Starting phenix.real_space_refine on Mon Jul 6 00:59:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rkv_24504/07_2026/7rkv_24504.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 135 5.16 5 C 19952 2.51 5 N 5287 2.21 5 O 5983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31357 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7026 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1010 Unresolved non-hydrogen dihedrals: 620 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 18, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 10, 'ARG:plan': 10, 'TYR:plan': 10, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "D" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.93, per 1000 atoms: 0.25 Number of scatterers: 31357 At special positions: 0 Unit cell: (133.826, 145.992, 212.905, 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 135 16.00 O 5983 8.00 N 5287 7.00 C 19952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 198 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG A1314 " - " ASN A 717 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 717 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 717 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7950 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 84 sheets defined 21.3% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.370A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.686A 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 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.098A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.660A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 342' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.153A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.687A 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 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.099A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.764A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A 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 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.099A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.762A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.704A pdb=" N LEU D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 126 through 131 Processing helix chain 'H' and resid 186 through 192 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 199 through 205 removed outlier: 3.705A pdb=" N LEU E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'G' and resid 199 through 205 removed outlier: 3.704A pdb=" N LEU G 203 " --> pdb=" O SER G 200 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 186 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.252A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.385A 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: 3.533A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.156A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.989A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.513A 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 removed outlier: 5.233A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.378A pdb=" N PHE A 377 " --> pdb=" O TYR E 103 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR E 103 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.957A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 719 through 728 removed outlier: 7.027A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.365A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1103 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.681A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.156A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.990A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.234A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.335A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.828A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.027A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.364A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.681A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 11.212A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.989A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.602A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.028A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.364A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.265A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.614A pdb=" N GLY D 109 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 134 through 136 removed outlier: 5.288A pdb=" N GLY D 153 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 196 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 155 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 194 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 157 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU