Starting phenix.real_space_refine on Fri Sep 19 01:37:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uht_64175/09_2025/9uht_64175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uht_64175/09_2025/9uht_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_64175/09_2025/9uht_64175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uht_64175/09_2025/9uht_64175.map" model { file = "/net/cci-nas-00/data/ceres_data/9uht_64175/09_2025/9uht_64175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uht_64175/09_2025/9uht_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-2.0-5805/lib/python3.9/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: 5.57, per 1000 atoms: 0.25 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: 1.52 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.50 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: 3.34 Time building geometry restraints manager: 2.10 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 23.230 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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= 0.308 Angle : 0.984 29.798 31088 Z= 0.553 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 aren 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 covalent geometry : bond 0.00526 (22650) covalent geometry : angle 0.97252 (31061) hydrogen bonds : bond 0.18475 ( 843) hydrogen bonds : angle 6.40981 ( 2324) metal coordination : bond 0.01950 ( 32) metal coordination : angle 5.20166 ( 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 : 0.503 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: 0.5605 time to fit residues: 221.1156 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 : 0.758 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN A 713 ASN B 65 GLN B 168 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 492 GLN F 519 ASN G 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.161641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.124333 restraints weight = 108277.255| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 7.18 r_work: 0.2998 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 22682 Z= 0.249 Angle : 0.777 15.502 31088 Z= 0.396 Chirality : 0.047 0.331 3605 Planarity : 0.005 0.058 3757 Dihedral : 13.062 89.316 3861 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.91 % Favored : 90.83 % Rotamer: Outliers : 5.91 % Allowed : 30.75 % Favored : 63.34 % 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 aren not related in a simple way. whole: -2.06 (0.16), residues: 2655 helix: 0.06 (0.17), residues: 986 sheet: -1.42 (0.33), residues: 229 loop : -2.50 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 21 TYR 0.017 0.002 TYR F 299 PHE 0.024 0.002 PHE E 422 TRP 0.026 0.002 TRP D 182 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00585 (22650) covalent geometry : angle 0.75914 (31061) hydrogen bonds : bond 0.06989 ( 843) hydrogen bonds : angle 5.46120 ( 2324) metal coordination : bond 0.01748 ( 32) metal coordination : angle 5.71236 ( 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: 134 poor density : 152 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7796 (t0) cc_final: 0.7446 (t0) REVERT: A 267 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8977 (mmmm) REVERT: A 523 ASP cc_start: 0.9018 (m-30) cc_final: 0.8742 (m-30) REVERT: A 892 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8565 (m-70) REVERT: B 23 GLU cc_start: 0.4723 (OUTLIER) cc_final: 0.4297 (mp0) REVERT: B 62 MET cc_start: 0.8047 (ttp) cc_final: 0.7746 (tmt) REVERT: C 70 LYS cc_start: 0.9297 (ttmt) cc_final: 0.8980 (tppt) REVERT: D 42 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4197 (pp) REVERT: D 157 GLN cc_start: 0.8202 (mt0) cc_final: 0.7647 (tm130) REVERT: E 462 LYS cc_start: 0.7708 (mptt) cc_final: 0.7471 (tptp) REVERT: E 576 MET cc_start: 0.0144 (tmm) cc_final: -0.0350 (ppp) REVERT: F 344 ASP cc_start: 0.5344 (m-30) cc_final: 0.5099 (m-30) REVERT: F 378 MET cc_start: 0.0879 (ptt) cc_final: -0.1855 (mtt) REVERT: F 492 GLN cc_start: -0.2524 (OUTLIER) cc_final: -0.2820 (pt0) REVERT: F 497 ARG cc_start: 0.3811 (mtt180) cc_final: 0.3207 (tmm160) REVERT: F 576 MET cc_start: 0.3228 (mmm) cc_final: 0.2920 (mpt) REVERT: G 20 GLN cc_start: 0.6658 (mm-40) cc_final: 0.5807 (mp10) REVERT: G 33 ASN cc_start: 0.7136 (t0) cc_final: 0.6929 (t0) REVERT: G 86 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5726 (mppt) outliers start: 134 outliers final: 49 residues processed: 268 average time/residue: 0.5619 time to fit residues: 172.4748 Evaluate side-chains 188 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 372 LEU Chi-restraints excluded: chain A residue 563 CYS 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 865 ASP Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 23 GLU 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 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 142 CYS 