Starting phenix.real_space_refine on Thu Oct 29 23:18:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7so9_25263/10_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.map" model { file = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_2026/7so9_25263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7so9_25263/10_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): 0.28s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34470 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7820 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 8, 'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 749 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 864 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Restraints were copied for chains: F, K, G, L, H, M, I, N, J, O, Q, R Time building chain proxies: 11.74, per 1000 atoms: 0.34 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 F 131 " - pdb=" SG CYS F 166 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.17 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.05 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.02 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.12 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.12 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.10 Simple disulfide: pdb=" SG CYS F 883 " - pdb=" SG CYS K 707 " distance=2.14 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.17 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.05 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.02 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.12 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.12 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.10 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 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: 1.38 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: 10.35 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5799 1.32 - 1.45: 9687 1.45 - 1.58: 19212 1.58 - 1.71: 0 1.71 - 1.84: 222 Bond restraints: 34920 Sorted by residual: bond pdb=" CA CYS F 15 " pdb=" C CYS F 15 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CA CYS K 15 " pdb=" C CYS K 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA CYS A 15 " pdb=" C CYS A 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" C GLN F 14 " pdb=" N CYS F 15 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.32e-02 5.74e+03 9.07e+00 bond pdb=" C GLN A 14 " pdb=" N CYS A 15 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.32e-02 5.74e+03 8.93e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 42540 1.68 - 3.36: 4176 3.36 - 5.03: 413 5.03 - 6.71: 349 6.71 - 8.39: 132 Bond angle restraints: 47610 Sorted by residual: angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.05e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.20e-01 1.93e+00 9.03e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 ... (remaining 47605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 19371 17.79 - 35.58: 549 35.58 - 53.37: 171 53.37 - 71.17: 51 71.17 - 88.96: 21 Dihedral angle restraints: 20163 sinusoidal: 7338 harmonic: 12825 Sorted by residual: dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 96 " pdb=" CB CYS O 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.55 52.45 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 20160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 5415 0.189 - 0.378: 81 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.945: 3 Chirality restraints: 5499 Sorted by residual: chirality pdb=" C1 FUC R 2 " pdb=" O6 NAG R 1 " pdb=" C2 FUC R 2 " pdb=" O5 FUC R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.90e+01 chirality pdb=" C1 FUC P 2 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 2 " pdb=" O5 FUC P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.88e+01 chirality pdb=" C1 FUC Q 2 " pdb=" O6 NAG Q 1 " pdb=" C2 FUC Q 2 " pdb=" O5 FUC Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.79e+01 ... (remaining 5496 not shown) Planarity restraints: 6153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.043 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 331 " -0.043 2.00e-02 2.50e+03 4.45e-02 2.48e+01 pdb=" CG ASN K 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN K 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN K 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG K1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 331 " -0.043 2.00e-02 2.50e+03 4.44e-02 2.47e+01 pdb=" CG ASN F 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN F 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN F 331 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F1305 " -0.054 2.00e-02 2.50e+03 ... (remaining 6150 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 990 2.70 - 3.25: 32359 3.25 - 3.80: 55640 3.80 - 4.35: 74882 4.35 - 4.90: 121794 Nonbonded interactions: 285665 Sorted by model distance: nonbonded pdb=" O SER H 55 " pdb=" OG SER H 56 " model vdw 2.154 3.040 nonbonded pdb=" O SER E 55 " pdb=" OG SER E 56 " model vdw 2.154 3.040 nonbonded pdb=" O SER M 55 " pdb=" OG SER M 56 " model vdw 2.154 3.040 nonbonded pdb=" O ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.221 3.040 nonbonded pdb=" O ASP G 61 " pdb=" OD1 ASP G 61 " model vdw 2.221 3.040 ... (remaining 285660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.960 