Starting phenix.real_space_refine on Fri Mar 6 20:37:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7so9_25263/03_2026/7so9_25263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7so9_25263/03_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_25263/03_2026/7so9_25263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7so9_25263/03_2026/7so9_25263.map" model { file = "/net/cci-nas-00/data/ceres_data/7so9_25263/03_2026/7so9_25263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7so9_25263/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 45 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: 10.13, per 1000 atoms: 0.29 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: 2.69 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: 1.80 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: 9.65 Time building geometry restraints manager: 3.69 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: 20394 17.79 - 35.58: 582 35.58 - 53.37: 174 53.37 - 71.17: 51 71.17 - 88.96: 21 Dihedral angle restraints: 21222 sinusoidal: 8397 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 21219 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: 0.06 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: 11.730 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.770 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 10.515 88.957 12843 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 covalent geometry : bond 0.01049 (34920) covalent geometry : angle 1.19036 (47610) SS BOND : bond 0.06095 ( 57) SS BOND : angle 3.77839 ( 114) hydrogen bonds : bond 0.16911 ( 1484) hydrogen bonds : angle 8.12863 ( 4065) link_BETA1-6 : bond 0.05753 ( 3) link_BETA1-6 : angle 2.26292 ( 9) link_NAG-ASN : bond 0.04824 ( 48) link_NAG-ASN : angle 3.16314 ( 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 : 1.136 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: 0.6978 time to fit residues: 496.6405 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 : 1.070 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.201614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191072 restraints weight = 30252.317| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 0.39 r_work: 0.3991 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35028 Z= 0.141 Angle : 0.612 18.870 47877 Z= 0.316 Chirality : 0.047 0.526 5499 Planarity : 0.004 0.041 6105 Dihedral : 4.752 37.077 5820 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.66 % Allowed : 7.30 % Favored : 91.04 % 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: 1.21 (0.12), residues: 4350 helix: 2.09 (0.21), residues: 666 sheet: 1.13 (0.14), residues: 1275 loop : 0.33 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K1107 TYR 0.023 0.002 TYR F1067 PHE 0.014 0.002 PHE A 898 TRP 0.010 0.001 TRP H 115 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00294 (34920) covalent geometry : angle 0.56943 (47610) SS BOND : bond 0.00583 ( 57) SS BOND : angle 0.95584 ( 114) hydrogen bonds : bond 0.05466 ( 1484) hydrogen bonds : angle 6.13888 ( 4065) link_BETA1-6 : bond 0.01201 ( 3) link_BETA1-6 : angle 1.55384 ( 9) link_NAG-ASN : bond 0.00723 ( 48) link_NAG-ASN : angle 4.05839 ( 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 526 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 469 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7501 (t0) REVERT: B 54 MET cc_start: 0.6628 (mmm) cc_final: 0.6420 (mmt) REVERT: F 586 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7439 (t0) REVERT: F 895 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: G 5 MET cc_start: 0.6573 (tpp) cc_final: 0.6357 (tpp) REVERT: K 895 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: M 46 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6447 (tp30) outliers start: 57 outliers final: 15 residues processed: 502 average time/residue: 0.6984 time to fit residues: 419.3433 Evaluate side-chains 429 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 409 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN 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 314 GLN 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 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: 0.5980 chunk 227 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 408 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 419 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN A1101 HIS D 27 GLN D 101 GLN F 207 HIS F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 926 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 K1113 GLN N 89 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.198073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.187173 restraints weight = 29901.296| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 0.40 r_work: 0.3951 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 35028 Z= 0.221 Angle : 0.696 20.709 47877 Z= 0.363 Chirality : 0.050 0.481 5499 Planarity : 0.005 0.049 6105 Dihedral : 5.116 27.812 5820 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.73 % Allowed : 8.03 % Favored : 89.24 % 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: 1.79 (0.20), residues: 666 sheet: 1.03 (0.14), residues: 1260 loop : 0.10 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K1107 TYR 0.026 0.002 TYR G 92 PHE 0.028 0.003 PHE A 898 TRP 0.012 0.002 TRP A 886 HIS 0.010 0.002 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00505 (34920) covalent geometry : angle 0.65579 (47610) SS BOND : bond 0.00696 ( 57) SS BOND : angle 1.17286 ( 114) hydrogen bonds : bond 0.06312 ( 1484) hydrogen bonds : angle 6.15417 ( 4065) link_BETA1-6 : bond 0.00360 ( 3) link_BETA1-6 : angle 