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 158 LEU 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 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 492 GLN Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 19 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 217 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 408 GLN A 497 ASN B 65 GLN 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 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.162837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.125726 restraints weight = 83872.916| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 7.05 r_work: 0.3051 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22682 Z= 0.132 Angle : 0.674 13.562 31088 Z= 0.340 Chirality : 0.043 0.230 3605 Planarity : 0.004 0.048 3757 Dihedral : 12.576 80.095 3831 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.97 % Favored : 91.77 % Rotamer: Outliers : 3.33 % Allowed : 31.80 % Favored : 64.87 % 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 aren not related in a simple way. whole: -1.78 (0.16), residues: 2655 helix: 0.36 (0.17), residues: 980 sheet: -1.04 (0.34), residues: 223 loop : -2.42 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.025 0.001 TYR E 543 PHE 0.019 0.001 PHE E 422 TRP 0.020 0.002 TRP B 182 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00285 (22650) covalent geometry : angle 0.65822 (31061) hydrogen bonds : bond 0.05305 ( 843) hydrogen bonds : angle 5.09206 ( 2324) metal coordination : bond 0.01562 ( 32) metal coordination : angle 5.02331 ( 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 224 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7676 (ttt-90) REVERT: A 29 ASP cc_start: 0.7928 (t0) cc_final: 0.7481 (t0) REVERT: A 110 MET cc_start: 0.8777 (mtp) cc_final: 0.8569 (mmm) REVERT: A 497 ASN cc_start: 0.8940 (t0) cc_final: 0.8715 (t0) REVERT: A 523 ASP cc_start: 0.8984 (m-30) cc_final: 0.8653 (m-30) REVERT: A 668 MET cc_start: 0.9149 (tpp) cc_final: 0.8785 (ttm) REVERT: A 892 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8456 (m-70) REVERT: A 899 MET cc_start: 0.8277 (ttt) cc_final: 0.8050 (tmm) REVERT: B 62 MET cc_start: 0.8093 (ttp) cc_final: 0.7193 (tmt) REVERT: D 42 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4234 (pp) REVERT: D 87 MET cc_start: 0.9392 (mmm) cc_final: 0.9152 (mmm) REVERT: D 157 GLN cc_start: 0.8098 (mt0) cc_final: 0.7562 (tm130) REVERT: D 189 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8792 (tt) REVERT: E 554 HIS cc_start: 0.4421 (OUTLIER) cc_final: 0.2279 (m170) REVERT: E 576 MET cc_start: -0.0087 (tmm) cc_final: -0.0608 (ppp) REVERT: F 68 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6740 (mpp) REVERT: F 235 LEU cc_start: 0.1897 (pp) cc_final: 0.0898 (mm) REVERT: F 344 ASP cc_start: 0.5486 (m-30) cc_final: 0.5154 (m-30) REVERT: F 378 MET cc_start: 0.1073 (ptt) cc_final: -0.1583 (mtt) REVERT: F 497 ARG cc_start: 0.3593 (mtt180) cc_final: 0.2958 (tmm160) REVERT: F 576 MET cc_start: 0.3174 (mmm) cc_final: 0.2737 (mpt) REVERT: G 20 GLN cc_start: 0.6727 (mm-40) cc_final: 0.5802 (mp10) outliers start: 75 outliers final: 32 residues processed: 209 average time/residue: 0.6579 time to fit residues: 155.8389 Evaluate side-chains 167 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 204 VAL 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 255 SER Chi-restraints excluded: chain A residue 367 SER 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 778 SER Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 142 CYS 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 359 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 25 ASP 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: 5.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 95 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN B 65 GLN B 118 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 HIS ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.162222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.126441 restraints weight = 127916.463| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 7.27 r_work: 0.2996 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2996 ------------------------------------------------------------------------------- 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 = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22682 Z= 0.160 Angle : 0.664 12.729 31088 Z= 0.336 Chirality : 0.043 0.240 3605 Planarity : 0.004 0.050 3757 Dihedral : 12.383 75.701 3820 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.19 % Favored : 91.54 % Rotamer: Outliers : 3.94 % Allowed : 31.54 % 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 aren not related in a simple way. whole: -1.66 (0.16), residues: 2655 helix: 0.46 (0.17), residues: 983 sheet: -0.82 (0.34), residues: 236 loop : -2.39 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 390 TYR 0.014 0.001 TYR B 71 PHE 0.017 