Starting phenix.real_space_refine on Mon Jul 6 09:18:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.map" model { file = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7so9_25263/07_2026/7so9_25263.cif" } resolution = 2.4 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= 0.004 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 21756 2.51 5 N 5640 2.21 5 O 6906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34470 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7820 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 8, 'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 749 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 864 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Restraints were copied for chains: F, K, G, L, H, M, I, N, J, O, Q, R Time building chain proxies: 10.22, per 1000 atoms: 0.30 Number of scatterers: 34470 At special positions: 0 Unit cell: (154.269, 152.583, 195.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6906 8.00 N 5640 7.00 C 21756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.17 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.12 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS K 883 " distance=2.14 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.10 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS F 707 " distance=2.14 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.17 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.17 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.17 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.05 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.05 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.02 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.02 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.12 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.12 Simple disulfide: pdb=" SG CYS K 707 " - pdb=" SG CYS F 883 " distance=2.14 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.12 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.12 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.10 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.10 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.17 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-6 " NAG P 1 " - " FUC P 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 2 " " NAG R 1 " - " FUC R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG A1313 " - " ASN A 616 " " NAG A1314 " - " ASN A 709 " " NAG A1315 " - " ASN A 234 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 282 " " NAG F1304 " - " ASN F 165 " " NAG F1305 " - " ASN F 331 " " NAG F1306 " - " ASN F 603 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F 717 " " NAG F1309 " - " ASN F 801 " " NAG F1310 " - " ASN F1074 " " NAG F1311 " - " ASN F1098 " " NAG F1312 " - " ASN F1134 " " NAG F1313 " - " ASN F 616 " " NAG F1314 " - " ASN F 709 " " NAG F1315 " - " ASN F 234 " " NAG K1301 " - " ASN K 61 " " NAG K1302 " - " ASN K 122 " " NAG K1303 " - " ASN K 282 " " NAG K1304 " - " ASN K 165 " " NAG K1305 " - " ASN K 331 " " NAG K1306 " - " ASN K 603 " " NAG K1307 " - " ASN K 657 " " NAG K1308 " - " ASN K 717 " " NAG K1309 " - " ASN K 801 " " NAG K1310 " - " ASN K1074 " " NAG K1311 " - " ASN K1098 " " NAG K1312 " - " ASN K1134 " " NAG K1313 " - " ASN K 616 " " NAG K1314 " - " ASN K 709 " " NAG K1315 " - " ASN K 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN F 343 " " NAG R 1 " - " ASN K 343 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 84 sheets defined 19.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.080A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.791A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.626A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 107 through 111 removed outlier: 4.005A pdb=" N TYR E 111 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.251A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.797A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.079A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 939 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.791A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.626A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 4.005A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 438 through 443 Processing helix chain 'K' and resid 502 through 505 Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.797A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 824 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.079A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 939 Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.791A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 982 Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K 995 " --> pdb=" O VAL K 991 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.626A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 107 through 111 removed outlier: 4.005A pdb=" N TYR M 111 " --> pdb=" O