1.36039 ( 9) link_NAG-ASN : bond 0.00893 ( 48) link_NAG-ASN : angle 4.19902 ( 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 511 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 417 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7500 (t0) REVERT: E 67 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6408 (mmm160) REVERT: B 54 MET cc_start: 0.6921 (mmm) cc_final: 0.6563 (mmt) REVERT: F 48 LEU cc_start: 0.8435 (mt) cc_final: 0.8106 (mp) REVERT: F 207 HIS cc_start: 0.7622 (m90) cc_final: 0.7385 (m-70) REVERT: F 586 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7477 (t70) REVERT: F 776 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8754 (tttt) REVERT: F 814 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5757 (pttt) REVERT: F 895 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: F 1045 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7906 (ttpt) REVERT: H 46 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: K 546 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7813 (tp) REVERT: K 895 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: K 985 ASP cc_start: 0.7557 (m-30) cc_final: 0.7352 (m-30) REVERT: M 46 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6498 (tp30) REVERT: N 4 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5026 (tpt) REVERT: N 9 SER cc_start: 0.6825 (t) cc_final: 0.6578 (p) REVERT: O 96 CYS cc_start: 0.6427 (p) cc_final: 0.6201 (p) outliers start: 94 outliers final: 38 residues processed: 470 average time/residue: 0.6755 time to fit residues: 381.2199 Evaluate side-chains 440 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 390 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 445 VAL Chi-restraints excluded: chain A residue 462 LYS 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 E residue 74 THR 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 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 814 LYS 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 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 571 ASP 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 339 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 335 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 935 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 955 ASN G 101 GLN I 89 GLN K 30 ASN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.199819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.189038 restraints weight = 29910.433| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 0.38 r_work: 0.3976 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35028 Z= 0.133 Angle : 0.588 20.088 47877 Z= 0.301 Chirality : 0.046 0.476 5499 Planarity : 0.004 0.044 6105 Dihedral : 4.706 29.454 5820 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.39 % Allowed : 9.08 % Favored : 88.54 % 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: 1.02 (0.12), residues: 4350 helix: 2.04 (0.20), residues: 666 sheet: 1.05 (0.14), residues: 1287 loop : 0.15 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K1107 TYR 0.019 0.002 TYR F1067 PHE 0.019 0.001 PHE A 898 TRP 0.010 0.001 TRP H 106 HIS 0.006 0.001 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00288 (34920) covalent geometry : angle 0.54560 (47610) SS BOND : bond 0.00364 ( 57) SS BOND : angle 0.84695 ( 114) hydrogen bonds : bond 0.05131 ( 1484) hydrogen bonds : angle 5.79479 ( 4065) link_BETA1-6 : bond 0.00393 ( 3) link_BETA1-6 : angle 1.40293 ( 9) link_NAG-ASN : bond 0.00636 ( 48) link_NAG-ASN : angle 4.00160 ( 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 498 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 416 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 895 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: E 67 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6395 (mmm160) REVERT: B 54 MET cc_start: 0.6743 (mmm) cc_final: 0.6426 (mmt) REVERT: F 48 LEU cc_start: 0.8333 (mt) cc_final: 0.8081 (mp) REVERT: F 207 HIS cc_start: 0.7621 (m90) cc_final: 0.7374 (m-70) REVERT: F 586 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7416 (t70) REVERT: F 895 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: H 46 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6444 (tp30) REVERT: K 586 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7418 (t0) REVERT: K 895 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: K 985 ASP cc_start: 0.7508 (m-30) cc_final: 0.7261 (m-30) REVERT: M 46 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: N 4 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5002 (tpt) REVERT: N 9 SER cc_start: 0.6954 (t) cc_final: 0.6670 (p) REVERT: O 96 CYS cc_start: 0.6430 (p) cc_final: 0.6160 (p) outliers start: 82 outliers final: 36 residues processed: 457 average time/residue: 0.6970 time to fit residues: 380.9033 Evaluate side-chains 440 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 394 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 470 THR 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 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 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 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 G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN 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 333 THR Chi-restraints excluded: chain K residue 340 GLU 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 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 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: 3.9990 chunk 100 optimal weight: 0.0470 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: 3.9990 chunk 51 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 