0.001 PHE E 422 TRP 0.015 0.002 TRP B 182 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00368 (22650) covalent geometry : angle 0.65004 (31061) hydrogen bonds : bond 0.05658 ( 843) hydrogen bonds : angle 4.96648 ( 2324) metal coordination : bond 0.01343 ( 32) metal coordination : angle 4.68665 ( 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 237 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 148 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7712 (tp-100) REVERT: A 75 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7424 (p90) REVERT: A 110 MET cc_start: 0.8758 (mtp) cc_final: 0.8535 (mmm) REVERT: A 523 ASP cc_start: 0.9006 (m-30) cc_final: 0.8685 (m-30) REVERT: A 553 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8452 (ttp80) REVERT: A 892 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8806 (m-70) REVERT: A 899 MET cc_start: 0.8356 (ttt) cc_final: 0.8036 (tmm) REVERT: B 62 MET cc_start: 0.7692 (ttp) cc_final: 0.7207 (tmm) REVERT: B 75 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8046 (tpp80) REVERT: D 42 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4320 (pp) REVERT: D 87 MET cc_start: 0.9395 (mmm) cc_final: 0.9183 (mmm) REVERT: D 157 GLN cc_start: 0.8244 (mt0) cc_final: 0.7796 (tm130) REVERT: E 554 HIS cc_start: 0.4334 (OUTLIER) cc_final: 0.2388 (m170) REVERT: E 576 MET cc_start: 0.0052 (tmm) cc_final: -0.0542 (ppp) REVERT: F 68 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6907 (mpp) REVERT: F 235 LEU cc_start: 0.2626 (pp) cc_final: 0.1603 (mm) REVERT: F 344 ASP cc_start: 0.5638 (m-30) cc_final: 0.5335 (m-30) REVERT: F 378 MET cc_start: 0.1449 (ptt) cc_final: -0.1108 (mtt) REVERT: F 429 MET cc_start: -0.3921 (tpp) cc_final: -0.4463 (tpt) REVERT: F 497 ARG cc_start: 0.3618 (mtt180) cc_final: 0.2780 (tmm160) REVERT: F 576 MET cc_start: 0.3354 (mmm) cc_final: 0.3014 (mpt) REVERT: G 20 GLN cc_start: 0.6687 (mm-40) cc_final: 0.5726 (mp10) REVERT: G 86 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5277 (mttt) outliers start: 89 outliers final: 43 residues processed: 224 average time/residue: 0.6595 time to fit residues: 166.9859 Evaluate side-chains 182 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 51 THR 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 115 SER 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 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 563 CYS 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 776 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 38 LEU 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 50 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 187 THR 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 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 68 MET Chi-restraints excluded: chain F residue 159 SER 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 18 THR 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 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: 5.9990 chunk 18 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 242 optimal weight: 40.0000 chunk 176 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 492 GLN A 497 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 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 = 0.4526 r_free = 0.4526 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.108997 restraints weight = 126818.455| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 7.10 r_work: 0.2886 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 22682 Z= 0.301 Angle : 0.744 13.370 31088 Z= 0.379 Chirality : 0.048 0.280 3605 Planarity : 0.005 0.048 3757 Dihedral : 12.503 74.484 3818 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.91 % Favored : 90.83 % Rotamer: Outliers : 5.12 % Allowed : 30.09 % 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 aren not related in a simple way. whole: -1.83 (0.16), residues: 2655 helix: 0.27 (0.17), residues: 986 sheet: -1.07 (0.34), residues: 241 loop : -2.44 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 129 TYR 0.016 0.002 TYR A 748 PHE 0.021 0.002 PHE A 753 TRP 0.027 0.002 TRP D 182 HIS 0.007 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00725 (22650) covalent geometry : angle 0.72728 (31061) hydrogen bonds : bond 0.07150 ( 843) hydrogen bonds : angle 5.15826 ( 2324) metal coordination : bond 0.01280 ( 32) metal coordination : angle 5.31619 ( 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 259 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 143 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7910 (t0) cc_final: 0.7544 (t0) REVERT: A 75 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7588 (p90) REVERT: A 497 ASN cc_start: 0.9041 (t0) cc_final: 0.8832 (t0) REVERT: A 523 ASP cc_start: 0.9045 (m-30) cc_final: 0.8557 (m-30) REVERT: A 553 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8448 (ttp80) REVERT: A 892 HIS cc_start: 0.9135 (OUTLIER) cc_final: 0.8811 (m-70) REVERT: B 62 MET cc_start: 0.7517 (ttp) cc_final: 0.7013 (tmm) REVERT: B 111 ARG cc_start: 0.8561 (pmm-80) cc_final: 0.7502 (ptt90) REVERT: D 34 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6033 (p) REVERT: D 42 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4215 (pp) REVERT: D 57 ARG cc_start: 0.8824 (ptp90) cc_final: 0.8439 (ptp90) REVERT: D 157 GLN cc_start: 0.8274 (mt0) cc_final: 0.7907 (tm130) REVERT: D 189 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8734 (tm) REVERT: E 554 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.2732 (m170) REVERT: E 576 MET cc_start: 0.0386 (tmm) cc_final: 0.0039 (pp-130) REVERT: F 68 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: F 235 LEU cc_start: 0.2895 (pp) cc_final: 0.1889 (mm) REVERT: F 344 ASP cc_start: 0.5641 (m-30) cc_final: 0.5308 (m-30) REVERT: F 348 VAL cc_start: 0.3858 (OUTLIER) cc_final: 0.3012 (m) REVERT: F 378 MET cc_start: 0.0805 (ptt) cc_final: -0.1047 (mtt) REVERT: F 497 ARG cc_start: 0.3713 (mtt180) cc_final: 0.2884 (tmm160) REVERT: F 576 MET cc_start: 0.3165 (mmm) cc_final: 0.2925 (mpt) REVERT: G 33 ASN cc_start: 0.7117 (t0) cc_final: 0.6801 (t0) outliers start: 116 outliers final: 53 residues processed: 246 average time/residue: 0.5872 time to fit residues: 165.0357 Evaluate side-chains 188 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 126 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 75 HIS 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 124 MET Chi-restraints excluded: chain A residue 147 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 239 SER Chi-restraints excluded: chain A residue 246 THR 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 553 ARG 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 807 LYS 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 23 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS 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 158 LEU Chi-restraints excluded: chain E residue 199 THR 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 462 LYS 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 68 MET Chi-restraints excluded: chain F residue 159 SER 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 348 VAL Chi-restraints excluded: chain F residue 555 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 37 optimal weight: 1.9990 chunk 217 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 172 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 171 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 534 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** 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** G 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.161880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.114924 restraints weight = 115409.842| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 7.27 r_work: 0.2951 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22682 Z= 0.126 Angle : 0.644 12.392 31088 Z= 0.325 Chirality : 0.042 0.220 3605 Planarity : 0.004 0.051 3757 Dihedral : 12.317 74.127 3817 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.51 % Favored : 92.30 % Rotamer: Outliers : 3.24 % Allowed : 31.93 % Favored : 64.83 % 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 aren not related in a simple way. whole: -1.49 (0.16), residues: 2655 helix: 0.59 (0.17), residues: 983 sheet: -0.90 (0.33), residues: 248 loop : -2.26 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 129 TYR 0.015 0.001 TYR A 831 PHE 0.014 0.001 PHE A 652 TRP 0.019 0.002 TRP D 182 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00270 (22650) covalent geometry : angle 0.62964 (31061) hydrogen bonds : bond 0.05007 ( 843) hydrogen bonds : angle 4.82397 ( 2324) metal coordination : bond 0.01217 ( 32) metal coordination : angle 4.57292 ( 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 211 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7662 (tp-100) REVERT: A 29 ASP cc_start: 0.7941 (t0) cc_final: 0.7442 (t0) REVERT: A 497 ASN cc_start: 0.8981 (t0) cc_final: 0.8764 (t0) REVERT: A 523 ASP cc_start: 0.9001 (m-30) cc_final: 0.8514 (m-30) REVERT: A 553 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (ttp80) REVERT: A 889 ARG cc_start: 0.8931 (ttt180) cc_final: 0.8682 (tpt-90) REVERT: A 892 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8812 (m-70) REVERT: B 23 GLU cc_start: 0.5224 (OUTLIER) cc_final: 0.4898 (pp20) REVERT: B 62 MET cc_start: 0.7207 (ttp) cc_final: 0.6809 (tmm) REVERT: B 71 TYR cc_start: 0.8458 (t80) cc_final: 0.8240 (t80) REVERT: B 111 ARG cc_start: 0.8423 (pmm-80) cc_final: 0.7383 (ptt90) REVERT: C 38 ASP cc_start: 0.9218 (m-30) cc_final: 0.8992 (m-30) REVERT: D 42 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4243 (pp) REVERT: D 57 ARG cc_start: 0.8902 (ptp90) cc_final: 0.8683 (ptp90) REVERT: D 157 GLN cc_start: 0.8499 (mt0) cc_final: 0.7912 (tm130) REVERT: D 189 