GLY M 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.698A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.043A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU F 324 " --> pdb=" O CYS F 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.202A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.615A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.575A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.709A pdb=" N ALA A 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS K 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN A 703 " --> pdb=" O LYS K 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.692A pdb=" N LYS A 790 " --> pdb=" O ASN F 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.645A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.797A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.595A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'F' and resid 27 through 31 removed outlier: 3.698A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA F 264 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 187 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.043A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU K 324 " --> pdb=" O CYS K 538 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 168 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU F 132 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS F 166 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN F 134 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN F 164 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.574A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 787 through 790 removed outlier: 3.692A pdb=" N LYS F 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.644A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.533A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.533A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.626A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.626A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.796A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.705A pdb=" N LEU I 11 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.705A pdb=" N LEU I 11 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.594A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.698A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA K 264 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR K 95 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 187 " --> pdb=" O ILE K 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 84 through 85 Processing sheet with id=AG8, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 168 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL K 595 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN K 317 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY K 593 " --> pdb=" O ASN K 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AH2, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.574A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.644A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AI2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.796A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AJ2, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.595A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 11 through 12 1592 hydrogen bonds defined for protein. 4065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.34 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5799 1.32 - 1.45: 9687 1.45 - 1.58: 19212 1.58 - 1.71: 0 1.71 - 1.84: 222 Bond restraints: 34920 Sorted by residual: bond pdb=" CA CYS F 15 " pdb=" C CYS F 15 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CA CYS K 15 " pdb=" C CYS K 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA CYS A 15 " pdb=" C CYS A 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" C GLN F 14 " pdb=" N CYS F 15 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.32e-02 5.74e+03 9.07e+00 bond pdb=" C GLN A 14 " pdb=" N CYS A 15 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.32e-02 5.74e+03 8.93e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 42540 1.68 - 3.36: 4176 3.36 - 5.03: 413 5.03 - 6.71: 349 6.71 - 8.39: 132 Bond angle restraints: 47610 Sorted by residual: angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.05e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.20e-01 1.93e+00 9.03e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 ... (remaining 47605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 19371 17.79 - 35.58: 549 35.58 - 53.37: 171 53.37 - 71.17: 51 71.17 - 88.96: 21 Dihedral angle restraints: 20163 sinusoidal: 7338 harmonic: 12825 Sorted by residual: dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 96 " pdb=" CB CYS O 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.55 52.45 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 20160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 5415 0.189 - 