D 192 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 134 through 136 removed outlier: 5.288A pdb=" N GLY D 153 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 196 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 155 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 194 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 157 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU D 192 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR D 208 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.543A pdb=" N ALA H 12 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE H 33 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS H 49 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.543A pdb=" N ALA H 12 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 119 through 123 removed outlier: 5.216A pdb=" N THR H 136 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 185 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL H 138 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU H 183 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 140 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER H 181 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER H 142 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA H 179 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 119 through 123 removed outlier: 5.216A pdb=" N THR H 136 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 185 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL H 138 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU H 183 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 140 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER H 181 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER H 142 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA H 179 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.658A pdb=" N TRP H 153 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.874A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.587A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG9, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY E 153 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL E 196 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 155 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER E 194 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 157 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 192 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY E 153 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL E 196 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 155 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER E 194 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 157 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 192 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR E 208 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AH4, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.566A pdb=" N ALA F 12 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE F 33 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.566A pdb=" N ALA F 12 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.218A pdb=" N THR F 136 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 185 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL F 138 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU F 183 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 140 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER F 181 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 142 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA F 179 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.218A pdb=" N THR F 136 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 185 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL F 138 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU F 183 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 140 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER F 181 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 142 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA F 179 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 158 through 160 removed outlier: 4.661A pdb=" N TRP F 153 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.874A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.600A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AI3, first strand: chain 'G' and resid 101 through 104 removed outlier: 3.565A pdb=" N GLY G 109 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY G 153 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL G 196 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 155 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER G 194 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS G 157 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU G 192 