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8653 (tm) REVERT: E 554 HIS cc_start: 0.4544 (OUTLIER) cc_final: 0.2930 (m170) REVERT: E 576 MET cc_start: 0.0426 (tmm) cc_final: -0.0273 (ppp) REVERT: F 68 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7259 (mpp) REVERT: F 235 LEU cc_start: 0.3364 (pp) cc_final: 0.2250 (mm) REVERT: F 344 ASP cc_start: 0.5674 (m-30) cc_final: 0.5379 (m-30) REVERT: F 348 VAL cc_start: 0.4219 (OUTLIER) cc_final: 0.3433 (m) REVERT: F 378 MET cc_start: 0.1213 (ptt) cc_final: -0.0634 (mtt) REVERT: F 429 MET cc_start: -0.4222 (tpp) cc_final: -0.4824 (tpt) REVERT: F 482 HIS cc_start: 0.0867 (OUTLIER) cc_final: -0.0076 (OUTLIER) REVERT: F 493 ILE cc_start: 0.2186 (OUTLIER) cc_final: 0.1775 (tt) REVERT: F 497 ARG cc_start: 0.3646 (mtt180) cc_final: 0.2860 (tmm160) REVERT: F 576 MET cc_start: 0.3237 (mmm) cc_final: 0.2998 (mpt) outliers start: 73 outliers final: 36 residues processed: 201 average time/residue: 0.6263 time to fit residues: 142.1927 Evaluate side-chains 177 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ARG 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 776 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 142 CYS 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 436 MET Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 495 VAL 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 68 MET Chi-restraints excluded: chain F residue 159 SER 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 348 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 223 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 186 optimal weight: 0.0170 chunk 254 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 226 optimal weight: 20.0000 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN ** E 537 GLN ** 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 107 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.162354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.117372 restraints weight = 103088.535| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 6.85 r_work: 0.3007 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22682 Z= 0.117 Angle : 0.624 11.734 31088 Z= 0.314 Chirality : 0.041 0.216 3605 Planarity : 0.004 0.051 3757 Dihedral : 12.220 74.837 3816 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.78 % Favored : 92.07 % Rotamer: Outliers : 3.42 % Allowed : 31.84 % Favored : 64.74 % 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 aren not related in a simple way. whole: -1.33 (0.16), residues: 2655 helix: 0.69 (0.18), residues: 988 sheet: -0.76 (0.36), residues: 219 loop : -2.14 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 497 TYR 0.015 0.001 TYR A 903 PHE 0.013 0.001 PHE A 652 TRP 0.028 0.002 TRP D 182 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00254 (22650) covalent geometry : angle 0.61099 (31061) hydrogen bonds : bond 0.04741 ( 843) hydrogen bonds : angle 4.68336 ( 2324) metal coordination : bond 0.01094 ( 32) metal coordination : angle 4.30513 ( 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: 77 poor density : 143 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7797 (tp-100) REVERT: A 29 ASP cc_start: 0.7943 (t0) cc_final: 0.7501 (t0) REVERT: A 75 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.6847 (p90) REVERT: A 523 ASP cc_start: 0.8957 (m-30) cc_final: 0.8495 (m-30) REVERT: A 553 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8389 (ttp80) REVERT: A 889 ARG cc_start: 0.8875 (ttt180) cc_final: 0.8640 (tpt-90) REVERT: A 892 HIS cc_start: 0.9106 (OUTLIER) cc_final: 0.8781 (m-70) REVERT: B 23 GLU cc_start: 0.5309 (OUTLIER) cc_final: 0.5023 (pp20) REVERT: B 61 LYS cc_start: 0.8686 (pptt) cc_final: 0.8461 (ptpt) REVERT: B 62 MET cc_start: 0.7246 (ttp) cc_final: 0.6428 (tmt) REVERT: B 71 TYR cc_start: 0.8416 (t80) cc_final: 0.8191 (t80) REVERT: B 111 ARG cc_start: 0.8416 (pmm-80) cc_final: 0.7406 (ptt90) REVERT: C 44 ASP cc_start: 0.7873 (t0) cc_final: 0.7613 (t0) REVERT: D 42 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4190 (pp) REVERT: D 80 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8752 (ttp80) REVERT: D 157 GLN cc_start: 0.8406 (mt0) cc_final: 0.7836 (tm130) REVERT: D 189 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8704 (tm) REVERT: E 554 HIS cc_start: 0.4724 (OUTLIER) cc_final: 0.3010 (m170) REVERT: E 576 MET cc_start: 0.0410 (tmm) cc_final: 0.0088 (pp-130) REVERT: F 235 LEU cc_start: 0.2708 (pp) cc_final: 0.1547 (mm) REVERT: F 344 ASP cc_start: 0.5606 (m-30) cc_final: 0.5276 (m-30) REVERT: F 348 VAL cc_start: 0.3513 (OUTLIER) cc_final: 0.2708 (m) REVERT: F 378 MET cc_start: 0.1592 (ptt) cc_final: -0.0546 (mtt) REVERT: F 429 MET cc_start: -0.4046 (tpp) cc_final: -0.4670 (tpt) REVERT: F 482 HIS cc_start: 0.0884 (OUTLIER) cc_final: -0.0206 (OUTLIER) REVERT: F 493 ILE cc_start: 0.2528 (OUTLIER) cc_final: 0.2161 (tt) REVERT: F 497 ARG cc_start: 0.3563 (mtt180) cc_final: 0.2692 (tmm160) REVERT: F 554 HIS