0.378: 81 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.945: 3 Chirality restraints: 5499 Sorted by residual: chirality pdb=" C1 FUC R 2 " pdb=" O6 NAG R 1 " pdb=" C2 FUC R 2 " pdb=" O5 FUC R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.90e+01 chirality pdb=" C1 FUC P 2 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 2 " pdb=" O5 FUC P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.88e+01 chirality pdb=" C1 FUC Q 2 " pdb=" O6 NAG Q 1 " pdb=" C2 FUC Q 2 " pdb=" O5 FUC Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.79e+01 ... (remaining 5496 not shown) Planarity restraints: 6153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.043 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 331 " -0.043 2.00e-02 2.50e+03 4.45e-02 2.48e+01 pdb=" CG ASN K 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN K 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN K 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG K1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 331 " -0.043 2.00e-02 2.50e+03 4.44e-02 2.47e+01 pdb=" CG ASN F 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN F 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN F 331 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F1305 " -0.054 2.00e-02 2.50e+03 ... (remaining 6150 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 990 2.70 - 3.25: 32359 3.25 - 3.80: 55640 3.80 - 4.35: 74882 4.35 - 4.90: 121794 Nonbonded interactions: 285665 Sorted by model distance: nonbonded pdb=" O SER H 55 " pdb=" OG SER H 56 " model vdw 2.154 3.040 nonbonded pdb=" O SER E 55 " pdb=" OG SER E 56 " model vdw 2.154 3.040 nonbonded pdb=" O SER M 55 " pdb=" OG SER M 56 " model vdw 2.154 3.040 nonbonded pdb=" O ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.221 3.040 nonbonded pdb=" O ASP G 61 " pdb=" OD1 ASP G 61 " model vdw 2.221 3.040 ... (remaining 285660 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.640 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.011 0.139 35028 Z= 0.598 Angle : 1.214 11.924 47877 Z= 0.817 Chirality : 0.069 0.945 5499 Planarity : 0.005 0.023 6105 Dihedral : 10.791 88.957 11784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.17 % Allowed : 0.79 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4350 helix: 0.49 (0.19), residues: 657 sheet: 1.05 (0.14), residues: 1299 loop : 0.19 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K1019 TYR 0.044 0.005 TYR D 92 PHE 0.022 0.004 PHE F 898 TRP 0.029 0.005 TRP H 106 HIS 0.004 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01049 / 0.58 (34920) covalent geometry : angle 1.19036 / 0.81 (47610) SS BOND : bond 0.06095 / 4.07 ( 57) SS BOND : angle 3.77839 / 2.82 ( 114) hydrogen bonds : bond 0.16911 / 11.44 ( 1484) hydrogen bonds : angle 8.12863 / 5.76 ( 4065) link_BETA1-6 : bond 0.05753 / 2.88 ( 3) link_BETA1-6 : angle 2.26292 / 1.38 ( 9) link_NAG-ASN : bond 0.04824 / 3.48 ( 48) link_NAG-ASN : angle 3.16314 / 2.07 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 593 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.8137 (t80) cc_final: 0.7897 (t80) REVERT: E 64 PHE cc_start: 0.7042 (m-80) cc_final: 0.6808 (m-80) REVERT: B 9 SER cc_start: 0.7038 (p) cc_final: 0.6768 (t) REVERT: B 54 MET cc_start: 0.6610 (mmm) cc_final: 0.6111 (mmt) REVERT: B 89 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6716 (tm-30) REVERT: I 47 LEU cc_start: 0.7097 (mt) cc_final: 0.6880 (mm) REVERT: I 54 MET cc_start: 0.6519 (mmm) cc_final: 0.6049 (mmt) REVERT: I 86 TYR cc_start: 0.5400 (m-80) cc_final: 0.5016 (m-10) REVERT: I 89 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6630 (tm130) REVERT: K 202 LYS cc_start: 0.6365 (mttt) cc_final: 0.5930 (mmtt) REVERT: N 9 SER cc_start: 0.7237 (p) cc_final: 0.6995 (t) REVERT: O 31 SER cc_start: 0.8344 (p) cc_final: 0.8143 (p) outliers start: 6 outliers final: 0 residues processed: 599 average time/residue: 0.6931 time to fit residues: 496.6655 Evaluate side-chains 411 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 540 ASN A 755 GLN A1011 GLN D 101 GLN E 117 GLN C 98 ASN F 314 GLN F 564 GLN F 644 GLN F 755 GLN F 804 GLN F 954 GLN F1005 GLN F1010 GLN F1011 GLN G 101 GLN H 117 GLN I 27 GLN J 98 ASN K 314 GLN K 498 GLN K 540 ASN K 606 ASN K 644 GLN K 755 GLN K 954 GLN K1005 GLN K1011 GLN M 117 GLN N 89 GLN O 98 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.201608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.191158 restraints weight = 30273.411| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 0.38 r_work: 0.3992 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35028 Z= 0.137 Angle : 0.614 18.675 47877 Z= 0.316 Chirality : 0.046 0.457 5499 Planarity : 0.004 0.039 6105 Dihedral : 4.484 23.030 4761 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.75 % Allowed : 7.18 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4350 helix: 2.07 (0.21), residues: 666 sheet: 1.14 (0.14), residues: 1269 loop : 0.33 