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY G 153 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL G 196 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 155 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER G 194 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS G 157 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU G 192 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR G 208 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI8, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.550A pdb=" N ALA L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.550A pdb=" N ALA L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.217A pdb=" N THR L 136 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU L 185 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL L 138 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU L 183 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU L 140 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 181 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER L 142 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA L 179 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.217A pdb=" N THR L 136 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU L 185 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL L 138 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU L 183 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU L 140 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 181 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER L 142 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA L 179 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.659A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) 1498 hydrogen bonds defined for protein. 3834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.94 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5115 1.31 - 1.44: 8794 1.44 - 1.57: 17985 1.57 - 1.70: 6 1.70 - 1.84: 168 Bond restraints: 32068 Sorted by residual: bond pdb=" CB ASN B 928 " pdb=" CG ASN B 928 " ideal model delta sigma weight residual 1.516 1.297 0.219 2.50e-02 1.60e+03 7.65e+01 bond pdb=" CB ASN C 928 " pdb=" CG ASN C 928 " ideal model delta sigma weight residual 1.516 1.298 0.218 2.50e-02 1.60e+03 7.61e+01 bond pdb=" CB ASN A 928 " pdb=" CG ASN A 928 " ideal model delta sigma weight residual 1.516 1.298 0.218 2.50e-02 1.60e+03 7.59e+01 bond pdb=" C PHE A1075 " pdb=" N THR A1076 " ideal model delta sigma weight residual 1.330 1.456 -0.126 1.45e-02 4.76e+03 7.58e+01 bond pdb=" C PHE C1075 " pdb=" N THR C1076 " ideal model delta sigma weight residual 1.330 1.456 -0.126 1.45e-02 4.76e+03 7.55e+01 ... (remaining 32063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 43579 5.64 - 11.28: 230 11.28 - 16.92: 34 16.92 - 22.56: 2 22.56 - 28.20: 6 Bond angle restraints: 43851 Sorted by residual: angle pdb=" C PHE A1075 " pdb=" N THR A1076 " pdb=" CA THR A1076 " ideal model delta sigma weight residual 122.09 96.63 25.46 1.48e+00 4.57e-01 2.96e+02 angle pdb=" C PHE B1075 " pdb=" N THR B1076 " pdb=" CA THR B1076 " ideal model delta sigma weight residual 122.09 96.64 25.45 1.48e+00 4.57e-01 2.96e+02 angle pdb=" C PHE C1075 " pdb=" N THR C1076 " pdb=" CA THR C1076 " ideal model delta sigma weight residual 122.09 96.64 25.45 1.48e+00 4.57e-01 2.96e+02 angle pdb=" CA GLN A 926 " pdb=" CB GLN A 926 " pdb=" CG GLN A 926 " ideal model delta sigma weight residual 114.10 142.30 -28.20 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLN B 926 " pdb=" CB GLN B 926 " pdb=" CG GLN B 926 " ideal model delta sigma weight residual 114.10 142.28 -28.18 2.00e+00 2.50e-01 1.99e+02 ... (remaining 43846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17635 18.00 - 36.00: 792 36.00 - 54.00: 155 54.00 - 72.00: 45 72.00 - 89.99: 22 Dihedral angle restraints: 18649 sinusoidal: 6278 harmonic: 12371 Sorted by residual: dihedral pdb=" C ASN A1134 " pdb=" N ASN A1134 " pdb=" CA ASN A1134 " pdb=" CB ASN A1134 " ideal model delta harmonic sigma weight residual -122.60 -156.11 33.51 0 2.50e+00 1.60e-01 1.80e+02 dihedral pdb=" N ASN A1134 " pdb=" C ASN A1134 " pdb=" CA ASN A1134 " pdb=" CB ASN A1134 " ideal model delta harmonic sigma weight residual 122.80 155.56 -32.76 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 18646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 5159 0.272 - 0.544: 31 0.544 - 0.815: 0 0.815 - 1.087: 0 1.087 - 1.359: 1 Chirality restraints: 5191 Sorted by residual: chirality pdb=" CA ASN A1134 " pdb=" N ASN A1134 " pdb=" C ASN A1134 " pdb=" CB ASN A1134 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.62e+01 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PHE B 342 " pdb=" N PHE B 342 " pdb=" C PHE B 342 " pdb=" CB PHE B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5188 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.352 