Starting phenix.real_space_refine on Fri Mar 6 02:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210.map" model { file = "/net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn3_25210/03_2026/7sn3_25210_neut.cif" } resolution = 3.1 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= 0.056 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 120 5.16 5 C 17474 2.51 5 N 4525 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27447 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7136 Classifications: {'peptide': 925} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 875} Chain breaks: 10 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 7133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7133 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 874} Chain breaks: 10 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 7055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7055 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 48, 'TRANS': 866} Chain breaks: 10 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.62, per 1000 atoms: 0.24 Number of scatterers: 27447 At special positions: 0 Unit cell: (147.675, 150.15, 186.45, 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 120 16.00 O 5328 8.00 N 4525 7.00 C 17474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1074 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG A1315 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG B1315 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C1074 " " NAG C1313 " - " ASN C1098 " " NAG C1314 " - " ASN C1134 " " NAG C1315 " - " ASN C 165 " " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN B 343 " " NAG K 1 " - " ASN C 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 55 sheets defined 23.2% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.567A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.507A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) 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: 3.723A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.723A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.746A 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: 4.319A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.259A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.907A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.946A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.535A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.502A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.652A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.789A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.613A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.702A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.428A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.970A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.880A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.858A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.693A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.766A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.589A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.571A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.089A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.511A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.340A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.806A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.759A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.468A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.529A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.750A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.750A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.507A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.663A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.863A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.781A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.781A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.610A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.173A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.108A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.773A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.141A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.725A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.974A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 356 removed outlier: 