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1107 TYR 0.023 0.002 TYR F1067 PHE 0.013 0.002 PHE A 592 TRP 0.010 0.001 TRP H 115 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (34920) covalent geometry : angle 0.57309 / 0.31 (47610) SS BOND : bond 0.00283 / 0.22 ( 57) SS BOND : angle 0.98074 / 0.73 ( 114) hydrogen bonds : bond 0.05384 / 3.64 ( 1484) hydrogen bonds : angle 6.10466 / 4.34 ( 4065) link_BETA1-6 : bond 0.01399 / 0.70 ( 3) link_BETA1-6 : angle 1.09365 / 0.61 ( 9) link_NAG-ASN : bond 0.00355 / 0.25 ( 48) link_NAG-ASN : angle 3.97198 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 468 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7467 (t0) REVERT: B 54 MET cc_start: 0.6591 (mmm) cc_final: 0.6378 (mmt) REVERT: F 586 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7396 (t0) REVERT: F 895 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: G 5 MET cc_start: 0.6523 (tpp) cc_final: 0.6298 (tpp) REVERT: K 895 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: M 46 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6410 (tp30) outliers start: 60 outliers final: 14 residues processed: 504 average time/residue: 0.6642 time to fit residues: 402.0037 Evaluate side-chains 426 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 407 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 284 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 227 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 408 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 419 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN A1101 HIS D 101 GLN F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 954 GLN G 101 GLN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN K 501 ASN K 804 GLN K 872 GLN K 954 GLN K1010 GLN K1011 GLN K1101 HIS N 89 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.200160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189359 restraints weight = 29900.707| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 0.39 r_work: 0.3976 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35028 Z= 0.145 Angle : 0.602 20.565 47877 Z= 0.310 Chirality : 0.046 0.454 5499 Planarity : 0.004 0.041 6105 Dihedral : 4.432 22.755 4761 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.36 % Allowed : 8.29 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4350 helix: 1.98 (0.20), residues: 684 sheet: 1.13 (0.14), residues: 1263 loop : 0.30 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F1107 TYR 0.021 0.002 TYR F1067 PHE 0.021 0.002 PHE A 898 TRP 0.009 0.001 TRP M 36 HIS 0.006 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34920) covalent geometry : angle 0.55954 / 0.30 (47610) SS BOND : bond 0.00388 / 0.28 ( 57) SS BOND : angle 0.87746 / 0.66 ( 114) hydrogen bonds : bond 0.05346 / 3.60 ( 1484) hydrogen bonds : angle 5.86769 / 4.17 ( 4065) link_BETA1-6 : bond 0.00626 / 0.31 ( 3) link_BETA1-6 : angle 1.22686 / 0.71 ( 9) link_NAG-ASN : bond 0.00768 / 0.54 ( 48) link_NAG-ASN : angle 4.04191 / 2.46 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 422 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7562 (t0) REVERT: E 67 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6380 (mmm160) REVERT: B 54 MET cc_start: 0.6816 (mmm) cc_final: 0.6546 (mmt) REVERT: F 48 LEU cc_start: 0.8368 (mt) cc_final: 0.8109 (mp) REVERT: F 586 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7510 (t70) REVERT: F 776 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8745 (tttt) REVERT: F 895 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: H 46 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: K 586 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7465 (t0) REVERT: K 895 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: M 46 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: N 4 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.4339 (tpt) REVERT: N 9 SER cc_start: 0.6796 (t) cc_final: 0.6557 (p) REVERT: O 96 CYS cc_start: 0.6296 (p) cc_final: 0.5975 (p) outliers start: 81 outliers final: 36 residues processed: 468 average time/residue: 0.6670 time to fit residues: 375.2136 Evaluate side-chains 445 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1010 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 339 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 221 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 335 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN A1023 ASN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 954 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 954 GLN K1010 GLN K1113 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.199048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188103 restraints weight = 29797.307| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 0.37 r_work: 0.3965 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35028 Z= 0.174 Angle : 0.633 20.114 47877 Z= 0.326 Chirality : 0.047 0.459 5499 Planarity : 0.005 0.062 6105 Dihedral : 4.623 23.712 