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C1303 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.327 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C7 NAG C1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1312 " -0.273 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C7 NAG A1312 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1312 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1312 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG A1312 " -0.017 2.00e-02 2.50e+03 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 90 2.44 - 3.06: 20054 3.06 - 3.67: 44883 3.67 - 4.29: 68483 4.29 - 4.90: 113438 Nonbonded interactions: 246948 Sorted by model distance: nonbonded pdb=" CG PRO B 412 " pdb=" OH TYR D 32 " model vdw 1.829 3.440 nonbonded pdb=" CD1 TRP L 95 " pdb=" CD2 LEU L 100 " model vdw 1.905 3.680 nonbonded pdb=" CG PRO C 412 " pdb=" OH TYR G 32 " model vdw 1.916 3.440 nonbonded pdb=" ND2 ASN B 801 " pdb=" O7 NAG B1311 " model vdw 2.038 3.120 nonbonded pdb=" CG1 VAL D 64 " pdb=" CB PHE D 68 " model vdw 2.083 3.860 ... (remaining 246943 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 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) selection = (chain 'B' and (resid 27 through 510 or (resid 511 through 512 and (name N or na \ me CA or name C or name O or name CB )) or resid 513 through 1311)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' } 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: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 35.820 Find NCS groups from input model: 0.850 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 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 0.219 32158 Z= 0.520 Angle : 1.405 31.084 44070 Z= 0.851 Chirality : 0.076 1.359 5191 Planarity : 0.012 0.301 5660 Dihedral : 11.740 89.994 10546 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 0.54 % Allowed : 4.88 % Favored : 94.58 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4212 helix: 1.05 (0.19), residues: 705 sheet: 0.35 (0.15), residues: 1200 loop : -0.39 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 466 TYR 0.045 0.003 TYR C 170 PHE 0.093 0.003 PHE C 374 TRP 0.074 0.005 TRP B1102 HIS 0.012 0.002 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.52 (32068) covalent geometry : angle 1.34330 / 0.84 (43851) SS BOND : bond 0.00833 / 0.47 ( 51) SS BOND : angle 2.33379 / 1.53 ( 102) hydrogen bonds : bond 0.17289 / 11.35 ( 1413) hydrogen bonds : angle 8.77667 / 6.24 ( 3834) link_NAG-ASN : bond 0.02043 / 1.12 ( 39) link_NAG-ASN : angle 7.90376 / 5.14 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 THR cc_start: 0.9386 (p) cc_final: 0.8874 (t) REVERT: C 883 THR cc_start: 0.9493 (p) cc_final: 0.9231 (t) REVERT: E 168 TRP cc_start: 0.0881 (m100) cc_final: 0.0576 (m100) REVERT: G 168 TRP cc_start: 0.0896 (m100) cc_final: 0.0518 (m100) outliers start: 16 outliers final: 3 residues processed: 250 average time/residue: 0.2204 time to fit residues: 87.7453 Evaluate side-chains 111 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN A1071 GLN B1005 GLN B1071 GLN C 603 ASN C1071 GLN D 39 GLN H 38 GLN H 93 GLN E 39 GLN F 28 HIS F 38 GLN G 39 GLN L 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.099038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065900 restraints weight = 148390.813| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.16 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32158 Z= 0.192 Angle : 0.681 15.470 44070 Z= 0.348 Chirality : 0.047 0.401 5191 Planarity : 0.005 0.049 5660 Dihedral : 4.931 56.855 4533 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.54 % Favored : 98.43 % Rotamer: Outliers : 1.46 % Allowed : 6.95 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.12), residues: 4212 helix: 1.83 (0.18), residues: 711 sheet: 0.45 (0.14), residues: 1284 loop : -0.09 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.022 0.002 TYR C 904 PHE 0.031 0.002 PHE D 29 TRP 0.040 0.002 TRP D 168 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (32068) covalent geometry : angle 0.65601 / 0.34 (43851) SS BOND : bond 0.00334 / 0.18 ( 51) SS BOND : angle 1.00571 / 0.67 ( 102) hydrogen bonds : bond 0.04405 / 2.90 ( 1413) hydrogen bonds : angle 5.99612 / 4.26 ( 3834) link_NAG-ASN : bond 0.00619 / 0.43 ( 39) link_NAG-ASN : angle 3.56977 / 2.40 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 780 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 131 LYS cc_start: 0.7597 (tttp) cc_final: 0.7380 (ptpp) REVERT: E 12 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7208 (t) REVERT: E 77 ASN cc_start: 0.5768 (OUTLIER) cc_final: 0.5502 (p0) REVERT: F 39 GLN cc_start: 0.6987 (mm-40) cc_final: 0.5982 (mm-40) REVERT: F 45 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7163 (tmt-80) REVERT: F 57 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7510 (p) REVERT: G 12 