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: 0.050 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.139 35028 Z= 0.598 Angle : 1.214 11.924 47877 Z= 0.817 Chirality : 0.069 0.945 5499 Planarity : 0.005 0.023 6105 Dihedral : 10.791 88.957 11784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.17 % Allowed : 0.79 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4350 helix: 0.49 (0.19), residues: 657 sheet: 1.05 (0.14), residues: 1299 loop : 0.19 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K1019 TYR 0.044 0.005 TYR D 92 PHE 0.022 0.004 PHE F 898 TRP 0.029 0.005 TRP H 106 HIS 0.004 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01049 / 0.58 (34920) covalent geometry : angle 1.19036 / 0.81 (47610) SS BOND : bond 0.06095 / 4.07 ( 57) SS BOND : angle 3.77839 / 2.72 ( 114) hydrogen bonds : bond 0.16911 / 11.44 ( 1484) hydrogen bonds : angle 8.12863 / 5.76 ( 4065) link_BETA1-6 : bond 0.05753 / 2.88 ( 3) link_BETA1-6 : angle 2.26292 / 1.38 ( 9) link_NAG-ASN : bond 0.04824 / 3.48 ( 48) link_NAG-ASN : angle 3.16314 / 2.07 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 593 time to evaluate : 1.183 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: 0.6804 time to fit residues: 488.8574 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 540 ASN A 755 GLN A1011 GLN D 101 GLN E 117 GLN C 98 ASN F 314 GLN F 564 GLN F 644 GLN F 755 GLN F 804 GLN F 954 GLN F1005 GLN F1010 GLN F1011 GLN G 101 GLN H 117 GLN I 27 GLN J 98 ASN K 314 GLN K 498 GLN K 540 ASN K 606 ASN K 644 GLN K 755 GLN K 954 GLN K1005 GLN K1011 GLN M 117 GLN N 89 GLN O 98 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.201608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.191158 restraints weight = 30273.411| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 0.38 r_work: 0.3993 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35028 Z= 0.137 Angle : 0.614 18.675 47877 Z= 0.316 Chirality : 0.046 0.457 5499 Planarity : 0.004 0.039 6105 Dihedral : 4.484 23.030 4761 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.75 % Allowed : 7.18 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4350 helix: 2.07 (0.21), residues: 666 sheet: 1.14 (0.14), residues: 1269 loop : 0.33 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1107 TYR 0.023 0.002 TYR F1067 PHE 0.013 0.002 PHE A 592 TRP 0.010 0.001 TRP H 115 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (34920) covalent geometry : angle 0.57309 / 0.31 (47610) SS BOND : bond 0.00283 / 0.22 ( 57) SS BOND : angle 0.98074 / 0.70 ( 114) hydrogen bonds : bond 0.05384 / 3.64 ( 1484) hydrogen bonds : angle 6.10466 / 4.34 ( 4065) link_BETA1-6 : bond 0.01399 / 0.70 ( 3) link_BETA1-6 : angle 1.09365 / 0.61 ( 9) link_NAG-ASN : bond 0.00355 / 0.25 ( 48) link_NAG-ASN : angle 3.97198 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 468 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 54 MET cc_start: 0.6590 (mmm) cc_final: 0.6379 (mmt) REVERT: F 586 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7395 (t0) REVERT: F 895 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: G 5 MET cc_start: 0.6520 (tpp) cc_final: 0.6295 (tpp) REVERT: K 895 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: M 46 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6410 (tp30) outliers start: 60 outliers final: 14 residues processed: 504 average time/residue: 0.6438 time to fit residues: 392.0300 Evaluate side-chains 426 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 407 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [284, 69, 227, 109, 88, 408, 63, 25, 289, 290, 419] chunk 284 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 227 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 408 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN A1101 HIS D 101 GLN F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 954 GLN G 101 GLN K 314 GLN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN K 501 ASN K 804 GLN K 872 GLN K 954 GLN K1010 GLN K1011 GLN K1101 HIS N 89 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.200161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189359 restraints weight = 29900.783| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 0.39 r_work: 0.3978 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35028 Z= 0.146 Angle : 0.602 20.567 47877 Z= 0.310 Chirality : 0.046 0.454 5499 Planarity : 0.004 0.041 6105 Dihedral : 4.432 22.756 4761 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.36 % Allowed : 8.29 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4350 helix: 1.98 (0.20), residues: 684 sheet: 1.13 (0.14), residues: 1263 loop : 0.30 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F1107 TYR 0.021 0.002 TYR F1067 PHE 0.021 0.002 PHE A 898 TRP 0.010 0.001 TRP M 36 HIS 0.006 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34920) covalent geometry : angle 0.55956 / 0.30 (47610) SS BOND : bond 0.00388 / 0.28 ( 57) SS BOND : angle 0.87724 / 0.63 ( 114) hydrogen bonds : bond 0.05346 / 3.60 ( 1484) hydrogen bonds : angle 5.86784 / 4.17 ( 4065) link_BETA1-6 : bond 0.00651 / 0.32 ( 3) link_BETA1-6 : angle 1.23490 / 0.72 ( 9) link_NAG-ASN : bond 0.00767 / 0.54 ( 48) link_NAG-ASN : angle 4.04207 / 2.46 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 422 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7552 (t0) REVERT: E 67 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6370 (mmm160) REVERT: B 54 MET cc_start: 0.6805 (mmm) cc_final: 0.6537 (mmt) REVERT: F 48 LEU cc_start: 0.8365 (mt) cc_final: 0.8107 (mp) REVERT: F 586 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7502 (t70) REVERT: F 776 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8743 (tttt) REVERT: F 895 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: H 46 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6392 (tp30) REVERT: K 586 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7456 (t0) REVERT: K 895 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: M 46 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6434 (tp30) REVERT: N 4 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.4338 (tpt) REVERT: N 9 SER cc_start: 0.6793 (t) cc_final: 0.6556 (p) REVERT: O 96 CYS cc_start: 0.6284 (p) cc_final: 0.5963 (p) outliers start: 81 outliers final: 36 residues processed: 468 average time/residue: 0.6655 time to fit residues: 375.6350 Evaluate side-chains 445 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1010 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [339, 94, 30, 120, 19, 139, 99, 248, 221, 281, 335] chunk 339 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 248 optimal weight: 0.0000 chunk 221 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 335 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN A1023 ASN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 954 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 954 GLN K1010 GLN K1113 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.198729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188004 restraints weight = 29822.572| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 0.38 r_work: 0.3966 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 1.11 restraints_weight: 0.2500 r_work: 0.3721 rms_B_bonded: 3.89 restraints_weight: 0.1250 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35028 Z= 0.173 Angle : 0.633 20.130 47877 Z= 0.326 Chirality : 0.047 0.457 5499 Planarity : 0.005 0.063 6105 Dihedral : 4.626 23.635 4761 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.73 % Allowed : 8.61 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 4350 helix: 1.82 (0.20), residues: 684 sheet: 1.07 (0.14), residues: 1263 loop : 0.16 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.023 0.002 TYR G 92 PHE 0.024 0.002 PHE A 898 TRP 0.011 0.002 TRP H 106 HIS 0.008 0.002 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (34920) covalent geometry : angle 0.59378 / 0.32 (47610) SS BOND : bond 0.00554 / 0.38 ( 57) SS BOND : angle 1.01123 / 0.72 ( 114) hydrogen bonds : bond 0.05646 / 3.79 ( 1484) hydrogen bonds : angle 5.88650 / 4.18 ( 4065) link_BETA1-6 : bond 0.00333 / 0.16 ( 3) link_BETA1-6 : angle 1.24852 / 0.72 ( 9) link_NAG-ASN : bond 0.00648 / 0.45 ( 48) link_NAG-ASN : angle 3.96034 / 2.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 410 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7916 (t0) REVERT: E 67 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6499 (mmm160) REVERT: B 54 MET cc_start: 0.7156 (mmm) cc_final: 0.6778 (mmt) REVERT: F 48 LEU cc_start: 0.8512 (mt) cc_final: 0.8190 (mp) REVERT: F 554 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: F 586 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (t70) REVERT: F 703 ASN cc_start: 0.6618 (t0) cc_final: 0.6406 (t160) REVERT: F 895 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: F 1045 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: H 46 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6873 (tp30) REVERT: K 895 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: K 985 ASP cc_start: 0.7889 (m-30) cc_final: 0.7681 (m-30) REVERT: K 1010 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: M 46 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: N 4 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.4758 (tpt) REVERT: N 9 SER cc_start: 0.7076 (t) cc_final: 0.6720 (p) REVERT: O 96 CYS cc_start: 0.6863 (p) cc_final: 0.6556 (p) outliers start: 94 outliers final: 45 residues processed: 455 average time/residue: 0.6541 time to fit residues: 359.7210 Evaluate side-chains 452 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 396 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 554 GLU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain 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 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: [149, 100, 53, 6, 388, 254, 294, 51, 87, 196, 357] chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 357 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 804 GLN A 926 GLN A 935 GLN A 954 GLN D 27 GLN D 101 GLN B 27 GLN B 89 GLN F 501 ASN F 532 ASN F 564 GLN F 613 GLN F 755 GLN F 926 GLN G 27 GLN G 101 GLN I 89 GLN K 30 ASN K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K1010 GLN L 27 GLN N 89 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.185627 restraints weight = 29790.636| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 0.40 r_work: 0.3936 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 35028 Z= 0.262 Angle : 0.737 20.451 47877 Z= 0.384 Chirality : 0.051 0.458 5499 Planarity : 0.005 0.042 6105 Dihedral : 5.027 25.591 4761 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.29 % Allowed : 8.70 % Favored : 88.02 % 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: 0.62 (0.12), residues: 4350 helix: 1.42 (0.20), residues: 684 sheet: 0.93 (0.14), residues: 1299 loop : -0.13 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 905 TYR 0.029 0.003 TYR G 92 PHE 0.033 0.003 PHE A 898 TRP 0.015 0.003 TRP K 152 HIS 0.012 0.002 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (34920) covalent geometry : angle 0.70058 / 0.38 (47610) SS BOND : bond 0.00721 / 0.52 ( 57) SS BOND : angle 1.36168 / 0.96 ( 114) hydrogen bonds : bond 0.06472 / 4.35 ( 1484) hydrogen bonds : angle 6.15720 / 4.37 ( 4065) link_BETA1-6 : bond 0.00413 / 0.21 ( 3) link_BETA1-6 : angle 1.49008 / 0.87 ( 9) link_NAG-ASN : bond 0.00697 / 0.49 ( 48) link_NAG-ASN : angle 4.08798 / 2.51 ( 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 512 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 399 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7497 (t0) REVERT: A 895 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: E 67 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6373 (mmm160) REVERT: F 554 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: F 586 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7541 (t70) REVERT: F 895 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: F 902 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7313 (tpp) REVERT: F 1045 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7927 (ttpt) REVERT: H 46 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: K 202 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5496 (mmtt) REVERT: K 895 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: K 947 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: L 46 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7125 (ptt-90) REVERT: M 46 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6538 (tp30) REVERT: M 70 MET cc_start: 0.6093 (mtt) cc_final: 0.5829 (mtt) REVERT: N 4 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5420 (tpt) REVERT: N 9 SER cc_start: 0.7049 (t) cc_final: 0.6771 (p) outliers start: 113 outliers final: 52 residues processed: 469 average time/residue: 0.6469 time to fit residues: 366.7409 Evaluate side-chains 453 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 386 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 554 GLU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP 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 902 MET 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 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 202 LYS 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 659 SER Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [33, 340, 152, 77, 183, 280, 425, 176, 108, 136, 119] chunk 33 optimal weight: 0.9980 chunk 340 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 425 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN F 955 ASN F1005 GLN G 27 GLN G 101 GLN I 89 GLN K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.198210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.187371 restraints weight = 29767.597| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 0.39 r_work: 0.3956 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35028 Z= 0.154 Angle : 0.618 20.010 47877 Z= 0.317 Chirality : 0.046 0.449 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.666 23.063 4761 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.62 % Allowed : 9.71 % 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: 0.80 (0.12), residues: 4350 helix: 1.88 (0.20), residues: 666 sheet: 0.98 (0.14), residues: 1287 loop : -0.05 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F1107 TYR 0.021 0.002 TYR G 92 PHE 0.022 0.002 PHE A 898 TRP 0.012 0.001 TRP H 106 HIS 0.007 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (34920) covalent geometry : angle 0.57888 / 0.31 (47610) SS BOND : bond 0.00436 / 0.31 ( 57) SS BOND : angle 1.00284 / 0.72 ( 114) hydrogen bonds : bond 0.05372 / 3.61 ( 1484) hydrogen bonds : angle 5.86777 / 4.16 ( 4065) link_BETA1-6 : bond 0.00348 / 0.17 ( 3) link_BETA1-6 : angle 1.42122 / 0.80 ( 9) link_NAG-ASN : bond 0.00648 / 0.45 ( 48) link_NAG-ASN : angle 3.92650 / 2.41 ( 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 491 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 401 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 895 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 46 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: B 54 MET cc_start: 0.7168 (mmm) cc_final: 0.6889 (mmt) REVERT: C 59 TYR cc_start: 0.8363 (m-80) cc_final: 0.8147 (m-80) REVERT: F 48 LEU cc_start: 0.8371 (mt) cc_final: 0.8110 (mp) REVERT: F 586 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7499 (t70) REVERT: F 895 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: F 1045 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7877 (ttpt) REVERT: H 46 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6531 (tp30) REVERT: K 202 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5346 (mmtt) REVERT: K 895 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: M 46 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6493 (tp30) REVERT: M 70 MET cc_start: 0.5986 (mtt) cc_final: 0.5738 (mtt) REVERT: N 4 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5408 (tpt) REVERT: N 9 SER cc_start: 0.7085 (t) cc_final: 0.6814 (p) outliers start: 90 outliers final: 50 residues processed: 455 average time/residue: 0.6495 time to fit residues: 357.5308 Evaluate side-chains 451 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 390 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 34 LEU 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 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER 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: [435, 147, 379, 73, 101, 302, 57, 362, 189, 6, 137] chunk 435 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 362 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 703 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 703 ASN K 755 GLN K 926 GLN K 954 GLN K1010 GLN K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.185977 restraints weight = 29552.572| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.39 r_work: 0.3936 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 35028 Z= 0.271 Angle : 0.754 20.619 47877 Z= 0.393 Chirality : 0.052 0.448 5499 Planarity : 0.005 0.046 6105 Dihedral : 5.136 25.599 4761 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.14 % Allowed : 9.57 % Favored : 87.29 % 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: 0.44 (0.12), residues: 4350 helix: 1.49 (0.20), residues: 666 sheet: 0.78 (0.14), residues: 1302 loop : -0.30 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F1107 TYR 0.031 0.003 TYR A 396 PHE 0.033 0.003 PHE A 898 TRP 0.013 0.002 TRP H 106 HIS 0.011 0.002 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (34920) covalent geometry : angle 0.71791 / 0.39 (47610) SS BOND : bond 0.00746 / 0.53 ( 57) SS BOND : angle 1.43586 / 1.00 ( 114) hydrogen bonds : bond 0.06561 / 4.41 ( 1484) hydrogen bonds : angle 6.21383 / 4.40 ( 4065) link_BETA1-6 : bond 0.00365 / 0.18 ( 3) link_BETA1-6 : angle 1.52698 / 0.88 ( 9) link_NAG-ASN : bond 0.00697 / 0.49 ( 48) link_NAG-ASN : angle 4.07615 / 2.50 ( 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 506 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 398 time to evaluate : 1.209 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: 0.7418 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: A 586 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7526 (t0) REVERT: A 895 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 1045 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7951 (ttpt) REVERT: E 46 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6268 (tp30) REVERT: B 54 MET cc_start: 0.7204 (mmm) cc_final: 0.6861 (mmt) REVERT: F 310 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8402 (ttpp) REVERT: F 586 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7606 (t70) REVERT: F 895 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: F 1045 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7937 (ttpt) REVERT: H 46 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6520 (tp30) REVERT: I 46 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7561 (tm) REVERT: K 202 LYS cc_start: 0.5781 (OUTLIER) cc_final: 0.5363 (mmtt) REVERT: K 858 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8106 (mt) REVERT: K 895 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: K 947 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7714 (ttpt) REVERT: L 46 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7077 (ptt-90) REVERT: M 38 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.5570 (ttm170) REVERT: M 46 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: N 4 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5647 (tpt) REVERT: N 9 SER cc_start: 0.7177 (t) cc_final: 0.6863 (p) REVERT: O 96 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7245 (p) outliers start: 108 outliers final: 58 residues processed: 463 average time/residue: 0.6531 time to fit residues: 365.7086 Evaluate side-chains 471 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 393 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 B residue 52 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 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 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 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 202 LYS 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 547 THR 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 858 LEU 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 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 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: [36, 76, 287, 211, 61, 373, 318, 16, 394, 289, 238] chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 287 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 373 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 394 optimal weight: 0.8980 chunk 289 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1010 GLN L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.199385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187182 restraints weight = 29864.278| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 0.42 r_work: 0.3949 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35028 Z= 0.119 Angle : 0.586 19.902 47877 Z= 0.299 Chirality : 0.045 0.441 5499 Planarity : 0.004 0.037 6105 Dihedral : 4.531 21.579 4761 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.12 % Allowed : 10.94 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 4350 helix: 1.98 (0.20), residues: 666 sheet: 0.91 (0.14), residues: 1296 loop : -0.11 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1107 TYR 0.029 0.001 TYR A 396 PHE 0.016 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/Z covalent geometry : bond 0.00250 / 0.12 (34920) covalent geometry : angle 0.54580 / 0.29 (47610) SS BOND : bond 0.00291 / 0.21 ( 57) SS BOND : angle 0.76859 / 0.56 ( 114) hydrogen bonds : bond 0.04873 / 3.28 ( 1484) hydrogen bonds : angle 5.74487 / 4.07 ( 4065) link_BETA1-6 : bond 0.00402 / 0.20 ( 3) link_BETA1-6 : angle 1.39794 / 0.78 ( 9) link_NAG-ASN : bond 0.00653 / 0.45 ( 48) link_NAG-ASN : angle 3.87286 / 2.38 ( 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 482 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 409 time to evaluate : 1.299 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: 0.7821 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 895 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: E 46 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: B 54 MET cc_start: 0.7133 (mmm) cc_final: 0.6904 (mmt) REVERT: F 48 LEU cc_start: 0.8346 (mt) cc_final: 0.8111 (mp) REVERT: F 586 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7546 (t70) REVERT: F 895 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: H 46 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: I 46 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (tm) REVERT: J 96 CYS cc_start: 0.6506 (p) cc_final: 0.6184 (p) REVERT: K 895 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: M 46 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6427 (tp30) outliers start: 73 outliers final: 40 residues processed: 453 average time/residue: 0.6532 time to fit residues: 357.1471 Evaluate side-chains 448 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 340 GLU 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 619 GLU 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 D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 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 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR 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 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 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 11 LEU 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: [158, 14, 83, 3, 254, 382, 162, 392, 359, 416, 403] chunk 158 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 392 optimal weight: 0.9980 chunk 359 optimal weight: 2.9990 chunk 416 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1010 GLN K1101 HIS 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 = 0.4152 r_free = 0.4152 target = 0.198045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.187557 restraints weight = 29491.979| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 0.37 r_work: 0.3957 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 35028 Z= 0.187 Angle : 0.659 20.229 47877 Z= 0.341 Chirality : 0.048 0.436 5499 Planarity : 0.005 0.038 6105 Dihedral : 4.763 23.878 4761 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.24 % Allowed : 10.79 % Favored : 86.97 % 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: 1.81 (0.20), residues: 666 sheet: 0.93 (0.14), residues: 1266 loop : -0.17 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 905 TYR 0.026 0.002 TYR G 92 PHE 0.027 0.002 PHE A 898 TRP 0.011 0.002 TRP H 106 HIS 0.008 0.002 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (34920) covalent geometry : angle 0.62164 / 0.33 (47610) SS BOND : bond 0.00551 / 0.40 ( 57) SS BOND : angle 1.18456 / 0.80 ( 114) hydrogen bonds : bond 0.05754 / 3.87 ( 1484) hydrogen bonds : angle 5.91469 / 4.19 ( 4065) link_BETA1-6 : bond 0.00322 / 0.16 ( 3) link_BETA1-6 : angle 1.43344 / 0.82 ( 9) link_NAG-ASN : bond 0.00675 / 0.47 ( 48) link_NAG-ASN : angle 3.93938 / 2.42 ( 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 470 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 393 time to evaluate : 1.315 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: symmetry clash REVERT: A 586 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 895 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: E 46 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: B 54 MET cc_start: 0.7228 (mmm) cc_final: 0.6966 (mmt) REVERT: F 48 LEU cc_start: 0.8362 (mt) cc_final: 0.8128 (mp) REVERT: F 586 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7545 (t70) REVERT: F 895 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: F 1045 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7902 (ttpt) REVERT: H 46 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6535 (tp30) REVERT: I 46 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7504 (tm) REVERT: J 96 CYS cc_start: 0.6635 (p) cc_final: 0.6349 (p) REVERT: K 895 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: M 46 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6512 (tp30) outliers start: 77 outliers final: 47 residues processed: 439 average time/residue: 0.6441 time to fit residues: 343.5492 Evaluate side-chains 451 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 394 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 462 LYS 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 D