4761 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.71 % Allowed : 8.64 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4350 helix: 1.81 (0.20), residues: 684 sheet: 1.07 (0.14), residues: 1263 loop : 0.17 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.023 0.002 TYR G 92 PHE 0.024 0.002 PHE A 898 TRP 0.011 0.002 TRP H 106 HIS 0.008 0.002 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (34920) covalent geometry : angle 0.59392 / 0.32 (47610) SS BOND : bond 0.00569 / 0.39 ( 57) SS BOND : angle 1.04869 / 0.81 ( 114) hydrogen bonds : bond 0.05651 / 3.80 ( 1484) hydrogen bonds : angle 5.89058 / 4.18 ( 4065) link_BETA1-6 : bond 0.00424 / 0.21 ( 3) link_BETA1-6 : angle 1.27649 / 0.73 ( 9) link_NAG-ASN : bond 0.00651 / 0.45 ( 48) link_NAG-ASN : angle 3.96002 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 408 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7535 (t0) REVERT: A 895 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: E 67 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6370 (mmm160) REVERT: B 54 MET cc_start: 0.6763 (mmm) cc_final: 0.6431 (mmt) REVERT: F 48 LEU cc_start: 0.8357 (mt) cc_final: 0.8101 (mp) REVERT: F 586 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7449 (t70) REVERT: F 776 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8732 (tttt) REVERT: F 895 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: F 1045 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7853 (ttpt) REVERT: G 5 MET cc_start: 0.6600 (tpp) cc_final: 0.6363 (tpp) REVERT: H 46 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6491 (tp30) REVERT: K 895 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: M 46 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6495 (tp30) REVERT: N 4 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.4731 (tpt) REVERT: N 9 SER cc_start: 0.6958 (t) cc_final: 0.6654 (p) REVERT: O 96 CYS cc_start: 0.6439 (p) cc_final: 0.6173 (p) outliers start: 93 outliers final: 45 residues processed: 453 average time/residue: 0.6822 time to fit residues: 372.2700 Evaluate side-chains 449 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 149 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 804 GLN A 926 GLN A 935 GLN A 954 GLN D 27 GLN D 101 GLN B 27 GLN B 89 GLN F 501 ASN F 532 ASN F 564 GLN F 613 GLN F 703 ASN F 755 GLN F 926 GLN G 27 GLN G 101 GLN I 89 GLN K 30 ASN K 314 GLN K 498 GLN K 501 ASN K 954 GLN K 955 ASN K1010 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.197226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.186478 restraints weight = 29829.331| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 0.38 r_work: 0.3948 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 35028 Z= 0.215 Angle : 0.689 20.254 47877 Z= 0.357 Chirality : 0.049 0.450 5499 Planarity : 0.005 0.039 6105 Dihedral : 4.891 24.772 4761 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.08 % Allowed : 8.93 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4350 helix: 1.56 (0.20), residues: 684 sheet: 0.94 (0.14), residues: 1284 loop : -0.06 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.026 0.002 TYR G 92 PHE 0.028 0.002 PHE A 898 TRP 0.017 0.002 TRP K 152 HIS 0.010 0.002 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (34920) covalent geometry : angle 0.65133 / 0.35 (47610) SS BOND : bond 0.00606 / 0.44 ( 57) SS BOND : angle 1.19000 / 0.92 ( 114) hydrogen bonds : bond 0.06094 / 4.09 ( 1484) hydrogen bonds : angle 6.04465 / 4.29 ( 4065) link_BETA1-6 : bond 0.00357 / 0.18 ( 3) link_BETA1-6 : angle 1.40686 / 0.81 ( 9) link_NAG-ASN : bond 0.00683 / 0.47 ( 48) link_NAG-ASN : angle 4.02846 / 2.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 407 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7471 (t0) REVERT: F 586 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7500 (t70) REVERT: F 895 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 902 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7286 (tpp) REVERT: F 1045 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7898 (ttpt) REVERT: H 46 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6559 (tp30) REVERT: K 895 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: K 947 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7695 (ttpt) REVERT: L 46 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7098 (ptt-90) REVERT: M 46 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6502 (tp30) REVERT: N 4 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5407 (tpt) REVERT: N 9 SER cc_start: 0.7053 (t) cc_final: 0.6794 (p) REVERT: O 96 CYS cc_start: 0.6484 (p) cc_final: 0.6239 (p) outliers start: 106 outliers final: 51 residues processed: 472 average time/residue: 0.6242 time to fit residues: 356.5825 Evaluate side-chains 454 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 392 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 33 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 183 optimal weight: 0.6980 