4.675A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.911A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.757A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.757A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.593A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.076A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.756A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.774A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.588A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 374 through 378 Processing sheet with id=AD6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD7, first strand: chain 'C' and resid 399 through 400 removed outlier: 3.940A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.989A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.730A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.730A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.575A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.847A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.382A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 39 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR D 58 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.300A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.618A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 51 removed outlier: 6.622A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 96 " --> pdb=" O PHE F 100F" (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE F 100F" --> pdb=" O LEU F 96 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 45 through 51 removed outlier: 6.622A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.765A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.917A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.404A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.404A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.250A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.523A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) 1129 hydrogen bonds defined for protein. 3054 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: 6.91 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8405 1.34 - 1.47: 7716 1.47 - 1.60: 11784 1.60 - 1.74: 5 1.74 - 1.87: 146 Bond restraints: 28056 Sorted by residual: bond pdb=" C ALA C 411 " pdb=" N PRO C 412 " ideal model delta sigma weight residual 1.331 1.391 -0.060 7.90e-03 1.60e+04 5.74e+01 bond pdb=" CD2 TYR L 32 " pdb=" CE2 TYR L 32 " ideal model delta sigma weight residual 1.382 1.228 0.154 3.00e-02 1.11e+03 2.64e+01 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.666 0.142 3.30e-02 9.18e+02 1.85e+01 bond pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 1.808 1.680 0.128 3.30e-02 9.18e+02 1.49e+01 bond pdb=" CA ASP D 100 " pdb=" CB ASP D 100 " ideal model delta sigma weight residual 1.534 1.619 -0.084 2.47e-02 1.64e+03 1.16e+01 ... (remaining 28051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 37435 3.28 - 6.56: 707 6.56 - 9.83: 56 9.83 - 13.11: 12 13.11 - 16.39: 4 Bond angle restraints: 38214 Sorted by residual: angle pdb=" N ASP D 100 " pdb=" CA ASP D 100 " pdb=" CB ASP D 100 " ideal model delta sigma weight residual 111.00 127.39 -16.39 1.81e+00 3.05e-01 8.20e+01 angle pdb=" CB TYR L 32 " pdb=" CG TYR L 32 " pdb=" CD2 TYR L 32 " ideal model delta sigma weight residual 120.80 109.27 11.53 1.50e+00 4.44e-01 5.91e+01 angle pdb=" N TYR L 32 " pdb=" CA TYR L 32 " pdb=" C TYR L 32 " ideal model delta sigma weight residual 107.80 120.39 -12.59 1.73e+00 3.34e-01 5.29e+01 angle pdb=" CG ARG E 91 " pdb=" CD ARG E 91 " pdb=" NE ARG E 91 " ideal model delta sigma weight residual 112.00 97.16 14.84 2.20e+00 2.07e-01 4.55e+01 angle pdb=" C PHE A 374 " pdb=" N SER A 375 " pdb=" CA SER A 375 " ideal model delta sigma weight residual 121.54 134.29 -12.75 1.91e+00 2.74e-01 4.45e+01 ... (remaining 38209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 16170 22.61 - 45.22: 944 45.22 - 67.84: 146 67.84 - 90.45: 41 90.45 - 113.06: 12 Dihedral angle restraints: 17313 sinusoidal: 7291 harmonic: 10022 Sorted by residual: dihedral pdb=" CA SER A 373 " pdb=" C SER A 373 " pdb=" N PHE A 374 " pdb=" CA PHE A 374 " ideal model delta harmonic sigma weight residual -180.00 -108.20 -71.80 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA TRP L 94 " pdb=" C TRP L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 -110.26 -69.74 0 5.00e+00 4.00e-02 1.95e+02 dihedral pdb=" CA TYR C 423 " pdb=" C TYR C 423 " pdb=" N LYS C 424 " pdb=" CA LYS C 424 " ideal model delta harmonic sigma weight residual 180.00 118.09 61.91 0 5.00e+00 4.00e-02 1.53e+02 ... (remaining 17310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 4507 0.261 - 0.522: 19 0.522 - 0.783: 3 0.783 - 1.044: 0 1.044 - 1.305: 1 Chirality restraints: 4530 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.81e+01 chirality pdb=" CB THR L 31 " pdb=" CA THR L 31 " pdb=" OG1 THR L 31 " pdb=" CG2 THR L 31 " both_signs ideal model delta sigma weight residual False 2.55 1.25 1.31 2.00e-01 2.50e+01 4.26e+01 ... (remaining 4527 not shown) Planarity restraints: 4889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 91 " -0.914 9.50e-02 1.11e+02 4.10e-01 1.03e+02 pdb=" NE ARG G 91 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG G 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 91 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " 0.044 2.00e-02 2.50e+03 5.78e-02 6.69e+01 pdb=" CG TYR L 32 " -0.136 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 100D" 0.667 9.50e-02 1.11e+02 2.99e-01 5.69e+01 pdb=" NE ARG D 100D" -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG D 100D" 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG D 100D" -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 100D" 0.011 2.00e-02 2.50e+03 ... (remaining 4886 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 174 2.52 - 3.11: 20888 3.11 - 3.71: 40279 3.71 - 4.30: 59746 4.30 - 4.90: 100680 Nonbonded interactions: 221767 Sorted by model distance: nonbonded pdb=" O ALA B 372 " pdb=" NH2 ARG F 100D" model vdw 1.922 3.120 nonbonded pdb=" O ALA C 372 " pdb=" NH2 ARG H 100D" model vdw 1.932 3.120 nonbonded pdb=" O ALA A 372 " pdb=" NH1 ARG D 100D" model vdw 1.942 3.120 nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.012 3.040 nonbonded pdb=" OG SER G 63 " pdb=" OG1 THR G 74 " model vdw 2.056 3.040 ... (remaining 221762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 437 or resid 509 through 1315)) selection = (chain 'B' and (resid 27 through 437 or resid 509 through 1315)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 5.560 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.180 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.009 0.154 28145 Z= 0.412 Angle : 1.145 16.390 38444 Z= 0.627 Chirality : 0.070 1.305 4530 Planarity : 0.012 0.410 4841 Dihedral : 14.894 113.062 10755 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 0.36 % Favored : 99.35 % Rotamer: Outliers : 0.10 % Allowed : 0.72 % Favored : 99.18 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 1.73 % Twisted General : 0.52 % 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: -0.84 (0.13), residues: 3373 helix: 0.67 (0.18), residues: 647 sheet: -0.08 (0.16), residues: 901 loop : -1.27 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 100D TYR 0.136 0.003 TYR L 32 PHE 0.048 0.003 PHE C 906 TRP 0.113 0.003 TRP F 36 HIS 0.012 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00941 (28056) covalent geometry : angle 1.10715 (38214) SS BOND : bond 0.01125 ( 34) SS BOND : angle 3.68682 ( 68) hydrogen bonds : bond 0.12229 ( 1096) hydrogen bonds : angle 8.44004 ( 3054) Misc. bond : bond 0.00202 ( 1) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 1.63763 ( 18) link_NAG-ASN : bond 0.00773 ( 48) link_NAG-ASN : angle 4.21475 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.7801 (mmm) cc_final: 0.7537 (mmt) REVERT: B 1050 MET cc_start: 0.8289 (ptm) cc_final: 0.8018 (ptm) REVERT: H 82 MET cc_start: 0.5004 (mmt) cc_final: 0.4346 (mmt) outliers start: 3 outliers final: 2 residues processed: 201 average time/residue: 0.1511 time to fit residues: 51.7247 Evaluate side-chains 138 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain C residue 657 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 613 GLN A 992 GLN B 613 GLN B 804 GLN C 207 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN H 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.162438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.113944 restraints weight = 45962.219| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.21 r_work: 0.3375 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28145 Z= 0.157 Angle : 0.708 11.865 38444 Z= 0.363 Chirality : 0.049 0.371 4530 Planarity : 0.005 0.080 4841 Dihedral : 8.762 74.536 4830 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.44 % Favored : 96.21 % Rotamer: Outliers : 0.68 % Allowed : 7.09 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.09 % 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: -0.13 (0.14), residues: 3373 helix: 2.07 (0.20), residues: 651 sheet: -0.11 (0.16), residues: 901 loop : -0.87 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.020 0.002 TYR C 265 PHE 0.020 0.002 PHE A 106 TRP 0.036 0.002 TRP F 36 HIS 0.010 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00348 (28056) covalent geometry : angle 0.67154 (38214) SS BOND : bond 0.00446 ( 34) SS BOND : angle 1.39453 ( 68) hydrogen bonds : bond 0.04376 ( 1096) hydrogen bonds : angle 6.68316 ( 3054) Misc. bond : bond 0.00094 ( 1) link_BETA1-4 : bond 0.00701 ( 6) link_BETA1-4 : angle 2.36468 ( 18) link_NAG-ASN : bond 0.00495 ( 48) link_NAG-ASN : angle 3.55061 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 SER cc_start: 0.9122 (p) cc_final: 0.8906 (m) REVERT: C 380 TYR cc_start: 0.6460 (m-10) cc_final: 0.6045 (m-10) REVERT: D 58 TYR cc_start: 0.5701 (m-80) cc_final: 0.5476 (m-80) REVERT: D 79 TYR cc_start: 0.4834 (m-10) cc_final: 0.4558 (m-80) REVERT: H 82 MET cc_start: 0.3908 (mmt) cc_final: 0.3606 (mmt) REVERT: H 103 TRP cc_start: 0.5100 (m100) cc_final: 0.4875 (m100) outliers start: 20 outliers final: 11 residues processed: 194 average time/residue: 0.1402 time to fit residues: 47.5659 Evaluate side-chains 153 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 120 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 286 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 580 GLN B 901 GLN C 207 HIS C 901 GLN C1002 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.169896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119565 restraints weight = 48673.096| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.80 r_work: 0.3385 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28145 Z= 0.152 Angle : 0.637 10.926 38444 Z= 0.325 Chirality : 0.047 0.331 4530 Planarity : 0.004 0.059 4841 Dihedral : 7.346 51.810 4830 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.89 % Rotamer: Outliers : 1.50 % Allowed : 9.34 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.00 (0.14), residues: 3373 helix: 2.15 (0.20), residues: 649 sheet: 0.01 (0.16), residues: 878 loop : -0.78 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.025 0.001 TYR B 369 PHE 0.015 0.002 PHE C1089 TRP 0.044 0.002 TRP F 36 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00347 (28056) covalent geometry : angle 0.60344 (38214) SS BOND : bond 0.00297 ( 34) SS BOND : angle 1.39617 ( 68) hydrogen bonds : bond 0.03931 ( 1096) hydrogen bonds : angle 6.22629 ( 3054) Misc. bond : bond 0.00036 ( 1) link_BETA1-4 : bond 0.00478 ( 6) link_BETA1-4 : angle 2.30757 ( 18) link_NAG-ASN : bond 0.00495 ( 48) link_NAG-ASN : angle 3.15734 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.6107 (m-40) cc_final: 0.5250 (t0) REVERT: C 568 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: C 574 ASP cc_start: 0.8090 (t0) cc_final: 0.7459 (m-30) REVERT: D 58 TYR cc_start: 0.5891 (m-80) cc_final: 0.5497 (m-80) REVERT: F 34 MET cc_start: 0.5194 (mmp) cc_final: 0.4467 (mmm) REVERT: F 39 GLN cc_start: 0.5927 (tt0) cc_final: 0.5042 (mm110) REVERT: G 44 PRO cc_start: 0.3423 (Cg_exo) cc_final: 0.3097 (Cg_endo) REVERT: H 45 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.5024 (mp) REVERT: H 103 TRP cc_start: 0.5295 (m100) cc_final: 0.4978 (m100) REVERT: L 2 ILE cc_start: 0.5606 (mt) cc_final: 0.5249 (tp) outliers start: 44 outliers final: 16 residues processed: 195 average time/residue: 0.1415 time to fit residues: 48.1343 Evaluate side-chains 152 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 81 optimal weight: 0.0770 chunk 225 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.170097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116310 restraints weight = 48345.547| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.32 r_work: 0.3362 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28145 Z= 0.136 Angle : 0.604 10.726 38444 Z= 0.308 Chirality : 0.046 0.333 4530 Planarity : 0.004 0.082 4841 Dihedral : 6.578 50.608 4828 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.38 % Favored : 96.38 % Rotamer: Outliers : 1.57 % Allowed : 10.50 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.11 (0.14), residues: 3373 helix: 2.28 (0.20), residues: 647 sheet: 0.09 (0.16), residues: 868 loop : -0.73 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.019 0.001 TYR C 265 PHE 0.015 0.001 PHE C1089 TRP 0.050 0.002 TRP F 36 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (28056) covalent