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7101 (t) REVERT: G 83 MET cc_start: -0.0163 (mtt) cc_final: -0.0397 (mtt) outliers start: 43 outliers final: 13 residues processed: 157 average time/residue: 0.2117 time to fit residues: 54.3154 Evaluate side-chains 124 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 404 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 57 optimal weight: 0.1980 chunk 302 optimal weight: 0.9990 chunk 389 optimal weight: 20.0000 chunk 365 optimal weight: 30.0000 chunk 316 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS C 207 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 56 HIS L 56 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.099327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065653 restraints weight = 145622.602| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 5.46 r_work: 0.2976 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32158 Z= 0.138 Angle : 0.562 15.094 44070 Z= 0.288 Chirality : 0.044 0.278 5191 Planarity : 0.004 0.045 5660 Dihedral : 4.383 54.475 4532 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 0.81 % Allowed : 8.75 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 4212 helix: 2.38 (0.19), residues: 705 sheet: 0.75 (0.14), residues: 1266 loop : -0.01 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.020 0.001 TYR B 904 PHE 0.021 0.001 PHE D 29 TRP 0.028 0.001 TRP D 168 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (32068) covalent geometry : angle 0.53908 / 0.28 (43851) SS BOND : bond 0.00147 / 0.08 ( 51) SS BOND : angle 0.72137 / 0.49 ( 102) hydrogen bonds : bond 0.03656 / 2.43 ( 1413) hydrogen bonds : angle 5.29654 / 3.76 ( 3834) link_NAG-ASN : bond 0.00515 / 0.32 ( 39) link_NAG-ASN : angle 3.11662 / 2.10 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8983 (mt-10) REVERT: B 740 MET cc_start: 0.9376 (tpt) cc_final: 0.9080 (tpp) REVERT: B 780 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9055 (mt-10) REVERT: C 697 MET cc_start: 0.9175 (ttm) cc_final: 0.8960 (ttm) REVERT: H 57 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7840 (p) REVERT: E 54 ASP cc_start: 0.9222 (t0) cc_final: 0.8889 (m-30) REVERT: F 45 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7270 (tmt-80) REVERT: G 54 ASP cc_start: 0.9071 (m-30) cc_final: 0.8754 (m-30) REVERT: G 168 TRP cc_start: 0.1707 (m100) cc_final: 0.1443 (m100) outliers start: 24 outliers final: 13 residues processed: 133 average time/residue: 0.2088 time to fit residues: 45.5804 Evaluate side-chains 108 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 258 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 342 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 926 GLN B 901 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.097602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063782 restraints weight = 147869.646| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 5.35 r_work: 0.2911 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32158 Z= 0.175 Angle : 0.563 15.433 44070 Z= 0.286 Chirality : 0.044 0.310 5191 Planarity : 0.004 0.046 5660 Dihedral : 4.289 54.562 4532 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 9.59 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4212 helix: 2.54 (0.20), residues: 687 sheet: 0.84 (0.15), residues: 1200 loop : 0.08 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1091 TYR 0.021 0.001 TYR B 904 PHE 0.022 0.001 PHE D 29 TRP 0.018 0.001 TRP E 168 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (32068) covalent geometry : angle 0.54472 / 0.28 (43851) SS BOND : bond 0.00165 / 0.10 ( 51) SS BOND : angle 0.64175 / 0.45 ( 102) hydrogen bonds : bond 0.03514 / 2.33 ( 1413) hydrogen bonds : angle 5.09400 / 3.61 ( 3834) link_NAG-ASN : bond 0.00524 / 0.35 ( 39) link_NAG-ASN : angle 2.79994 / 1.87 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9367 (tpt) cc_final: 0.9080 (tpp) REVERT: B 780 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9071 (mt-10) REVERT: H 45 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7355 (tmt-80) REVERT: H 57 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7890 (p) REVERT: H 65 ARG cc_start: 0.5134 (ptt90) cc_final: 0.4751 (ptt90) REVERT: E 54 ASP cc_start: 0.9311 (t0) cc_final: 0.9007 (m-30) REVERT: E 168 TRP cc_start: 0.1241 (m100) cc_final: 0.0955 (m100) REVERT: F 45 ARG cc_start: 0.7911 (ttt180) cc_final: 0.7308 (tmt-80) REVERT: F 57 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7857 (p) REVERT: F 65 ARG cc_start: 0.4999 (ptt90) cc_final: 0.3907 (ptt90) REVERT: G 54 ASP cc_start: 0.9088 (m-30) cc_final: 0.8765 (m-30) REVERT: L 57 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7705 (p) outliers start: 38 outliers final: 16 residues processed: 133 average time/residue: 0.2102 time to fit residues: 46.2209 Evaluate side-chains 112 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 