chunk 280 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN F 955 ASN F1005 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.197791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187226 restraints weight = 29708.080| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 0.38 r_work: 0.3958 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35028 Z= 0.176 Angle : 0.638 20.124 47877 Z= 0.329 Chirality : 0.047 0.446 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.732 23.578 4761 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.73 % Allowed : 9.71 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4350 helix: 1.65 (0.20), residues: 684 sheet: 0.92 (0.14), residues: 1299 loop : -0.08 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.023 0.002 TYR G 92 PHE 0.025 0.002 PHE A 898 TRP 0.012 0.002 TRP H 106 HIS 0.008 0.002 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (34920) covalent geometry : angle 0.59951 / 0.32 (47610) SS BOND : bond 0.00502 / 0.36 ( 57) SS BOND : angle 1.01987 / 0.78 ( 114) hydrogen bonds : bond 0.05609 / 3.77 ( 1484) hydrogen bonds : angle 5.90634 / 4.19 ( 4065) link_BETA1-6 : bond 0.00319 / 0.16 ( 3) link_BETA1-6 : angle 1.43072 / 0.81 ( 9) link_NAG-ASN : bond 0.00655 / 0.45 ( 48) link_NAG-ASN : angle 3.94352 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 402 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7465 (t0) REVERT: A 895 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: E 46 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6298 (tp30) REVERT: B 54 MET cc_start: 0.7146 (mmm) cc_final: 0.6881 (mmt) REVERT: C 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.8148 (m-80) REVERT: F 48 LEU cc_start: 0.8416 (mt) cc_final: 0.8153 (mp) REVERT: F 586 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7511 (t70) REVERT: F 895 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: F 1045 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: H 46 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: K 895 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: M 46 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: N 9 SER cc_start: 0.7119 (t) cc_final: 0.6872 (p) REVERT: O 96 CYS cc_start: 0.6467 (p) cc_final: 0.6230 (p) outliers start: 94 outliers final: 47 residues processed: 457 average time/residue: 0.6586 time to fit residues: 363.2956 Evaluate side-chains 451 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 395 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 615 VAL Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 435 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 379 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 362 optimal weight: 0.0270 chunk 189 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 703 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 926 GLN K 954 GLN K1010 GLN K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.197433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.186862 restraints weight = 29777.205| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 0.38 r_work: 0.3951 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.3623 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 35028 Z= 0.188 Angle : 0.659 20.275 47877 Z= 0.340 Chirality : 0.048 0.439 5499 Planarity : 0.005 0.050 6105 Dihedral : 4.805 24.243 4761 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 9.89 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4350 helix: 1.74 (0.20), residues: 666 sheet: 0.87 (0.14), residues: 1299 loop : -0.13 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F1107 TYR 0.028 0.002 TYR A 396 PHE 0.026 0.002 PHE A 898 TRP 0.012 0.002 TRP H 106 HIS 0.009 0.002 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (34920) covalent geometry : angle 0.62076 / 0.33 (47610) SS BOND : bond 0.00552 / 0.40 ( 57) SS BOND : angle 1.13946 / 0.87 ( 114) hydrogen bonds : bond 0.05790 / 3.89 ( 1484) hydrogen bonds : angle 5.94546 / 4.22 ( 4065) link_BETA1-6 : bond 0.00343 / 0.17 ( 3) link_BETA1-6 : angle 1.42730 / 0.81 ( 9) link_NAG-ASN : bond 0.00672 / 0.47 ( 48) link_NAG-ASN : angle 3.95146 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 400 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8732 (mt) cc_final: 0.8347 (mp) REVERT: A 586 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8049 (t0) REVERT: E 46 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: B 54 MET cc_start: 0.7684 (mmm) cc_final: 0.7278 (mmt) REVERT: F 48 LEU cc_start: 0.8567 (mt) cc_final: 0.8260 (mp) REVERT: F 310 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (ttpp) REVERT: F 501 ASN cc_start: 0.8460 (m-40) cc_final: 0.8210 (m110) REVERT: F 586 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8045 (t70) REVERT: F 703 ASN cc_start: 0.7105 (t0) cc_final: 0.6738 (t160) REVERT: F 895 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: F 1045 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8054 (ttpt) REVERT: H 46 