geometry : angle 0.57260 (38214) SS BOND : bond 0.00271 ( 34) SS BOND : angle 1.53673 ( 68) hydrogen bonds : bond 0.03678 ( 1096) hydrogen bonds : angle 5.97367 ( 3054) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 2.22945 ( 18) link_NAG-ASN : bond 0.00469 ( 48) link_NAG-ASN : angle 2.91826 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.6185 (m-40) cc_final: 0.5193 (t0) REVERT: C 63 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7595 (p) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5311 (t80) REVERT: C 241 LEU cc_start: 0.7583 (mp) cc_final: 0.6708 (pp) REVERT: C 436 TRP cc_start: 0.5645 (p90) cc_final: 0.5312 (p90) REVERT: C 568 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: D 58 TYR cc_start: 0.5908 (m-80) cc_final: 0.5502 (m-80) REVERT: F 39 GLN cc_start: 0.5981 (tt0) cc_final: 0.5167 (mm-40) REVERT: G 44 PRO cc_start: 0.3381 (Cg_exo) cc_final: 0.3055 (Cg_endo) REVERT: H 103 TRP cc_start: 0.5362 (m100) cc_final: 0.4953 (m100) REVERT: L 2 ILE cc_start: 0.5671 (mt) cc_final: 0.5303 (tp) REVERT: L 75 ILE cc_start: -0.0703 (OUTLIER) cc_final: -0.0944 (mm) outliers start: 46 outliers final: 26 residues processed: 189 average time/residue: 0.1424 time to fit residues: 46.6343 Evaluate side-chains 172 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 290 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 214 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 279 optimal weight: 30.0000 chunk 282 optimal weight: 10.0000 chunk 81 optimal weight: 0.0070 chunk 250 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.170041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115954 restraints weight = 48464.908| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.33 r_work: 0.3371 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28145 Z= 0.123 Angle : 0.580 11.003 38444 Z= 0.296 Chirality : 0.046 0.320 4530 Planarity : 0.004 0.083 4841 Dihedral : 6.175 50.695 4828 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 1.81 % Allowed : 11.01 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.22 (0.14), residues: 3373 helix: 2.39 (0.20), residues: 647 sheet: 0.16 (0.16), residues: 887 loop : -0.68 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.018 0.001 TYR C 265 PHE 0.025 0.001 PHE B 643 TRP 0.043 0.002 TRP F 100C HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00276 (28056) covalent geometry : angle 0.55160 (38214) SS BOND : bond 0.00393 ( 34) SS BOND : angle 1.56716 ( 68) hydrogen bonds : bond 0.03538 ( 1096) hydrogen bonds : angle 5.82696 ( 3054) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00458 ( 6) link_BETA1-4 : angle 2.10561 ( 18) link_NAG-ASN : bond 0.00544 ( 48) link_NAG-ASN : angle 2.73668 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.5892 (p0) REVERT: A 342 PHE cc_start: 0.6602 (m-80) cc_final: 0.6342 (m-80) REVERT: B 121 ASN cc_start: 0.6078 (m-40) cc_final: 0.5154 (t0) REVERT: C 63 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7642 (p) REVERT: C 133 PHE cc_start: 0.6075 (m-80) cc_final: 0.4853 (t80) REVERT: C 436 TRP cc_start: 0.5601 (p90) cc_final: 0.5307 (p90) REVERT: C 568 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: C 574 ASP cc_start: 0.8062 (t0) cc_final: 0.7455 (m-30) REVERT: D 58 TYR cc_start: 0.5922 (m-80) cc_final: 0.5541 (m-80) REVERT: F 39 GLN cc_start: 0.6129 (tt0) cc_final: 0.5296 (mm-40) REVERT: G 35 TRP cc_start: 0.4994 (m100) cc_final: 0.4650 (m100) REVERT: G 44 PRO cc_start: 0.3337 (Cg_exo) cc_final: 0.3023 (Cg_endo) REVERT: H 45 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5037 (mp) REVERT: H 103 TRP cc_start: 0.5458 (m100) cc_final: 0.4973 (m100) REVERT: L 2 ILE cc_start: 0.5739 (mt) cc_final: 0.5400 (tp) outliers start: 53 outliers final: 28 residues processed: 195 average time/residue: 0.1369 time to fit residues: 47.0935 Evaluate side-chains 177 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 4 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 156 optimal weight: 0.0050 chunk 101 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 66 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.169990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115624 restraints weight = 48462.866| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.37 r_work: 0.3401 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28145 Z= 0.112 Angle : 0.566 10.236 38444 Z= 0.288 Chirality : 0.045 0.317 4530 Planarity : 0.004 0.074 4841 Dihedral : 5.865 51.049 