cc_start: 0.0949 (OUTLIER) cc_final: 0.0254 (p-80) REVERT: F 555 SER cc_start: 0.0824 (OUTLIER) cc_final: -0.1020 (p) REVERT: F 576 MET cc_start: 0.3366 (mmm) cc_final: 0.3083 (mpt) REVERT: G 20 GLN cc_start: 0.6337 (mm-40) cc_final: 0.5634 (mp10) REVERT: G 52 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6939 (tmmt) outliers start: 77 outliers final: 34 residues processed: 208 average time/residue: 0.6402 time to fit residues: 150.5238 Evaluate side-chains 180 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 75 HIS 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 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 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ARG 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 892 HIS Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 153 LEU 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 80 ARG Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 462 LYS 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 75 HIS Chi-restraints excluded: chain F residue 159 SER 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 348 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 251 optimal weight: 40.0000 chunk 195 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 194 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 1 optimal weight: 0.0370 chunk 204 optimal weight: 10.0000 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN D 65 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.160404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.112448 restraints weight = 96299.978| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 6.71 r_work: 0.2926 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22682 Z= 0.220 Angle : 0.689 12.058 31088 Z= 0.346 Chirality : 0.044 0.254 3605 Planarity : 0.005 0.052 3757 Dihedral : 12.312 74.093 3815 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.27 % Favored : 91.58 % Rotamer: Outliers : 3.11 % Allowed : 32.24 % Favored : 64.65 % 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 aren not related in a simple way. whole: -1.50 (0.16), residues: 2655 helix: 0.53 (0.17), residues: 987 sheet: -0.92 (0.35), residues: 228 loop : -2.20 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 129 TYR 0.017 0.002 TYR A 903 PHE 0.019 0.002 PHE A 741 TRP 0.024 0.002 TRP D 182 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00524 (22650) covalent geometry : angle 0.67468 (31061) hydrogen bonds : bond 0.06192 ( 843) hydrogen bonds : angle 4.84243 ( 2324) metal coordination : bond 0.01066 ( 32) metal coordination : angle 4.84366 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 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 208 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 138 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7961 (t0) cc_final: 0.7587 (t0) REVERT: A 75 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7304 (p90) REVERT: A 523 ASP cc_start: 0.8985 (m-30) cc_final: 0.8494 (m-30) REVERT: A 553 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8460 (ttp80) REVERT: A 892 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8859 (m-70) REVERT: B 23 GLU cc_start: 0.5263 (mm-30) cc_final: 0.4906 (pp20) REVERT: B 62 MET cc_start: 0.7204 (ttp) cc_final: 0.6791 (tmm) REVERT: B 71 TYR cc_start: 0.8492 (t80) cc_final: 0.8240 (t80) REVERT: B 111 ARG cc_start: 0.8451 (pmm-80) cc_final: 0.7476 (ptt90) REVERT: D 157 GLN cc_start: 0.8524 (mt0) cc_final: 0.7976 (tm130) REVERT: D 189 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8666 (tm) REVERT: E 554 HIS cc_start: 0.4905 (OUTLIER) cc_final: 0.3180 (m170) REVERT: E 576 MET cc_start: 0.0383 (tmm) cc_final: 0.0112 (pp-130) REVERT: F 235 LEU cc_start: 0.3148 (pp) cc_final: 0.2013 (mm) REVERT: F 344 ASP cc_start: 0.5680 (m-30) cc_final: 0.5383 (m-30) REVERT: F 348 VAL cc_start: 0.3766 (OUTLIER) cc_final: 0.2959 (m) REVERT: F 378 MET cc_start: 0.1401 (ptt) cc_final: -0.0512 (mtt) REVERT: F 429 MET cc_start: -0.4208 (tpp) cc_final: -0.4809 (tpt) REVERT: F 482 HIS cc_start: 0.0847 (OUTLIER) cc_final: -0.0105 (OUTLIER) REVERT: F 493 ILE cc_start: 0.2369 (OUTLIER) cc_final: 0.1919 (tt) REVERT: F 497 ARG cc_start: 0.3504 (mtt180) cc_final: 0.2621 (tmm160) REVERT: F 576 MET cc_start: 0.3334 (mmm) cc_final: 0.3073 (mpt) REVERT: G 20 GLN cc_start: 0.6308 (mm-40) cc_final: 0.5538 (mp10) outliers start: 70 outliers final: 36 residues processed: 201 average time/residue: 0.6014 time to fit residues: 137.4335 Evaluate side-chains 171 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 75 HIS 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 246 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ARG 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 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 B residue 153 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 159 SER 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 348 