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: I 46 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (tm) REVERT: K 858 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mt) REVERT: K 895 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: K 947 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: L 46 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7451 (ptt-90) REVERT: M 46 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: O 96 CYS cc_start: 0.6969 (p) cc_final: 0.6710 (p) outliers start: 99 outliers final: 55 residues processed: 457 average time/residue: 0.6872 time to fit residues: 377.8080 Evaluate side-chains 463 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 395 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 547 THR Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 858 LEU Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 36 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 373 optimal weight: 0.7980 chunk 318 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 238 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.199283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188106 restraints weight = 29824.347| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 0.39 r_work: 0.3965 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35028 Z= 0.129 Angle : 0.589 19.919 47877 Z= 0.301 Chirality : 0.046 0.436 5499 Planarity : 0.004 0.040 6105 Dihedral : 4.505 22.109 4761 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.47 % Allowed : 10.47 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4350 helix: 1.99 (0.20), residues: 666 sheet: 0.96 (0.14), residues: 1296 loop : -0.04 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1107 TYR 0.026 0.002 TYR F 396 PHE 0.018 0.001 PHE A 898 TRP 0.011 0.001 TRP H 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (34920) covalent geometry : angle 0.54904 / 0.29 (47610) SS BOND : bond 0.00346 / 0.25 ( 57) SS BOND : angle 0.88077 / 0.63 ( 114) hydrogen bonds : bond 0.04996 / 3.36 ( 1484) hydrogen bonds : angle 5.70283 / 4.05 ( 4065) link_BETA1-6 : bond 0.00365 / 0.18 ( 3) link_BETA1-6 : angle 1.37941 / 0.77 ( 9) link_NAG-ASN : bond 0.00657 / 0.46 ( 48) link_NAG-ASN : angle 3.84759 / 2.36 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 403 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7518 (t0) REVERT: E 46 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6267 (tp30) REVERT: B 54 MET cc_start: 0.7133 (mmm) cc_final: 0.6853 (mmt) REVERT: F 48 LEU cc_start: 0.8349 (mt) cc_final: 0.8103 (mp) REVERT: F 586 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7528 (t70) REVERT: F 895 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: H 46 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6509 (tp30) REVERT: I 46 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7411 (tm) REVERT: J 96 CYS cc_start: 0.6539 (p) cc_final: 0.6254 (p) REVERT: K 895 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: M 46 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6444 (tp30) outliers start: 85 outliers final: 53 residues processed: 449 average time/residue: 0.6732 time to fit residues: 365.1151 Evaluate side-chains 454 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 158 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 254 optimal weight: 7.9990 chunk 382 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 359 optimal weight: 0.8980 chunk 416 optimal weight: 10.0000 chunk 403 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.200231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.188270 restraints weight = 29795.042| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 0.42 r_work: 0.3964 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35028 Z= 0.111 Angle : 0.566 19.859 47877 Z= 0.287 Chirality : 0.045 0.428 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.304 20.752 4761 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 10.94 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 4350 helix: 2.12 (0.21), residues: 663 sheet: 1.03 (0.14), residues: 1296 loop : 0.03 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.025 0.001 TYR K 396 PHE 0.016 0.001 PHE A 898 TRP 0.010 0.001 TRP H 106 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (34920) covalent geometry : angle 0.52498 / 0.28 (47610) SS BOND : bond 0.00311 / 0.22 ( 57) SS BOND : angle 0.90928 / 0.64 ( 114) hydrogen bonds : bond 0.04636 / 3.12 ( 1484) hydrogen bonds : angle 5.52252 / 3.92 ( 4065) link_BETA1-6 : bond 0.00478 / 0.24 ( 3) link_BETA1-6 : angle 1.29595 / 0.72 ( 9) link_NAG-ASN : bond 0.00665 / 0.46 ( 48) link_NAG-ASN : angle 3.80133 / 2.