Starting phenix.real_space_refine on Fri Mar 6 14:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkv_24504/03_2026/7rkv_24504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkv_24504/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rkv_24504/03_2026/7rkv_24504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkv_24504/03_2026/7rkv_24504.map" model { file = "/net/cci-nas-00/data/ceres_data/7rkv_24504/03_2026/7rkv_24504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkv_24504/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 42 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 dihedrals: 42 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.92, per 1000 atoms: 0.22 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 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: 1.27 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: 10.83 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 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: 18378 18.00 - 36.00: 832 36.00 - 54.00: 186 54.00 - 72.00: 50 72.00 - 89.99: 22 Dihedral angle restraints: 19468 sinusoidal: 7097 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 19465 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.200 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 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:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 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 : 11.812 89.994 11365 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 covalent geometry : bond 0.00879 (32068) covalent geometry : angle 1.34330 (43851) SS BOND : bond 0.00833 ( 51) SS BOND : angle 2.33379 ( 102) hydrogen bonds : bond 0.17289 ( 1413) hydrogen bonds : angle 8.77667 ( 3834) link_NAG-ASN : bond 0.02043 ( 39) link_NAG-ASN : angle 7.90376 ( 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 : 1.104 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: 0.1920 time to fit residues: 76.2855 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 : 1.117 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4067 r_free = 0.4067 target = 0.099720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066948 restraints weight = 147770.770| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.58 r_work: 0.3162 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32158 Z= 0.195 Angle : 0.677 15.581 44070 Z= 0.346 Chirality : 0.047 0.405 5191 Planarity : 0.005 0.049 5660 Dihedral : 6.107 56.546 5352 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.52 % Favored : 98.46 % Rotamer: Outliers : 1.46 % Allowed : 6.92 % Favored : 91.63 % 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: 0.53 (0.12), residues: 4212 helix: 1.83 (0.18), residues: 711 sheet: 0.42 (0.14), residues: 1290 loop : -0.10 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 65 TYR 0.023 0.002 TYR C1110 PHE 0.030 0.002 PHE D 29 TRP 0.039 0.002 TRP D 168 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00418 (32068) covalent geometry : angle 0.64877 (43851) SS BOND : bond 0.00595 ( 51) SS BOND : angle 0.99087 ( 102) hydrogen bonds : bond 0.04372 ( 1413) hydrogen bonds : angle 5.98172 ( 3834) link_NAG-ASN : bond 0.00623 ( 39) link_NAG-ASN : angle 3.72964 ( 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 : 1.134 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: 0.9253 (mt-10) cc_final: 0.8956 (mt-10) REVERT: D 131 LYS cc_start: 0.7592 (tttp) cc_final: 0.7383 (ptpp) REVERT: E 12 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7180 (t) REVERT: E 168 TRP cc_start: 0.1044 (m100) cc_final: 0.0843 (m100) REVERT: F 39 GLN cc_start: 0.6873 (mm-40) cc_final: 0.5898 (mm-40) REVERT: F 45 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7147 (tmt-80) REVERT: F 57 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7436 (p) REVERT: G 83 MET cc_start: -0.0352 (mtt) cc_final: -0.0572 (mtt) outliers start: 43 outliers final: 13 residues processed: 157 average time/residue: 0.1903 time to fit residues: 48.2134 Evaluate side-chains 122 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 F residue 57 SER 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: 8.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 389 optimal weight: 10.0000 chunk 365 optimal weight: 40.0000 chunk 316 optimal weight: 7.9990 chunk 339 optimal weight: 30.