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain G residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 235 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 266 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** 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 107 ASN ** 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 = 0.4556 r_free = 0.4556 target = 0.161857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.118631 restraints weight = 96937.656| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 6.35 r_work: 0.3032 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3974 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= 0.124 Angle : 0.648 12.755 31088 Z= 0.323 Chirality : 0.042 0.217 3605 Planarity : 0.004 0.051 3757 Dihedral : 12.199 73.870 3815 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.51 % Favored : 92.34 % Rotamer: Outliers : 2.54 % Allowed : 32.94 % Favored : 64.52 % 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 aren not related in a simple way. whole: -1.36 (0.16), residues: 2655 helix: 0.66 (0.17), residues: 986 sheet: -0.85 (0.34), residues: 246 loop : -2.15 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 497 TYR 0.016 0.001 TYR A 903 PHE 0.014 0.001 PHE A 652 TRP 0.023 0.002 TRP D 182 HIS 0.005 0.001 HIS E 482 Details of bonding type rmsd covalent geometry : bond 0.00277 (22650) covalent geometry : angle 0.63558 (31061) hydrogen bonds : bond 0.04888 ( 843) hydrogen bonds : angle 4.65543 ( 2324) metal coordination : bond 0.01088 ( 32) metal coordination : angle 4.39312 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 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 189 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7839 (tp-100) REVERT: A 29 ASP cc_start: 0.7947 (t0) cc_final: 0.7614 (t0) REVERT: A 75 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7163 (p90) REVERT: A 523 ASP cc_start: 0.8972 (m-30) cc_final: 0.8505 (m-30) REVERT: B 23 GLU cc_start: 0.5159 (mm-30) cc_final: 0.4861 (pp20) REVERT: B 62 MET cc_start: 0.7203 (ttp) cc_final: 0.6719 (tmm) REVERT: B 71 TYR cc_start: 0.8491 (t80) cc_final: 0.8278 (t80) REVERT: B 111 ARG cc_start: 0.8346 (pmm-80) cc_final: 0.7396 (ptt90) REVERT: D 157 GLN cc_start: 0.8514 (mt0) cc_final: 0.7963 (tm-30) REVERT: D 189 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8661 (tm) REVERT: E 554 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.3067 (m170) REVERT: E 576 MET cc_start: 0.0366 (tmm) cc_final: 0.0146 (pp-130) REVERT: F 235 LEU cc_start: 0.2789 (pp) cc_final: 0.1679 (mm) REVERT: F 344 ASP cc_start: 0.5688 (m-30) cc_final: 0.5334 (m-30) REVERT: F 348 VAL cc_start: 0.2911 (OUTLIER) cc_final: 0.2180 (m) REVERT: F 378 MET cc_start: 0.1548 (ptt) cc_final: -0.0687 (ttt) REVERT: F 429 MET cc_start: -0.4093 (tpp) cc_final: -0.4681 (tpt) REVERT: F 482 HIS cc_start: 0.0953 (OUTLIER) cc_final: -0.0105 (OUTLIER) REVERT: F 493 ILE cc_start: 0.2686 (OUTLIER) cc_final: 0.2233 (tt) REVERT: F 497 ARG cc_start: 0.3326 (mtt180) cc_final: 0.2459 (tmm160) REVERT: F 554 HIS cc_start: 0.0533 (OUTLIER) cc_final: 0.0171 (p-80) REVERT: F 576 MET cc_start: 0.3465 (mmm) cc_final: 0.3148 (mpt) REVERT: F 590 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3368 (mt) REVERT: G 20 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5551 (mp10) REVERT: G 52 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7397 (tmmt) outliers start: 57 outliers final: 36 residues processed: 182 average time/residue: 0.6115 time to fit residues: 126.0316 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 : 0.766 ------------------------------------------------------------------------------- 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 75 HIS 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 257 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP 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 B residue 79 LYS 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 D residue 34 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 159 SER 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 348 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 493 ILE 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 52 LYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 22 optimal weight: 0.0570 chunk 93 optimal weight: 0.0470 chunk 94 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 197 optimal weight: 0.0060 chunk 243 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.6214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** E 537 GLN ** 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 107 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.162508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.118077 restraints weight = 103648.668| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 6.32 r_work: 0.3030 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4083 