residue 98 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 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 F residue 1045 LYS 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 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain 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 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: [385, 136, 92, 244, 394, 1, 417, 406, 60, 87, 393] chunk 385 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 244 optimal weight: 0.9990 chunk 394 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 417 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1010 GLN L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.199841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.189521 restraints weight = 29712.190| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 0.37 r_work: 0.3976 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35028 Z= 0.122 Angle : 0.582 19.846 47877 Z= 0.297 Chirality : 0.045 0.429 5499 Planarity : 0.004 0.037 6105 Dihedral : 4.441 21.218 4761 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.80 % Allowed : 11.14 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4350 helix: 2.04 (0.20), residues: 663 sheet: 0.98 (0.14), residues: 1296 loop : -0.07 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.017 0.002 TYR K1067 PHE 0.017 0.001 PHE A 898 TRP 0.011 0.001 TRP H 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (34920) covalent geometry : angle 0.54201 / 0.29 (47610) SS BOND : bond 0.00314 / 0.23 ( 57) SS BOND : angle 0.85900 / 0.58 ( 114) hydrogen bonds : bond 0.04836 / 3.26 ( 1484) hydrogen bonds : angle 5.66075 / 4.02 ( 4065) link_BETA1-6 : bond 0.00273 / 0.14 ( 3) link_BETA1-6 : angle 1.35472 / 0.75 ( 9) link_NAG-ASN : bond 0.00660 / 0.46 ( 48) link_NAG-ASN : angle 3.83287 / 2.35 ( 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 467 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 1.544 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: 0.7789 (OUTLIER) cc_final: 0.7514 (t0) REVERT: A 895 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: E 46 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6261 (tp30) REVERT: B 54 MET cc_start: 0.7230 (mmm) cc_final: 0.6922 (mmt) REVERT: F 48 LEU cc_start: 0.8316 (mt) cc_final: 0.8091 (mp) REVERT: F 586 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7538 (t70) REVERT: F 895 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: H 46 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: I 46 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7414 (tm) REVERT: J 96 CYS cc_start: 0.6548 (p) cc_final: 0.6302 (p) REVERT: K 858 LEU cc_start: 0.8233 (mt) cc_final: 0.7962 (mp) REVERT: K 895 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: M 46 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6412 (tp30) outliers start: 62 outliers final: 38 residues processed: 446 average time/residue: 0.6416 time to fit residues: 347.1991 Evaluate side-chains 439 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 392 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 314 GLN 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 705 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 B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 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 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 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU 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: [199, 282, 386, 151, 330, 214, 250, 387, 79, 72, 173] chunk 199 optimal weight: 6.9990 chunk 282 optimal weight: 10.0000 chunk 386 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 330 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 250 optimal weight: 0.0030 chunk 387 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 954 GLN D 27 GLN D 101 GLN B 89 GLN F 501 ASN F 532 ASN F 703 ASN F 755 GLN G 27 GLN G 101 GLN I 89 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1010 GLN K1101 HIS ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.200170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189721 restraints weight = 29705.430| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 0.38 r_work: 0.3981 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35028 Z= 0.117 Angle : 0.578 19.850 47877 Z= 0.294 Chirality : 0.045 0.419 5499 Planarity : 0.004 0.044 6105 Dihedral : 4.331 21.132 4761 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 11.23 % Favored : 87.00 % 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: 0.90 (0.12), residues: 4350 helix: 2.09 (0.20), residues: 666 sheet: 1.03 (0.14), residues: 1296 loop : -0.03 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.034 0.001 TYR K 396 PHE 0.017 0.001 PHE A 898 TRP 0.011 0.001 TRP H 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (34920) covalent geometry : angle 0.53804 / 0.29 (47610) SS BOND : bond 0.00319 / 0.23 ( 57) SS BOND : angle 0.85388 / 0.58 ( 114) hydrogen bonds : bond 0.04717 / 3.18 ( 1484) hydrogen bonds : angle 5.55576 / 3.94 ( 4065) link_BETA1-6 : bond 0.00509 / 0.25 ( 3) link_BETA1-6 : angle 1.28384 / 0.72 ( 9) link_NAG-ASN : bond 0.00665 / 0.46 ( 48) link_NAG-ASN : angle 3.80861 / 2.34 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13410.84 seconds wall clock time: 228 minutes 20.11 seconds (13700.11 seconds total)