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 405 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8503 (mt) cc_final: 0.8234 (mp) REVERT: A 586 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7520 (t0) REVERT: E 46 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6262 (tp30) REVERT: B 54 MET cc_start: 0.7266 (mmm) cc_final: 0.6989 (mmt) REVERT: F 48 LEU cc_start: 0.8336 (mt) cc_final: 0.8089 (mp) REVERT: F 586 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7567 (t70) REVERT: F 895 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: H 46 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6535 (tp30) REVERT: I 46 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7383 (tm) REVERT: K 586 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7528 (t0) REVERT: K 858 LEU cc_start: 0.8226 (mt) cc_final: 0.8023 (mp) REVERT: K 895 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: M 46 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6425 (tp30) outliers start: 73 outliers final: 44 residues processed: 445 average time/residue: 0.6683 time to fit residues: 359.6542 Evaluate side-chains 443 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 390 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 444 LYS Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 385 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 394 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 417 optimal weight: 20.0000 chunk 406 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.197748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187318 restraints weight = 29527.973| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 0.38 r_work: 0.3949 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 35028 Z= 0.222 Angle : 0.690 20.199 47877 Z= 0.358 Chirality : 0.049 0.432 5499 Planarity : 0.005 0.038 6105 Dihedral : 4.821 24.781 4761 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.30 % Allowed : 10.67 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4350 helix: 1.77 (0.20), residues: 666 sheet: 0.94 (0.14), residues: 1323 loop : -0.14 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 905 TYR 0.048 0.003 TYR K 396 PHE 0.029 0.002 PHE A 898 TRP 0.012 0.002 TRP H 106 HIS 0.010 0.002 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (34920) covalent geometry : angle 0.65426 / 0.35 (47610) SS BOND : bond 0.00627 / 0.45 ( 57) SS BOND : angle 1.33265 / 1.01 ( 114) hydrogen bonds : bond 0.06064 / 4.08 ( 1484) hydrogen bonds : angle 5.94594 / 4.21 ( 4065) link_BETA1-6 : bond 0.00326 / 0.16 ( 3) link_BETA1-6 : angle 1.44574 / 0.84 ( 9) link_NAG-ASN : bond 0.00694 / 0.48 ( 48) link_NAG-ASN : angle 3.91829 / 2.40 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 384 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7519 (t0) REVERT: A 1045 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7829 (ttpt) REVERT: E 46 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: B 54 MET cc_start: 0.7230 (mmm) cc_final: 0.6918 (mmt) REVERT: F 48 LEU cc_start: 0.8380 (mt) cc_final: 0.8128 (mp) REVERT: F 586 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7552 (t70) REVERT: F 895 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: F 1045 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7903 (ttpt) REVERT: H 46 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: I 46 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7511 (tm) REVERT: K 895 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: M 46 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6526 (tp30) outliers start: 79 outliers final: 44 residues processed: 431 average time/residue: 0.6536 time to fit residues: 341.3110 Evaluate side-chains 429 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 615 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 444 LYS Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 199 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 330 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 250 optimal weight: 0.1980 chunk 387 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.190025 restraints weight = 29678.850| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 0.38 r_work: 0.3983 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35028 Z= 0.116 Angle : 0.572 19.763 47877 Z= 0.291 Chirality : 0.045 0.419 5499 Planarity : 0.004 0.037 6105 Dihedral : 4.368 20.963 4761 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.69 % Allowed : 11.29 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4350 helix: 2.09 (0.21), residues: 663 sheet: 1.04 (0.14), residues: 1293 loop : -0.02 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.039 0.001 TYR K 396 PHE 0.016 0.001 PHE A 898 TRP 0.010 0.001 TRP H 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (34920) covalent geometry : angle 0.53264 / 0.28 (47610) SS BOND : bond 0.00297 / 0.21 ( 57) SS BOND : angle 0.87458 / 0.62 ( 114) hydrogen bonds : bond 0.04701 / 3.17 ( 1484) hydrogen bonds : angle 5.57215 / 3.95 ( 4065) link_BETA1-6 : bond 0.00407 / 0.20 ( 3) link_BETA1-6 : angle 1.36042 / 0.75 ( 9) link_NAG-ASN : bond 0.00665 / 0.46 ( 48) link_NAG-ASN : angle 3.79387 / 2.33 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13799.22 seconds wall clock time: 235 minutes 33.78 seconds (14133.78 seconds total)