102 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 326 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 137 optimal weight: 40.0000 chunk 349 optimal weight: 20.0000 chunk 295 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 416 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 655 HIS A1088 HIS B 655 HIS B1088 HIS B1113 GLN C 121 ASN C 655 HIS ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS D 39 GLN H 38 GLN H 51 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 39 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 38 GLN F 51 ASN G 3 GLN G 39 GLN G 185 GLN L 38 GLN L 51 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.095188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061186 restraints weight = 149086.383| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 5.32 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 32158 Z= 0.322 Angle : 0.696 16.621 44070 Z= 0.352 Chirality : 0.046 0.298 5191 Planarity : 0.005 0.044 5660 Dihedral : 4.601 46.867 4528 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 10.37 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.13), residues: 4212 helix: 2.24 (0.20), residues: 687 sheet: 0.63 (0.15), residues: 1197 loop : -0.01 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 75 TYR 0.024 0.002 TYR B 904 PHE 0.017 0.002 PHE D 29 TRP 0.013 0.002 TRP B 64 HIS 0.009 0.002 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.32 (32068) covalent geometry : angle 0.67731 / 0.35 (43851) SS BOND : bond 0.00226 / 0.14 ( 51) SS BOND : angle 0.78769 / 0.56 ( 102) hydrogen bonds : bond 0.04166 / 2.76 ( 1413) hydrogen bonds : angle 5.47539 / 3.88 ( 3834) link_NAG-ASN : bond 0.00662 / 0.44 ( 39) link_NAG-ASN : angle 3.13472 / 2.07 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9198 (tpt) cc_final: 0.8916 (tpp) REVERT: D 34 MET cc_start: 0.5761 (tpt) cc_final: 0.5550 (tpt) REVERT: D 72 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6145 (ttt180) REVERT: H 45 ARG cc_start: 0.7921 (ttt180) cc_final: 0.6903 (mmm160) REVERT: H 57 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7933 (p) REVERT: H 65 ARG cc_start: 0.5079 (ptt90) cc_final: 0.4568 (ptt90) REVERT: E 54 ASP cc_start: 0.9457 (t0) cc_final: 0.9147 (m-30) REVERT: E 83 MET cc_start: 0.1557 (mpp) cc_final: 0.0835 (mmt) REVERT: F 45 ARG cc_start: 0.7898 (ttt180) cc_final: 0.7215 (tmt-80) REVERT: F 57 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7821 (p) REVERT: G 54 ASP cc_start: 0.9130 (m-30) cc_final: 0.8831 (m-30) REVERT: L 45 ARG cc_start: 0.7950 (ttt180) cc_final: 0.6882 (mmm160) outliers start: 51 outliers final: 31 residues processed: 139 average time/residue: 0.2229 time to fit residues: 50.0477 Evaluate side-chains 118 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 285 optimal weight: 0.9990 chunk 389 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 195 optimal weight: 0.9980 chunk 334 optimal weight: 40.0000 chunk 205 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1113 GLN C1113 GLN H 28 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 82 GLN F 28 HIS G 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.096307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063104 restraints weight = 147414.305| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.51 r_work: 0.3030 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32158 Z= 0.145 Angle : 0.543 15.591 44070 Z= 0.274 Chirality : 0.044 0.251 5191 Planarity : 0.004 0.045 5660 Dihedral : 4.188 37.904 4528 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.12 % Allowed : 11.22 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 4212 helix: 2.56 (0.20), residues: 687 sheet: 0.75 (0.15), residues: 1173 loop : 0.03 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.013 0.001 TYR E 105 PHE 0.015 0.001 PHE D 29 TRP 0.017 0.001 TRP G 168 HIS 0.008 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (32068) covalent geometry : angle 0.52365 / 0.27 (43851) SS BOND : bond 0.00179 / 0.09 ( 51) SS BOND : angle 0.64443 / 0.44 ( 102) hydrogen bonds : bond 0.03460 / 2.29 ( 1413) hydrogen bonds : angle 5.10246 / 3.62 ( 3834) link_NAG-ASN : bond 0.00358 / 0.22 ( 39) link_NAG-ASN : angle 2.85062 / 1.91 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9398 (tpt) cc_final: 0.9069 (tpp) REVERT: C 697 MET cc_start: 0.9312 (ttp) cc_final: 0.9052 (ttp) REVERT: H 45 ARG cc_start: 0.7888 (ttt180) cc_final: 0.6877 (mmm160) REVERT: H 57 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7828 (p) REVERT: H 65 ARG cc_start: 0.5039 (ptt90) cc_final: 0.4516 (ptt90) REVERT: E 54 ASP cc_start: 0.9384 (t0) cc_final: 0.9067 (m-30) REVERT: F 45 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7177 (tmt-80) REVERT: F 65 ARG cc_start: 0.4391 (ptt90) cc_final: 0.3885 (ptt90) REVERT: G 54 ASP cc_start: 0.9167 (m-30) cc_final: 0.8829 (m-30) REVERT: G 168 