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= 0.117 Angle : 0.636 11.816 31088 Z= 0.316 Chirality : 0.041 0.206 3605 Planarity : 0.004 0.052 3757 Dihedral : 12.113 74.257 3815 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 2.15 % Allowed : 33.55 % Favored : 64.30 % 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 aren not related in a simple way. whole: -1.24 (0.16), residues: 2655 helix: 0.73 (0.17), residues: 996 sheet: -0.84 (0.34), residues: 246 loop : -2.06 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 57 TYR 0.014 0.001 TYR A 903 PHE 0.012 0.001 PHE A 652 TRP 0.022 0.002 TRP D 182 HIS 0.004 0.001 HIS E 482 Details of bonding type rmsd covalent geometry : bond 0.00258 (22650) covalent geometry : angle 0.62463 (31061) hydrogen bonds : bond 0.04573 ( 843) hydrogen bonds : angle 4.53438 ( 2324) metal coordination : bond 0.01171 ( 32) metal coordination : angle 4.12389 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 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 186 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7822 (tp-100) REVERT: A 29 ASP cc_start: 0.7888 (t0) cc_final: 0.7524 (t0) REVERT: A 75 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.6760 (p90) REVERT: A 161 ASP cc_start: 0.8854 (m-30) cc_final: 0.8650 (m-30) REVERT: A 523 ASP cc_start: 0.8921 (m-30) cc_final: 0.8411 (m-30) REVERT: B 23 GLU cc_start: 0.5196 (mm-30) cc_final: 0.4875 (pp20) REVERT: B 62 MET cc_start: 0.7212 (ttp) cc_final: 0.6725 (tmm) REVERT: B 71 TYR cc_start: 0.8429 (t80) cc_final: 0.8200 (t80) REVERT: B 111 ARG cc_start: 0.8362 (pmm-80) cc_final: 0.7402 (ptt90) REVERT: D 157 GLN cc_start: 0.8542 (mt0) cc_final: 0.7959 (tm-30) REVERT: D 189 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8654 (tm) REVERT: E 554 HIS cc_start: 0.4390 (OUTLIER) cc_final: 0.2950 (m170) REVERT: E 576 MET cc_start: 0.0492 (tmm) cc_final: 0.0268 (pp-130) REVERT: F 235 LEU cc_start: 0.2914 (pp) cc_final: 0.1879 (mm) REVERT: F 344 ASP cc_start: 0.5837 (m-30) cc_final: 0.5470 (m-30) REVERT: F 348 VAL cc_start: 0.2818 (OUTLIER) cc_final: 0.2114 (m) REVERT: F 378 MET cc_start: 0.1357 (ptt) cc_final: -0.0757 (ttt) REVERT: F 429 MET cc_start: -0.4260 (tpp) cc_final: -0.4782 (tpt) REVERT: F 482 HIS cc_start: 0.1145 (OUTLIER) cc_final: 0.0067 (p90) REVERT: F 493 ILE cc_start: 0.2707 (OUTLIER) cc_final: 0.2247 (tt) REVERT: F 497 ARG cc_start: 0.3194 (mtt180) cc_final: 0.2316 (tmm160) REVERT: F 554 HIS cc_start: 0.0471 (OUTLIER) cc_final: 0.0079 (p-80) REVERT: F 576 MET cc_start: 0.3284 (mmm) cc_final: 0.2895 (mpt) REVERT: F 590 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.3608 (mt) REVERT: G 20 GLN cc_start: 0.6191 (mm-40) cc_final: 0.5494 (mp10) outliers start: 48 outliers final: 31 residues processed: 181 average time/residue: 0.6090 time to fit residues: 125.2383 Evaluate side-chains 169 residues out of total 2329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 75 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 115 SER 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 257 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 79 LYS 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 D residue 34 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain F residue 75 HIS 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 228 THR Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 493 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 136 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 210 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 167 optimal weight: 0.0070 chunk 119 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 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 = 0.4541 r_free = 0.4541 target = 0.160479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.114561 restraints weight = 95880.016| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 6.68 r_work: 0.2940 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22682 Z= 0.219 Angle : 0.691 13.247 31088 Z= 0.347 Chirality : 0.044 0.259 3605 Planarity : 0.005 0.051 3757 Dihedral : 12.149 73.705 3813 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.54 % Rotamer: Outliers : 2.23 % Allowed : 33.42 % Favored : 64.35 % 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 aren not related in a simple way. whole: -1.40 (0.16), residues: 2655 helix: 0.56 (0.17), residues: 994 sheet: -0.83 (0.34), residues: 245 loop : -2.15 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.015 0.002 TYR A 903 PHE 0.018 0.002 PHE A 741 TRP 0.023 0.002 TRP D 182 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00523 (22650) covalent geometry : angle 0.67838 (31061) hydrogen bonds : bond 0.06053 ( 843) hydrogen bonds : angle 4.72493 ( 2324) metal coordination : bond 0.01063 ( 32) metal coordination : angle 4.58895 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10518.91 seconds wall clock time: 179 minutes 8.43 seconds (10748.43 seconds total)