926 GLN A 954 GLN D 27 GLN D 101 GLN B 27 GLN B 89 GLN F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN K 501 ASN K 755 GLN K 926 GLN K 954 GLN K 955 ASN K1010 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.186165 restraints weight = 29802.630| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 0.38 r_work: 0.3947 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 35028 Z= 0.245 Angle : 0.722 20.625 47877 Z= 0.376 Chirality : 0.051 0.480 5499 Planarity : 0.005 0.046 6105 Dihedral : 5.364 37.017 5820 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.17 % Allowed : 8.90 % Favored : 87.93 % 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: 0.69 (0.12), residues: 4350 helix: 1.65 (0.20), residues: 666 sheet: 0.95 (0.14), residues: 1299 loop : -0.11 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1107 TYR 0.030 0.003 TYR G 92 PHE 0.031 0.003 PHE A 898 TRP 0.012 0.002 TRP A 353 HIS 0.011 0.002 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00562 (34920) covalent geometry : angle 0.68404 (47610) SS BOND : bond 0.00682 ( 57) SS BOND : angle 1.30871 ( 114) hydrogen bonds : bond 0.06409 ( 1484) hydrogen bonds : angle 6.12365 ( 4065) link_BETA1-6 : bond 0.00288 ( 3) link_BETA1-6 : angle 1.56326 ( 9) link_NAG-ASN : bond 0.00708 ( 48) link_NAG-ASN : angle 4.16338 ( 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 517 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 408 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: A 586 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7471 (t0) REVERT: A 895 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: F 310 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8329 (ttpp) REVERT: F 554 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: F 586 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7512 (t70) REVERT: F 895 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: F 1045 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7920 (ttpt) REVERT: H 46 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: K 895 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: K 947 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: L 46 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7099 (ptt-90) REVERT: M 46 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6517 (tp30) REVERT: N 4 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5445 (tpt) REVERT: N 9 SER cc_start: 0.7096 (t) cc_final: 0.6823 (p) outliers start: 109 outliers final: 50 residues processed: 474 average time/residue: 0.7070 time to fit residues: 399.4495 Evaluate side-chains 455 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 391 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain A residue 471 GLU 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 895 GLN 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 69 THR Chi-restraints excluded: chain F residue 108 THR 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 554 GLU 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 659 SER 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 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 47 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 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 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 947 LYS Chi-restraints excluded: chain L residue 21 LEU 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: 0.9990 chunk 340 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 804 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 314 GLN F 501 ASN F 532 ASN F 755 GLN F1005 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN K 501 ASN K 755 GLN K 954 GLN K 955 ASN 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 = 0.4154 r_free = 0.4154 target = 0.198167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.186403 restraints weight = 29685.446| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 0.40 r_work: 0.3942 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35028 Z= 0.169 Angle : 0.635 20.226 47877 Z= 0.327 Chirality : 0.047 0.467 5499 Planarity : 0.004 0.037 6105 Dihedral : 5.039 36.091 5820 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.88 % Allowed : 9.45 % Favored : 87.67 % 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: 0.74 (0.12), residues: 4350 helix: 1.81 (0.20), residues: 666 sheet: 0.96 (0.14), residues: 1278 loop : -0.10 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K1107 TYR 0.024 0.002 TYR A 396 PHE 0.024 0.002 PHE A 898 TRP 0.012 0.002 TRP H 106 HIS 0.008 0.002 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00376 (34920) covalent geometry : angle 0.59496 (47610) SS BOND : bond 0.00483 ( 57) SS BOND : angle 1.04956 ( 114) hydrogen bonds : bond 0.05568 ( 1484) hydrogen bonds : angle 5.91924 ( 4065) link_BETA1-6 : bond 0.00193 ( 3) link_BETA1-6 : angle 1.59792 ( 9) link_NAG-ASN : bond 0.00662 ( 48) link_NAG-ASN : angle 4.02351 ( 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 510 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 411 time to evaluate : 1.249 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 471 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: A 586 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7465 (t0) REVERT: A 895 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: A 1045 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7769 (ttpt) REVERT: E 46 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: B 54 MET cc_start: 0.7175 (mmm) cc_final: 0.6896 (mmt) REVERT: C 59 TYR cc_start: 0.8372 (m-80) cc_final: 0.8167 (m-80) REVERT: F 48 LEU cc_start: 0.8392 (mt) cc_final: 0.8123 (mp) REVERT: F 586 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7509 (t70) REVERT: F 895 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: F 1045 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7856 (ttpt) REVERT: H 46 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6484 (tp30) REVERT: I 46 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7425 (tm) REVERT: K 895 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: K 947 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7698 (ttpt) REVERT: L 46 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7090 (ptt-90) REVERT: M 46 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6509 (tp30) REVERT: N 9 SER cc_start: 0.7186 (t) cc_final: 0.6893 (p) outliers start: 99 outliers final: 50 residues processed: 471 average time/residue: 0.6886 time to fit residues: 387.1421 Evaluate side-chains 463 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 399 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 615 VAL 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 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1045 LYS 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 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 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 808 ASP 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 G residue 95 SER 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 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 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 791 THR 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 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 47 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 435 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 379 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 302 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 314 GLN F 501 ASN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 37 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 = 0.4140 r_free = 0.4140 target = 0.196999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.186441 restraints weight = 29584.102| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 0.38 r_work: 0.3941 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 35028 Z= 0.229 Angle : 0.711 20.615 47877 Z= 0.369 Chirality : 0.050 0.462 5499 Planarity : 0.005 0.051 6105 Dihedral : 5.456 48.033 5820 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.29 % Allowed : 9.60 % Favored : 87.11 % 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: 0.51 (0.12), residues: 4350 helix: 1.56 (0.20), residues: 666 sheet: 0.81 (0.14), residues: 1317 loop : -0.25 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F1107 TYR 0.028 0.003 TYR G 92 PHE 0.030 0.003 PHE A 898 TRP 0.012 0.002 TRP H 106 HIS 0.010 0.002 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00524 (34920) covalent geometry : angle 0.67320 (47610) SS BOND : bond 0.00651 ( 57) SS BOND : angle 1.30069 ( 114) hydrogen bonds : bond 0.06252 ( 1484) hydrogen bonds : angle 6.11092 ( 4065) link_BETA1-6 : bond 0.00260 ( 3) link_BETA1-6 : angle 1.68257 ( 9) link_NAG-ASN : bond 0.00697 ( 48) link_NAG-ASN : angle 4.10017 ( 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 523 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 410 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: A 586 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7509 (t0) REVERT: A 895 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: A 1045 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7964 (ttpt) REVERT: E 46 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: B 54 MET cc_start: 0.7214 (mmm) cc_final: 0.6934 (mmt) REVERT: F 310 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8353 (ttpp) REVERT: F 586 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7589 (t70) REVERT: F 895 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: F 1045 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7931 (ttpt) REVERT: H 46 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: K 895 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: K 947 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7714 (ttpt) REVERT: L 46 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7077 (ptt-90) REVERT: M 46 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6548 (tp30) REVERT: N 4 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5639 (tpt) REVERT: O 96 CYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (p) outliers start: 113 outliers final: 58 residues processed: 473 average time/residue: 0.6857 time to fit residues: 386.7516 Evaluate side-chains 474 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 400 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 471 GLU 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 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 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU 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 F residue 108 THR 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 576 VAL 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 808 ASP 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 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 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 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 791 THR Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain L residue 21 LEU 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 4 MET Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 373 optimal weight: 0.5980 chunk 318 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 394 