TRP cc_start: 0.0589 (m100) cc_final: -0.0028 (m100) REVERT: L 45 ARG cc_start: 0.7900 (ttt180) cc_final: 0.6866 (mmm160) REVERT: L 57 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7877 (p) outliers start: 33 outliers final: 16 residues processed: 115 average time/residue: 0.2082 time to fit residues: 39.4366 Evaluate side-chains 102 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 387 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 393 optimal weight: 50.0000 chunk 310 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 224 optimal weight: 30.0000 chunk 403 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 420 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN F 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.105389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072891 restraints weight = 169900.645| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 7.24 r_work: 0.2816 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 32158 Z= 0.286 Angle : 0.655 16.680 44070 Z= 0.327 Chirality : 0.046 0.561 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.419 38.053 4528 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.56 % Allowed : 11.12 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4212 helix: 2.35 (0.20), residues: 687 sheet: 0.62 (0.15), residues: 1179 loop : -0.06 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 72 TYR 0.018 0.001 TYR B 904 PHE 0.013 0.001 PHE L 144 TRP 0.012 0.001 TRP D 168 HIS 0.008 0.001 HIS F 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (32068) covalent geometry : angle 0.63639 / 0.32 (43851) SS BOND : bond 0.00240 / 0.14 ( 51) SS BOND : angle 0.72933 / 0.51 ( 102) hydrogen bonds : bond 0.03837 / 2.54 ( 1413) hydrogen bonds : angle 5.34016 / 3.77 ( 3834) link_NAG-ASN : bond 0.00554 / 0.32 ( 39) link_NAG-ASN : angle 3.03844 / 2.03 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7364 (mmm160) REVERT: F 45 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7643 (tmt-80) REVERT: F 65 ARG cc_start: 0.4454 (ptt90) cc_final: 0.4058 (ptt90) REVERT: G 83 MET cc_start: 0.4673 (mpp) cc_final: 0.4185 (mmt) REVERT: L 57 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7671 (p) outliers start: 46 outliers final: 27 residues processed: 123 average time/residue: 0.2040 time to fit residues: 41.5730 Evaluate side-chains 105 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 97 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.107036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074924 restraints weight = 168721.682| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 7.47 r_work: 0.2872 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32158 Z= 0.138 Angle : 0.549 15.878 44070 Z= 0.275 Chirality : 0.044 0.433 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.145 40.846 4528 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.22 % Allowed : 11.53 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4212 helix: 2.54 (0.20), residues: 705 sheet: 0.71 (0.15), residues: 1170 loop : 0.01 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.013 0.001 TYR A 170 PHE 0.022 0.001 PHE H 144 TRP 0.039 0.001 TRP E 168 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (32068) covalent geometry : angle 0.53047 / 0.27 (43851) SS BOND : bond 0.00180 / 0.09 ( 51) SS BOND : angle 0.62352 / 0.43 ( 102) hydrogen bonds : bond 0.03397 / 2.24 ( 1413) hydrogen bonds : angle 5.06978 / 3.58 ( 3834) link_NAG-ASN : bond 0.00310 / 0.19 ( 39) link_NAG-ASN : angle 2.80802 / 1.89 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9417 (tpt) cc_final: 0.9086 (tpp) REVERT: G 83 MET cc_start: 0.4787 (mpp) cc_final: 0.4280 (mmt) REVERT: L 57 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7785 (p) outliers start: 36 outliers final: 22 residues processed: 119 average time/residue: 0.1986 time to fit residues: 38.6455 Evaluate side-chains 102 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 195 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 410 optimal weight: 30.0000 chunk 323 optimal weight: 30.0000 chunk 204 optimal weight: 6.9990 chunk 413 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 66 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.095785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058902 restraints weight = 153258.714| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 5.90 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 32158 Z= 0.424 Angle : 0.809 16.928 44070 Z= 0.402 Chirality : 0.048 0.454 5191 Planarity : 0.005 0.045 5660 Dihedral : 4.825 37.944 4528 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.49 % Allowed : 11.56 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4212 helix: 1.86 (0.19), residues: 705 sheet: 0.52 (0.15), residues: 1167 loop : -0.35 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 65 TYR 0.021 0.002 TYR B 904 PHE 