4828 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Rotamer: Outliers : 1.91 % Allowed : 11.25 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.37 (0.14), residues: 3373 helix: 2.50 (0.20), residues: 647 sheet: 0.28 (0.16), residues: 893 loop : -0.59 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.027 0.001 TYR B 369 PHE 0.022 0.001 PHE B 643 TRP 0.059 0.002 TRP H 100C HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00247 (28056) covalent geometry : angle 0.53940 (38214) SS BOND : bond 0.00280 ( 34) SS BOND : angle 1.29962 ( 68) hydrogen bonds : bond 0.03419 ( 1096) hydrogen bonds : angle 5.68617 ( 3054) Misc. bond : bond 0.00003 ( 1) link_BETA1-4 : bond 0.00437 ( 6) link_BETA1-4 : angle 1.98485 ( 18) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 2.63749 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.5946 (p0) REVERT: A 342 PHE cc_start: 0.6657 (m-80) cc_final: 0.6369 (m-80) REVERT: B 121 ASN cc_start: 0.6009 (m-40) cc_final: 0.5154 (t0) REVERT: B 200 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5998 (p90) REVERT: C 63 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7639 (p) REVERT: C 133 PHE cc_start: 0.6028 (m-80) cc_final: 0.4849 (t80) REVERT: C 436 TRP cc_start: 0.5607 (p90) cc_final: 0.5272 (p90) REVERT: C 568 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: C 574 ASP cc_start: 0.8057 (t0) cc_final: 0.7532 (m-30) REVERT: D 36 TRP cc_start: 0.3651 (m100) cc_final: 0.3279 (m100) REVERT: D 58 TYR cc_start: 0.5871 (m-80) cc_final: 0.5508 (m-80) REVERT: F 34 MET cc_start: 0.5131 (mmp) cc_final: 0.4152 (mmm) REVERT: F 39 GLN cc_start: 0.6062 (tt0) cc_final: 0.5370 (mm110) REVERT: F 82 MET cc_start: 0.5188 (mmt) cc_final: 0.4073 (mpp) REVERT: G 35 TRP cc_start: 0.5144 (m100) cc_final: 0.4735 (m100) REVERT: G 44 PRO cc_start: 0.3443 (Cg_exo) cc_final: 0.3114 (Cg_endo) REVERT: H 45 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.5019 (mp) REVERT: H 103 TRP cc_start: 0.5463 (m100) cc_final: 0.4854 (m100) REVERT: L 2 ILE cc_start: 0.5763 (mt) cc_final: 0.5420 (tp) outliers start: 56 outliers final: 31 residues processed: 204 average time/residue: 0.1419 time to fit residues: 50.3626 Evaluate side-chains 187 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 293 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 153 optimal weight: 0.0470 chunk 202 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 237 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 66 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.161386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112600 restraints weight = 45138.523| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.24 r_work: 0.3309 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28145 Z= 0.106 Angle : 0.550 9.381 38444 Z= 0.280 Chirality : 0.045 0.312 4530 Planarity : 0.004 0.066 4841 Dihedral : 5.594 51.355 4828 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.44 % Favored : 96.35 % Rotamer: Outliers : 1.67 % Allowed : 11.96 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.47 (0.14), residues: 3373 helix: 2.56 (0.20), residues: 648 sheet: 0.39 (0.17), residues: 881 loop : -0.54 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.019 0.001 TYR G 49 PHE 0.020 0.001 PHE B 168 TRP 0.051 0.001 TRP F 100C HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00234 (28056) covalent geometry : angle 0.52455 (38214) SS BOND : bond 0.00268 ( 34) SS BOND : angle 1.04089 ( 68) hydrogen bonds : bond 0.03317 ( 1096) hydrogen bonds : angle 5.52239 ( 3054) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 1.85077 ( 18) link_NAG-ASN : bond 0.00655 ( 48) link_NAG-ASN : angle 2.60396 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6574 (OUTLIER) cc_final: 0.6014 (p0) REVERT: A 342 PHE cc_start: 0.6821 (m-80) cc_final: 0.6502 (m-80) REVERT: B 121 ASN cc_start: 0.5930 (m-40) cc_final: 0.5089 (t0) REVERT: B 200 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.6046 (p90) REVERT: C 133 PHE cc_start: 0.6021 (m-80) cc_final: 0.4902 (t80) REVERT: C 436 TRP cc_start: 0.5624 (p90) cc_final: 0.5356 (p90) REVERT: C 568 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: D 36 TRP cc_start: 0.3724 (m100) cc_final: 0.3463 (m100) REVERT: D 58 TYR cc_start: 0.6034 (m-80) cc_final: 0.5674 (m-80) REVERT: F 34 MET cc_start: 0.5130 (mmp) cc_final: 0.4113 (mmm) REVERT: F 38 ARG cc_start: 0.4859 (ptp90) cc_final: 0.3050 (ttp80) REVERT: F 39 GLN cc_start: 0.6094 (tt0) cc_final: 0.5338 (mm110) REVERT: G 35 TRP cc_start: 0.5135 (m100) cc_final: 0.4926 (m100) REVERT: G 44 PRO cc_start: 0.3163 (Cg_exo) cc_final: 0.2827 (Cg_endo) REVERT: H 103 TRP cc_start: 0.5468 (m100) cc_final: 0.5248 (m100) REVERT: L 2 ILE cc_start: 0.5808 (mt) cc_final: 0.5487 (tp) outliers start: 49 outliers final: 34 residues processed: 201 average time/residue: 0.1406 time to fit residues: 49.0344 Evaluate side-chains 191 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 190 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 335 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B 388 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.164547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3639 r_free = 0.3639 target = 0.112321 restraints weight = 48490.415| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.81 r_work: 0.3271 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 28145 Z= 0.426 Angle : 0.794 10.772 38444 Z= 0.404 Chirality : 0.055 0.411 4530 Planarity : 0.005 0.072 4841 Dihedral : 6.546 50.545 4828 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 1.70 % Allowed : 12.54 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: -0.23 (0.14), residues: 3373 helix: 1.63 (0.20), residues: 642 sheet: -0.09 (0.16), residues: 884 loop : -0.82 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.039 0.003 TYR B 369 PHE 0.031 0.003 PHE B1089 TRP 0.050 0.003 TRP F 100C HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01020 (28056) covalent geometry : angle 0.76534 (38214) SS BOND : bond 0.00932 ( 34) SS BOND : angle 1.65654 ( 68) hydrogen bonds : bond 0.04706 ( 1096) hydrogen bonds : angle 6.31291 ( 3054) Misc. bond : bond 0.00094 ( 1) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 2.15975 ( 18) link_NAG-ASN : bond 0.00605 ( 48) link_NAG-ASN : angle 3.33323 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.5931 (p0) REVERT: A 342 PHE cc_start: 0.6704 (m-80) cc_final: 0.6413 (m-80) REVERT: B 121 ASN cc_start: 0.6586 (m-40) cc_final: 0.5631 (t0) REVERT: B 983 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7671 (mtp180) REVERT: C 574 ASP cc_start: 0.8118 (t0) cc_final: 0.7833 (m-30) REVERT: C 902 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7885 (tpt) REVERT: D 36 TRP cc_start: 0.3649 (m100) cc_final: 0.3343 (m100) REVERT: D 58 TYR cc_start: 0.5912 (m-80) cc_final: 0.5579 (m-80) REVERT: F 38 ARG cc_start: 0.4864 (ptp90) cc_final: 0.2974 (ttp80) REVERT: H 45 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4639 (mp) REVERT: L 2 ILE cc_start: 0.5961 (mt) cc_final: 0.5656 (tp) outliers start: 50 outliers final: 34 residues processed: 187 average time/residue: 0.1408 time to fit residues: 45.3662 Evaluate side-chains 174 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 254 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN C 334 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.168449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114726 restraints weight = 48309.015| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.46 r_work: 0.3358 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28145 Z= 0.124 Angle : 0.600 9.806 38444 Z= 0.307 Chirality : 0.046 0.306 4530 Planarity : 0.004 0.061 4841 Dihedral : 5.862 48.720 4828 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 1.33 % Allowed : 13.33 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.03 (0.14), residues: 3373 helix: 2.11 (0.20), residues: 642 sheet: -0.03 (0.17), residues: 874 loop : -0.69 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.018 0.001 TYR C 265 PHE 0.019 0.001 PHE B 168 TRP 0.062 0.002 TRP H 100C HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00275 (28056) covalent geometry : angle 0.57263 (38214) SS BOND : bond 0.00304 ( 34) SS BOND : angle 1.06362 ( 68) hydrogen bonds : bond 0.03566 ( 1096) hydrogen bonds : angle 5.81089 ( 3054) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.00362 ( 6) link_BETA1-4 : angle 1.80733 ( 18) link_NAG-ASN : bond 0.00524 ( 48) link_NAG-ASN : angle 2.85953 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6640 (OUTLIER) cc_final: 0.6054 (p0) REVERT: A 342 PHE cc_start: 0.6766 (m-80) cc_final: 0.6487 (m-80) REVERT: B 121 ASN cc_start: 0.6244 (m-40) cc_final: 0.5350 (t0) REVERT: B 983 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7636 (mtp180) REVERT: C 133 PHE cc_start: 0.6115 (m-80) cc_final: 0.4874 (t80) REVERT: C 568 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: C 574 ASP cc_start: 0.8102 (t0) cc_final: 0.7637 (m-30) REVERT: C 917 TYR cc_start: 0.8036 (m-80) cc_final: 0.7805 (m-80) REVERT: D 32 TYR cc_start: 0.5859 (m-10) cc_final: 0.5132 (m-80) REVERT: D 36 TRP cc_start: 0.3584 (m100) cc_final: 0.3313 (m100) REVERT: D 58 TYR cc_start: 0.5889 (m-80) cc_final: 0.5567 (m-80) REVERT: F 38 ARG cc_start: 0.5072 (ptp90) cc_final: 0.3267 (ttp80) REVERT: F 39 GLN cc_start: 0.5866 (tt0) cc_final: 0.5024 (mm110) REVERT: G 35 TRP cc_start: 0.5116 (m100) cc_final: 0.4784 (m100) REVERT: H 45 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4588 (mp) REVERT: L 2 ILE cc_start: 0.5972 (mt) cc_final: 0.5669 (tp) outliers start: 39 outliers final: 29 residues processed: 182 average time/residue: 0.1447 time to fit residues: 45.3000 Evaluate side-chains 178 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 96 optimal weight: 0.0970 chunk 85 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 245 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 339 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 overall best weight: 2.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.155623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101702 restraints weight = 45090.534| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.62 r_work: 0.3165 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28145 Z= 0.226 Angle : 0.636 10.217 38444 Z= 0.323 Chirality : 0.048 0.325 4530 Planarity : 0.004 0.065 4841 Dihedral : 5.906 48.801 4828 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 1.19 % Allowed : 13.57 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: -0.06 (0.14), residues: 3373 helix: 2.06 (0.20), residues: 638 sheet: -0.06 (0.17), residues: 887 loop : -0.77 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 100D TYR 0.025 0.002 TYR C 265 PHE 0.022 0.002 PHE C 168 TRP 0.086 0.002 TRP H 100C HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00537 (28056) covalent geometry : angle 0.60828 (38214) SS BOND : bond 0.00383 ( 34) SS BOND : angle 1.14188 ( 68) hydrogen bonds : bond 0.03816 ( 1096) hydrogen bonds : angle 5.88006 ( 3054) Misc. bond : bond 0.00066 ( 1) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 1.82421 ( 18) link_NAG-ASN : bond 0.00499 ( 48) link_NAG-ASN : angle 2.93889 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6148 (p0) REVERT: A 342 PHE cc_start: 0.6922 (m-80) cc_final: 0.6678 (m-80) REVERT: B 121 ASN cc_start: 0.6400 (m-40) cc_final: 0.5541 (t0) REVERT: B 983 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7706 (mtp180) REVERT: C 574 ASP cc_start: 0.8186 (t0) cc_final: 0.7804 (m-30) REVERT: D 32 TYR cc_start: 0.5801 (m-10) cc_final: 0.5168 (m-80) REVERT: D 36 TRP cc_start: 0.3560 (m100) cc_final: 0.3278 (m100) REVERT: D 58 TYR cc_start: 0.5961 (m-80) cc_final: 0.5653 (m-80) REVERT: F 38 ARG cc_start: 0.5132 (ptp90) cc_final: 0.3189 (ttp80) REVERT: H 45 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4552 (mp) REVERT: L 2 ILE cc_start: 0.6145 (mt) cc_final: 0.5827 (tp) outliers start: 35 outliers final: 31 residues processed: 170 average time/residue: 0.1492 time to fit residues: 43.2758 Evaluate side-chains 176 residues out of total 3003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 254 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.157227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104657 restraints weight = 44950.097| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.77 r_work: 0.3185 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28145 Z= 0.121 Angle : 0.587 10.069 38444 Z= 0.300 Chirality : 0.045 0.293 4530 Planarity : 0.004 0.060 4841 Dihedral : 5.655 50.307 4828 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 1.19 % Allowed : 13.67 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: 0.12 (0.14), residues: 3373 helix: 2.26 (0.20), residues: 643 sheet: 0.02 (0.17), residues: 891 loop : -0.67 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.016 0.001 TYR C 265 PHE 0.018 0.001 PHE B 168 TRP 0.089 0.002 TRP H 100C HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00271 (28056) covalent geometry : angle 0.56121 (38214) SS BOND : bond 0.00268 ( 34) SS BOND : angle 1.04902 ( 68) hydrogen bonds : bond 0.03449 ( 1096) hydrogen bonds : angle 5.67389 ( 3054) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.68652 ( 18) link_NAG-ASN : bond 0.00530 ( 48) link_NAG-ASN : angle 2.71648 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9448.43 seconds wall clock time: 161 minutes 27.22 seconds (9687.22 seconds total)