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 314 GLN F 501 ASN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.199194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.188786 restraints weight = 29813.777| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 0.40 r_work: 0.3964 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35028 Z= 0.124 Angle : 0.591 20.111 47877 Z= 0.301 Chirality : 0.046 0.455 5499 Planarity : 0.004 0.041 6105 Dihedral : 4.868 43.776 5820 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.12 % Allowed : 11.14 % Favored : 86.74 % 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: 0.75 (0.12), residues: 4350 helix: 1.95 (0.20), residues: 666 sheet: 0.91 (0.14), residues: 1296 loop : -0.10 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K1107 TYR 0.028 0.002 TYR F 396 PHE 0.017 0.001 PHE A 898 TRP 0.012 0.001 TRP H 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (34920) covalent geometry : angle 0.54961 (47610) SS BOND : bond 0.00324 ( 57) SS BOND : angle 0.79411 ( 114) hydrogen bonds : bond 0.04938 ( 1484) hydrogen bonds : angle 5.73731 ( 4065) link_BETA1-6 : bond 0.00264 ( 3) link_BETA1-6 : angle 1.56096 ( 9) link_NAG-ASN : bond 0.00669 ( 48) link_NAG-ASN : angle 3.93659 ( 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 485 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 412 time to evaluate : 1.032 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: 0.7850 (OUTLIER) cc_final: 0.7551 (t0) REVERT: A 895 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: E 46 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: B 54 MET cc_start: 0.7220 (mmm) cc_final: 0.6945 (mmt) REVERT: F 48 LEU cc_start: 0.8337 (mt) cc_final: 0.8093 (mp) REVERT: F 586 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7530 (t70) REVERT: F 895 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: H 46 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: I 46 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7422 (tm) REVERT: K 895 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: M 46 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6485 (tp30) outliers start: 73 outliers final: 37 residues processed: 459 average time/residue: 0.6846 time to fit residues: 375.6887 Evaluate side-chains 449 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER 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 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 F residue 108 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 732 THR Chi-restraints excluded: chain F residue 808 ASP 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 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 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 445 VAL Chi-restraints excluded: chain K residue 571 ASP 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 21 LEU 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 52 SER Chi-restraints excluded: chain O residue 96 CYS 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: 9.9990 chunk 83 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 254 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 392 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 416 optimal weight: 9.9990 chunk 403 optimal weight: 3.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 314 GLN F 501 ASN F 532 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN K 394 ASN 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.198982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.188534 restraints weight = 29707.452| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 0.39 r_work: 0.3965 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35028 Z= 0.135 Angle : 0.599 20.247 47877 Z= 0.306 Chirality : 0.046 0.445 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.805 45.085 5820 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.18 % Allowed : 11.14 % Favored : 86.68 % 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: 0.81 (0.12), residues: 4350 helix: 1.97 (0.20), residues: 666 sheet: 0.97 (0.14), residues: 1293 loop : -0.07 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.032 0.002 TYR K 396 PHE 0.020 0.002 PHE A 898 TRP 0.011 0.001 TRP H 106 HIS 0.007 0.001 HIS K1048 Details of bonding type rmsd covalent geometry : bond 0.00295 (34920) covalent geometry : angle 0.55824 (47610) SS BOND : bond 0.00383 ( 57) SS BOND : angle 0.97147 ( 114) hydrogen bonds : bond 0.05095 ( 1484) hydrogen bonds : angle 5.69932 ( 4065) link_BETA1-6 : bond 0.00292 ( 3) link_BETA1-6 : angle 1.52263 ( 9) link_NAG-ASN : bond 0.00678 ( 48) link_NAG-ASN : angle 3.93734 ( 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 475 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 1.282 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: 0.7819 (OUTLIER) cc_final: 0.7537 (t0) REVERT: A 895 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: E 46 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: B 54 MET cc_start: 0.7190 (mmm) cc_final: 0.6928 (mmt) REVERT: F 48 LEU cc_start: 0.8346 (mt) cc_final: 0.8103 (mp) REVERT: F 586 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7509 (t70) REVERT: F 895 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: H 46 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6543 (tp30) REVERT: I 46 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7439 (tm) REVERT: K 586 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7494 (t0) REVERT: M 46 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6471 (tp30) outliers start: 75 outliers final: 46 residues processed: 449 average time/residue: 0.6664 time to fit residues: 360.5945 Evaluate side-chains 454 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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 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 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 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 791 THR 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 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 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 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 931 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 30 SER 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 11 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: 3.9990 chunk 1 optimal weight: 0.0070 chunk 417 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 393 optimal weight: 7.