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 901 GLN B 207 HIS B 901 GLN C 207 HIS C 901 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.097343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063007 restraints weight = 148976.427| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.35 r_work: 0.2897 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32158 Z= 0.239 Angle : 0.638 16.457 44070 Z= 0.328 Chirality : 0.046 0.322 5191 Planarity : 0.005 0.045 5660 Dihedral : 5.248 55.373 5351 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 1.25 % Allowed : 8.88 % Favored : 89.86 % 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: 0.80 (0.13), residues: 4212 helix: 2.40 (0.19), residues: 687 sheet: 0.62 (0.14), residues: 1230 loop : -0.04 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.030 0.002 TYR B 904 PHE 0.020 0.002 PHE D 29 TRP 0.028 0.002 TRP D 168 HIS 0.009 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00523 (32068) covalent geometry : angle 0.61737 (43851) SS BOND : bond 0.00198 ( 51) SS BOND : angle 0.78640 ( 102) hydrogen bonds : bond 0.04048 ( 1413) hydrogen bonds : angle 5.46656 ( 3834) link_NAG-ASN : bond 0.00657 ( 39) link_NAG-ASN : angle 3.15771 ( 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 140 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.019 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: A 697 MET cc_start: 0.9235 (ttm) cc_final: 0.9024 (ttm) REVERT: B 740 MET cc_start: 0.9395 (tpt) cc_final: 0.9091 (tpp) REVERT: B 780 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9065 (mt-10) REVERT: C 697 MET cc_start: 0.9250 (ttm) cc_final: 0.9041 (ttm) REVERT: C 740 MET cc_start: 0.9477 (tpp) cc_final: 0.9254 (tpp) REVERT: H 45 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7357 (tmt-80) REVERT: H 57 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7891 (p) REVERT: H 65 ARG cc_start: 0.4838 (ptt90) cc_final: 0.4257 (ptt90) REVERT: E 54 ASP cc_start: 0.9309 (t0) cc_final: 0.9018 (m-30) REVERT: E 168 TRP cc_start: 0.1802 (m100) cc_final: 0.0836 (m100) REVERT: G 54 ASP cc_start: 0.9100 (m-30) cc_final: 0.8789 (m-30) REVERT: G 168 TRP cc_start: 0.1764 (m100) cc_final: 0.1512 (m100) outliers start: 37 outliers final: 26 residues processed: 128 average time/residue: 0.1818 time to fit residues: 38.4869 Evaluate side-chains 115 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 734 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 327 VAL 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 734 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain G residue 12 VAL 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 57 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: 0.8980 chunk 33 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.097582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.063706 restraints weight = 147038.475| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 5.25 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32158 Z= 0.136 Angle : 0.532 15.531 44070 Z= 0.271 Chirality : 0.044 0.280 5191 Planarity : 0.004 0.046 5660 Dihedral : 4.812 54.736 5351 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.12 % Allowed : 10.20 % Favored : 88.68 % 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: 0.93 (0.13), residues: 4212 helix: 2.55 (0.20), residues: 687 sheet: 0.68 (0.14), residues: 1236 loop : 0.05 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 75 TYR 0.017 0.001 TYR L 76 PHE 0.021 0.001 PHE D 29 TRP 0.014 0.001 TRP D 168 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00299 (32068) covalent geometry : angle 0.51037 (43851) SS BOND : bond 0.00162 ( 51) SS BOND : angle 0.63200 ( 102) hydrogen bonds : bond 0.03448 ( 1413) hydrogen bonds : angle 5.13224 ( 3834) link_NAG-ASN : bond 0.00423 ( 39) link_NAG-ASN : angle 2.91679 ( 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 141 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8842 (ttm) cc_final: 0.8545 (ttm) REVERT: A 740 MET cc_start: 0.9324 (tpp) cc_final: 0.8989 (tpp) REVERT: B 740 MET cc_start: 0.9171 (tpt) cc_final: 0.8919 (tpp) REVERT: B 780 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8545 (mt-10) REVERT: C 697 MET cc_start: 0.8893 (ttm) cc_final: 0.8663 (ttp) REVERT: C 740 MET cc_start: 0.9327 (tpp) cc_final: 0.9028 (tpp) REVERT: H 57 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7828 (p) REVERT: H 65 ARG cc_start: 0.4782 (ptt90) cc_final: 0.4397 (ptt90) REVERT: E 54 ASP cc_start: 0.9364 (t0) cc_final: 0.9040 (m-30) REVERT: E 83 MET cc_start: 0.1317 (mpp) cc_final: 0.0773 (mmt) REVERT: E 168 TRP cc_start: 0.1239 (m100) cc_final: 0.0375 (m100) REVERT: F 45 ARG cc_start: 0.7806 (ttt180) cc_final: 0.7139 (tmt-80) REVERT: F 57 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7739 (p) REVERT: F 65 ARG cc_start: 0.4950 (ptt90) cc_final: 0.3747 (ptt90) REVERT: G 54 ASP cc_start: 0.9122 (m-30) cc_final: 0.8810 (m-30) REVERT: G 168 TRP cc_start: 0.1370 (m100) cc_final: 0.1163 (m100) REVERT: L 57 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7773 (p) outliers start: 33 outliers final: 13 residues processed: 136 average time/residue: 0.1927 time to fit residues: 42.5952 Evaluate side-chains 112 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 666 ILE 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 801 ASN 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 H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 12 VAL 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: 6.9990 chunk 393 optimal weight: 40.0000 chunk 326 optimal weight: 30.0000 chunk 206 optimal weight: 20.0000 chunk 137 optimal weight: 0.0470 chunk 349 optimal weight: 20.0000 chunk 295 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 416 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 655 HIS A1088 HIS B 655 HIS B1113 GLN C 121 ASN C 655 HIS C1088 HIS C1113 GLN D 39 GLN H 38 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 38 GLN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN L 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.095648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062070 restraints weight = 147617.841| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.01 r_work: 0.2869 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 32158 Z= 0.260 Angle : 0.628 16.269 44070 Z= 0.316 Chirality : 0.045 0.290 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.974 55.398 5347 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.63 % Allowed : 10.44 % Favored : 87.93 % 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: 2.43 (0.20), residues: 687 sheet: 0.75 (0.15), residues: 1161 loop : 0.03 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 75 TYR 0.021 0.001 TYR B 904 PHE 0.019 0.002 PHE L 144 TRP 0.015 0.001 TRP D 168 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00573 (32068) covalent geometry : angle 0.60948 (43851) SS BOND : bond 0.00196 ( 51) SS BOND : angle 0.69479 ( 102) hydrogen bonds : bond 0.03811 ( 1413) hydrogen bonds : angle 5.25878 ( 3834) link_NAG-ASN : bond 0.00556 ( 39) link_NAG-ASN : angle 2.97946 ( 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 142 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.054 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: A 697 MET cc_start: 0.9309 (ttm) cc_final: 0.9027 (ttm) REVERT: A 740 MET cc_start: 0.9557 (tpp) cc_final: 0.9139 (tpp) REVERT: B 740 MET cc_start: 0.9423 (tpt) cc_final: 0.9106 (tpp) REVERT: C 740 MET cc_start: 0.9565 (tpp) cc_final: 0.9239 (tpp) REVERT: D 72 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5701 (mtt180) REVERT: H 45 ARG cc_start: 0.7943 (ttt180) cc_final: 0.6905 (mmm160) REVERT: H 57 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7917 (p) REVERT: H 65 ARG cc_start: 0.4850 (ptt90) cc_final: 0.4320 (ptt90) REVERT: E 54 ASP cc_start: 0.9361 (t0) cc_final: 0.9087 (m-30) REVERT: F 45 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7300 (tmt-80) REVERT: F 57 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7778 (p) REVERT: G 54 ASP cc_start: 0.9116 (m-30) cc_final: 0.8841 (m-30) REVERT: G 83 MET cc_start: 0.1255 (mpp) cc_final: 0.0854 (mmt) REVERT: G 168 TRP cc_start: 0.1732 (m100) cc_final: 0.1483 (m100) REVERT: L 45 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7030 (mmm160) outliers start: 48 outliers final: 27 residues processed: 134 average time/residue: 0.1802 time to fit residues: 40.2194 Evaluate side-chains 116 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL 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 663 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET 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 781 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 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 79 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain L residue 17 SER 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: 0.8980 chunk 389 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 413 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN H 28 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.107652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.076131 restraints weight = 168278.861| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 7.86 r_work: 0.2892 rms_B_bonded: 5.65 restraints_weight: 2.0000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32158 Z= 0.132 Angle : 0.520 15.376 44070 Z= 0.264 Chirality : 0.044 0.262 5191 Planarity : 0.004 0.045 5660 Dihedral : 4.542 52.476 5347 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.36 % Allowed : 10.98 % 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: 1.00 (0.13), residues: 4212 helix: 2.69 (0.20), residues: 684 sheet: 0.70 (0.15), residues: 1212 loop : 0.10 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 65 TYR 0.016 0.001 TYR L 76 PHE 0.015 0.001 PHE D 29 TRP 0.015 0.001 TRP D 168 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00294 (32068) covalent geometry : angle 0.50017 (43851) SS BOND : bond 0.00186 ( 51) SS BOND : angle 0.63059 ( 102) hydrogen bonds : bond 0.03299 ( 1413) hydrogen bonds : angle 5.00156 ( 3834) link_NAG-ASN : bond 0.00342 ( 39) link_NAG-ASN : angle 2.80025 ( 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 142 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.187 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 242 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 740 MET cc_start: 0.9505 (tpp) cc_final: 0.9152 (tpp) REVERT: A 1029 MET cc_start: 0.9258 (tpp) cc_final: 0.8666 (ttm) REVERT: B 740 MET cc_start: 0.9392 (tpt) cc_final: 0.9081 (tpp) REVERT: C 740 MET cc_start: 0.9492 (tpp) cc_final: 0.9201 (tpp) REVERT: H 45 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7270 (mmm160) REVERT: H 57 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (p) REVERT: H 65 ARG cc_start: 0.4633 (ptt90) cc_final: 0.4224 (ptt90) REVERT: F 57 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7727 (p) REVERT: F 65 ARG cc_start: 0.5570 (ptt90) cc_final: 0.4999 (ptt90) REVERT: G 83 MET cc_start: 0.4281 (mpp) cc_final: 0.3798 (mmt) REVERT: L 57 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (p) outliers start: 40 outliers final: 22 residues processed: 135 average time/residue: 0.1704 time to fit residues: 38.5606 Evaluate side-chains 115 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL 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 875 SER 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 1050 MET 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 D residue 221 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 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: 7.9990 chunk 352 optimal weight: 10.0000 chunk 393 optimal weight: 40.0000 chunk 310 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 224 optimal weight: 40.0000 chunk 403 optimal weight: 0.4980 chunk 266 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 420 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS H 28 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.096139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062278 restraints weight = 148899.462| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.04 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32158 Z= 0.188 Angle : 0.563 16.854 44070 Z= 0.282 Chirality : 0.044 0.442 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.596 50.202 5347 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 11.29 % Favored : 87.22 % 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: 1.01 (0.13), residues: 4212 helix: 2.63 (0.20), residues: 687 sheet: 0.77 (0.15), residues: 1173 loop : 0.08 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 65 TYR 0.013 0.001 TYR E 105 PHE 0.015 0.001 PHE D 29 TRP 0.032 0.001 TRP E 168 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00416 (32068) covalent geometry : angle 0.54505 (43851) SS BOND : bond 0.00187 ( 51) SS BOND : angle 0.60515 ( 102) hydrogen bonds : bond 0.03432 ( 1413) hydrogen bonds : angle 5.02591 ( 3834) link_NAG-ASN : bond 0.00336 ( 39) link_NAG-ASN : angle 2.81745 ( 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 139 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.990 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: A 242 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 740 MET cc_start: 0.9341 (tpp) cc_final: 0.8946 (tpp) REVERT: A 1029 MET cc_start: 0.9297 (tpp) cc_final: 0.8729 (ttm) REVERT: B 740 MET cc_start: 0.9201 (tpt) cc_final: 0.8911 (tpp) REVERT: C 740 MET cc_start: 0.9332 (tpp) cc_final: 0.8998 (tpp) REVERT: F 57 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7782 (p) REVERT: G 3 GLN cc_start: 0.6107 (tp40) cc_final: 0.5858 (tp40) REVERT: G 83 MET cc_start: 0.1046 (mpp) cc_final: 0.0764 (mmt) outliers start: 44 outliers final: 25 residues processed: 133 average time/residue: 0.1905 time to fit residues: 41.9289 Evaluate side-chains 118 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU 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 734 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL 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 866 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL 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 1050 MET 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 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 24 LEU 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: 10.0000 chunk 88 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 152 optimal weight: 0.0470 chunk 369 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 28 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.106740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.075427 restraints weight = 168838.769| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 6.45 r_work: 0.2856 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32158 Z= 0.179 Angle : 0.560 15.761 44070 Z= 0.280 Chirality : 0.044 0.454 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.574 51.317 5347 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.49 % Allowed : 11.42 % 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: 1.04 (0.13), residues: 4212 helix: 2.64 (0.20), residues: 687 sheet: 0.84 (0.15), residues: 1146 loop : 0.08 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.015 0.001 TYR C 873 PHE 0.017 0.001 PHE H 144 TRP 0.049 0.002 TRP E 168 HIS 0.008 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00395 (32068) covalent geometry : angle 0.54124 (43851) SS BOND : bond 0.00198 ( 51) SS BOND : angle 0.61458 ( 102) hydrogen bonds : bond 0.03411 ( 1413) hydrogen bonds : angle 5.01959 ( 3834) link_NAG-ASN : bond 0.00317 ( 39) link_NAG-ASN : angle 2.79107 ( 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 141 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 1.054 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: A 242 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 740 MET cc_start: 0.9525 (tpp) cc_final: 0.9100 (tpp) REVERT: A 1029 MET cc_start: 0.9347 (tpp) cc_final: 0.8747 (ttm) REVERT: B 740 MET cc_start: 0.9412 (tpt) cc_final: 0.9079 (tpp) REVERT: B 869 MET cc_start: 0.9378 (mtm) cc_final: 0.9167 (pmm) REVERT: C 740 MET cc_start: 0.9537 (tpp) cc_final: 0.9194 (tpp) REVERT: H 57 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7902 (p) REVERT: H 65 ARG cc_start: 0.5142 (ptt90) cc_final: 0.4239 (ptt90) REVERT: F 57 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7819 (p) outliers start: 44 outliers final: 23 residues processed: 134 average time/residue: 0.1821 time to fit residues: 40.3039 Evaluate side-chains 116 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL 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 731 MET 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 611 LEU 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 D residue 221 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL 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: 1.9990 chunk 392 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 323 optimal weight: 30.0000 chunk 204 optimal weight: 3.9990 chunk 413 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 400 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 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 = 0.3979 r_free = 0.3979 target = 0.095870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062904 restraints weight = 146811.934| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.23 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32158 Z= 0.168 Angle : 0.554 15.384 44070 Z= 0.277 Chirality : 0.044 0.421 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.519 51.486 5347 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.08 % Allowed : 11.76 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.58 (0.20), residues: 705 sheet: 0.82 (0.15), residues: 1152 loop : 0.07 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.016 0.001 TYR C 873 PHE 0.018 0.001 PHE H 144 TRP 0.038 0.001 TRP E 168 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00374 (32068) covalent geometry : angle 0.53645 (43851) SS BOND : bond 0.00181 ( 51) SS BOND : angle 0.61946 ( 102) hydrogen bonds : bond 0.03342 ( 1413) hydrogen bonds : angle 4.97774 ( 3834) link_NAG-ASN : bond 0.00302 ( 39) link_NAG-ASN : angle 2.75425 ( 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 124 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 1.100 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: A 697 MET cc_start: 0.8870 (ttm) cc_final: 0.8659 (ttm) REVERT: A 740 MET cc_start: 0.9264 (tpp) cc_final: 0.8832 (tpp) REVERT: A 1029 MET cc_start: 0.9311 (tpp) cc_final: 0.8776 (ttm) REVERT: B 740 MET cc_start: 0.9205 (tpt) cc_final: 0.8901 (tpp) REVERT: B 869 MET cc_start: 0.9285 (mtm) cc_final: 0.8987 (pmm) REVERT: C 740 MET cc_start: 0.9332 (tpp) cc_final: 0.8983 (tpp) REVERT: H 57 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7931 (p) REVERT: E 3 GLN cc_start: 0.6416 (tp40) cc_final: 0.6193 (tp40) REVERT: F 57 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7769 (p) outliers start: 32 outliers final: 23 residues processed: 118 average time/residue: 0.1852 time to fit residues: 36.4605 Evaluate side-chains 110 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL 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 731 MET 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 101 ILE Chi-restraints excluded: chain C residue 611 LEU 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 115 ASP 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 F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 280 optimal weight: 2.9990 chunk 135 optimal weight: 50.0000 chunk 171 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 51 ASN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.096607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059823 restraints weight = 151715.236| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 5.87 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 32158 Z= 0.341 Angle : 0.721 16.488 44070 Z= 0.358 Chirality : 0.047 0.441 5191 Planarity : 0.005 0.078 5660 Dihedral : 5.272 55.277 5347 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.08 % Allowed : 11.69 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.58 (0.13), residues: 4212 helix: 1.96 (0.20), residues: 723 sheet: 0.72 (0.15), residues: 1134 loop : -0.24 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 65 TYR 0.016 0.002 TYR B 904 PHE 0.018 0.002 PHE D 68 TRP 0.040 0.002 TRP E 168 HIS 0.009 0.002 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00747 (32068) covalent geometry : angle 0.70368 (43851) SS BOND : bond 0.00271 ( 51) SS BOND : angle 0.81791 ( 102) hydrogen bonds : bond 0.04022 ( 1413) hydrogen bonds : angle 5.46263 ( 3834) link_NAG-ASN : bond 0.00453 ( 39) link_NAG-ASN : angle 3.13375 ( 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 113 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9470 (tpp) cc_final: 0.8829 (ttm) REVERT: B 869 MET cc_start: 0.9405 (mtm) cc_final: 0.8978 (pmm) REVERT: C 869 MET cc_start: 0.9404 (mtm) cc_final: 0.8986 (pmm) REVERT: H 45 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7713 (tpt170) REVERT: F 45 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7158 (mmm160) REVERT: F 57 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7769 (p) REVERT: L 45 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7202 (mmm160) outliers start: 32 outliers final: 27 residues processed: 108 average time/residue: 0.2017 time to fit residues: 35.4840 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 : 1.159 ------------------------------------------------------------------------------- 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 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL 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 731 MET 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 101 ILE Chi-restraints excluded: chain C residue 611 LEU 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 1104 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 406 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 66 HIS ** 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** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.093899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061303 restraints weight = 142655.676| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.75 r_work: 0.2814 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32158 Z= 0.252 Angle : 0.633 16.126 44070 Z= 0.316 Chirality : 0.046 0.417 5191 Planarity : 0.005 0.106 5660 Dihedral : 4.946 51.393 5347 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.12 % Allowed : 11.86 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.28 (0.20), residues: 705 sheet: 0.63 (0.15), residues: 1152 loop : -0.22 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 65 TYR 0.015 0.001 TYR E 53 PHE 0.020 0.001 PHE H 144 TRP 0.037 0.002 TRP E 168 HIS 0.007 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00558 (32068) covalent geometry : angle 0.61471 (43851) SS BOND : bond 0.00230 ( 51) SS BOND : angle 0.74396 ( 102) hydrogen bonds : bond 0.03712 ( 1413) hydrogen bonds : angle 5.31932 ( 3834) link_NAG-ASN : bond 0.00274 ( 39) link_NAG-ASN : angle 2.99530 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8266.68 seconds wall clock time: 141 minutes 54.94 seconds (8514.94 seconds total)