0.020 0.002 PHE H 144 TRP 0.050 0.002 TRP E 168 HIS 0.010 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.42 (32068) covalent geometry : angle 0.79193 / 0.40 (43851) SS BOND : bond 0.00332 / 0.20 ( 51) SS BOND : angle 0.89495 / 0.63 ( 102) hydrogen bonds : bond 0.04314 / 2.87 ( 1413) hydrogen bonds : angle 5.73389 / 4.05 ( 3834) link_NAG-ASN : bond 0.00551 / 0.37 ( 39) link_NAG-ASN : angle 3.25852 / 2.17 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7830 (tpt170) REVERT: L 45 ARG cc_start: 0.8126 (ttt180) cc_final: 0.7296 (mmm160) REVERT: L 57 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7662 (p) REVERT: L 65 ARG cc_start: 0.5457 (ptt90) cc_final: 0.5220 (ptt90) outliers start: 44 outliers final: 36 residues processed: 121 average time/residue: 0.2196 time to fit residues: 43.1820 Evaluate side-chains 118 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 280 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 171 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 334 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 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 = 0.3944 r_free = 0.3944 target = 0.094421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061552 restraints weight = 143532.633| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.66 r_work: 0.2847 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32158 Z= 0.149 Angle : 0.584 15.603 44070 Z= 0.292 Chirality : 0.045 0.399 5191 Planarity : 0.004 0.058 5660 Dihedral : 4.390 41.119 4528 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.92 % Allowed : 12.14 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 4212 helix: 2.34 (0.20), residues: 705 sheet: 0.58 (0.15), residues: 1140 loop : -0.22 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 65 TYR 0.015 0.001 TYR A 170 PHE 0.026 0.001 PHE H 144 TRP 0.067 0.002 TRP G 168 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (32068) covalent geometry : angle 0.56584 / 0.29 (43851) SS BOND : bond 0.00218 / 0.11 ( 51) SS BOND : angle 0.70339 / 0.48 ( 102) hydrogen bonds : bond 0.03643 / 2.40 ( 1413) hydrogen bonds : angle 5.29592 / 3.74 ( 3834) link_NAG-ASN : bond 0.00324 / 0.20 ( 39) link_NAG-ASN : angle 2.86297 / 1.92 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9618 (tpp) cc_final: 0.9123 (tpp) REVERT: A 869 MET cc_start: 0.9461 (mtm) cc_final: 0.9107 (pmm) REVERT: B 869 MET cc_start: 0.9050 (pmm) cc_final: 0.8844 (pmm) REVERT: C 869 MET cc_start: 0.9429 (mtm) cc_final: 0.9179 (pmm) REVERT: H 45 ARG cc_start: 0.8174 (ttt180) cc_final: 0.7696 (tpt170) REVERT: E 3 GLN cc_start: 0.6202 (tp40) cc_final: 0.5911 (tm-30) REVERT: E 83 MET cc_start: 0.1370 (mpp) cc_final: 0.1129 (mmp) REVERT: F 83 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7743 (mp10) REVERT: G 83 MET cc_start: 0.2014 (mpp) cc_final: 0.1689 (mmt) REVERT: L 45 ARG cc_start: 0.7943 (ttt180) cc_final: 0.6934 (mmm160) REVERT: L 57 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.7879 (p) REVERT: L 65 ARG cc_start: 0.5773 (ptt90) cc_final: 0.4423 (ptt90) REVERT: L 83 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7922 (mp10) outliers start: 27 outliers final: 21 residues processed: 104 average time/residue: 0.2111 time to fit residues: 35.8470 Evaluate side-chains 100 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 406 optimal weight: 30.0000 chunk 43 optimal weight: 0.0470 chunk 325 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 349 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 140 optimal weight: 0.0870 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 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 = 0.3944 r_free = 0.3944 target = 0.094311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061119 restraints weight = 141813.371| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.89 r_work: 0.2832 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32158 Z= 0.134 Angle : 0.556 15.053 44070 Z= 0.277 Chirality : 0.045 0.383 5191 Planarity : 0.004 0.043 5660 Dihedral : 4.138 40.747 4528 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.88 % Allowed : 12.03 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4212 helix: 2.58 (0.20), residues: 702 sheet: 0.66 (0.15), residues: 1158 loop : -0.11 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.021 0.001 TYR G 105 PHE 0.032 0.001 PHE D 68 TRP 0.036 0.001 TRP G 168 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (32068) covalent geometry : angle 0.53890 / 0.27 (43851) SS BOND : bond 0.00183 / 0.10 ( 51) SS BOND : angle 0.64694 / 0.45 ( 102) hydrogen bonds : bond 0.03312 / 2.19 ( 1413) hydrogen bonds : angle 5.07372 / 3.58 ( 3834) link_NAG-ASN : bond 0.00299 / 0.18 ( 39) link_NAG-ASN : angle 2.69047 / 1.82 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9076.02 seconds wall clock time: 155 minutes 53.03 seconds (9353.03 seconds total)