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F1010 GLN F1011 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.198184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.187672 restraints weight = 29533.024| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 0.38 r_work: 0.3955 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 35028 Z= 0.189 Angle : 0.656 20.343 47877 Z= 0.339 Chirality : 0.048 0.447 5499 Planarity : 0.005 0.038 6105 Dihedral : 5.133 54.796 5820 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.18 % Allowed : 11.11 % Favored : 86.71 % 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: 0.70 (0.12), residues: 4350 helix: 1.81 (0.20), residues: 666 sheet: 0.96 (0.14), residues: 1272 loop : -0.15 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 905 TYR 0.044 0.002 TYR K 396 PHE 0.026 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 covalent geometry : bond 0.00427 (34920) covalent geometry : angle 0.61765 (47610) SS BOND : bond 0.00542 ( 57) SS BOND : angle 1.17106 ( 114) hydrogen bonds : bond 0.05760 ( 1484) hydrogen bonds : angle 5.89858 ( 4065) link_BETA1-6 : bond 0.00233 ( 3) link_BETA1-6 : angle 1.60460 ( 9) link_NAG-ASN : bond 0.00694 ( 48) link_NAG-ASN : angle 3.98240 ( 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 475 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 1.141 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: 0.7866 (OUTLIER) cc_final: 0.7545 (t0) REVERT: A 895 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: E 46 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6302 (tp30) REVERT: B 54 MET cc_start: 0.7301 (mmm) cc_final: 0.6990 (mmt) REVERT: F 48 LEU cc_start: 0.8344 (mt) cc_final: 0.8107 (mp) REVERT: F 586 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7541 (t70) REVERT: F 895 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: H 46 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: I 46 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7503 (tm) REVERT: M 46 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6542 (tp30) REVERT: O 96 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7301 (p) outliers start: 75 outliers final: 48 residues processed: 449 average time/residue: 0.6746 time to fit residues: 363.3089 Evaluate side-chains 446 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 389 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 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 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 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 732 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU 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 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 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 931 ILE Chi-restraints excluded: chain L residue 21 LEU 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 11 LEU Chi-restraints excluded: chain N residue 47 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 199 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 330 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 250 optimal weight: 0.0970 chunk 387 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 474 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 271 GLN F 314 GLN F 501 ASN F 532 ASN F 755 GLN F 787 GLN G 27 GLN G 101 GLN I 89 GLN K 271 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN K1101 HIS ** 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 = 0.4155 r_free = 0.4155 target = 0.198332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.187807 restraints weight = 29456.110| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 0.37 r_work: 0.3959 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 35028 Z= 0.179 Angle : 0.764 59.194 47877 Z= 0.409 Chirality : 0.048 0.702 5499 Planarity : 0.004 0.038 6105 Dihedral : 5.124 54.748 5820 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.07 % Allowed : 11.17 % Favored : 86.77 % Cbeta Deviations : 0.02 % 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: 0.69 (0.12), residues: 4350 helix: 1.76 (0.20), residues: 666 sheet: 0.97 (0.14), residues: 1272 loop : -0.15 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K1107 TYR 0.038 0.002 TYR K 396 PHE 0.025 0.002 PHE A 898 TRP 0.011 0.001 TRP H 106 HIS 0.007 0.001 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.00396 (34920) covalent geometry : angle 0.73165 (47610) SS BOND : bond 0.00471 ( 57) SS BOND : angle 1.14354 ( 114) hydrogen bonds : bond 0.05674 ( 1484) hydrogen bonds : angle 5.89452 ( 4065) link_BETA1-6 : bond 0.00266 ( 3) link_BETA1-6 : angle 1.57401 ( 9) link_NAG-ASN : bond 0.00691 ( 48) link_NAG-ASN : angle 3.98205 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13081.28 seconds wall clock time: 222 minutes 45.27 seconds (13365.27 seconds total)