 - 139: 9.181 distance: 138 - 140: 6.334 distance: 139 - 141: 3.368 distance: 140 - 141: 5.335