Starting phenix.real_space_refine on Wed May 28 17:03:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.map" model { file = "/net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vye_43658/05_2025/8vye_43658.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.064 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 138 5.16 5 C 18702 2.51 5 N 5868 2.21 5 O 6432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31140 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 494 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 102} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 453 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 90} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 574 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 517 Classifications: {'peptide': 126} Incomplete info: {'backbone_only': 105} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 261 Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 446 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 87} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 170 Chain: "H" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 525 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 445 Classifications: {'peptide': 105} Incomplete info: {'backbone_only': 85} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 176 Chain: "E" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7234 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 560 Chain: "E" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Restraints were copied for chains: I, R, K, O, M, T, F, P, N, U, J, S, G, Q Time building chain proxies: 21.77, per 1000 atoms: 0.70 Number of scatterers: 31140 At special positions: 0 Unit cell: (203.163, 193.89, 190.518, 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 138 16.00 O 6432 8.00 N 5868 7.00 C 18702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 E1301 " - " ASN E 324 " " NAG E1302 " - " ASN E 596 " " NAG E1303 " - " ASN E 650 " " NAG E1304 " - " ASN E1067 " " NAG E1305 " - " ASN E1091 " " NAG E1306 " - " ASN E1127 " " NAG E1307 " - " ASN E 609 " " NAG E1308 " - " ASN E 702 " " NAG E1309 " - " ASN E 794 " " NAG E1310 " - " ASN E 710 " " NAG E1311 " - " ASN E 336 " " NAG E1312 " - " ASN E 275 " " NAG E1313 " - " ASN E 122 " " NAG E1314 " - " ASN E 165 " " NAG E1315 " - " ASN E 149 " " NAG E1316 " - " ASN E 17 " " NAG E1317 " - " ASN E 234 " " NAG E1318 " - " ASN E 246 " " NAG E1319 " - " ASN E 61 " " NAG K1301 " - " ASN K 324 " " NAG K1302 " - " ASN K 596 " " NAG K1303 " - " ASN K 650 " " NAG K1304 " - " ASN K1067 " " NAG K1305 " - " ASN K1091 " " NAG K1306 " - " ASN K1127 " " NAG K1307 " - " ASN K 609 " " NAG K1308 " - " ASN K 702 " " NAG K1309 " - " ASN K 794 " " NAG K1310 " - " ASN K 710 " " NAG K1311 " - " ASN K 336 " " NAG K1312 " - " ASN K 275 " " NAG K1313 " - " ASN K 122 " " NAG K1314 " - " ASN K 165 " " NAG K1315 " - " ASN K 149 " " NAG K1316 " - " ASN K 17 " " NAG K1317 " - " ASN K 234 " " NAG K1318 " - " ASN K 246 " " NAG K1319 " - " ASN K 61 " " NAG O1301 " - " ASN O 324 " " NAG O1302 " - " ASN O 596 " " NAG O1303 " - " ASN O 650 " " NAG O1304 " - " ASN O1067 " " NAG O1305 " - " ASN O1091 " " NAG O1306 " - " ASN O1127 " " NAG O1307 " - " ASN O 609 " " NAG O1308 " - " ASN O 702 " " NAG O1309 " - " ASN O 794 " " NAG O1310 " - " ASN O 710 " " NAG O1311 " - " ASN O 336 " " NAG O1312 " - " ASN O 275 " " NAG O1313 " - " ASN O 122 " " NAG O1314 " - " ASN O 165 " " NAG O1315 " - " ASN O 149 " " NAG O1316 " - " ASN O 17 " " NAG O1317 " - " ASN O 234 " " NAG O1318 " - " ASN O 246 " " NAG O1319 " - " ASN O 61 " Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 4.4 seconds 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 78 sheets defined 18.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 331 through 336 Processing helix chain 'K' and resid 342 through 346 removed outlier: 3.663A pdb=" N TRP K 346 " --> pdb=" O VAL K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN K 381 " --> pdb=" O THR K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 403 removed outlier: 3.910A pdb=" N ARG K 401 " --> pdb=" O ASP K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 409 through 415 Processing helix chain 'K' and resid 431 through 436 removed outlier: 3.747A pdb=" N SER K 436 " --> pdb=" O ASN K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 498 Processing helix chain 'K' and resid 609 through 613 Processing helix chain 'K' and resid 730 through 737 Processing helix chain 'K' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU K 747 " --> pdb=" O SER K 743 " (cutoff:3.500A) Processing helix chain 'K' and resid 748 through 750 No H-bonds generated for 'chain 'K' and resid 748 through 750' Processing helix chain 'K' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP K 768 " --> pdb=" O ALA K 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL K 774 " --> pdb=" O ASN K 770 " (cutoff:3.500A) Processing helix chain 'K' and resid 809 through 819 Processing helix chain 'K' and resid 846 through 849 Processing helix chain 'K' and resid 859 through 878 Processing helix chain 'K' and resid 879 through 883 Processing helix chain 'K' and resid 890 through 901 Processing helix chain 'K' and resid 905 through 911 removed outlier: 4.209A pdb=" N LEU K 909 " --> pdb=" O THR K 905 " (cutoff:3.500A) Processing helix chain 'K' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE K 927 " --> pdb=" O ALA K 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN K 928 " --> pdb=" O ILE K 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP K 929 " --> pdb=" O GLY K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL K 944 " --> pdb=" O LYS K 940 " (cutoff:3.500A) Processing helix chain 'K' and resid 959 through 961 No H-bonds generated for 'chain 'K' and resid 959 through 961' Processing helix chain 'K' and resid 969 through 977 Processing helix chain 'K' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL K 984 " --> pdb=" O PRO K 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG K 988 " --> pdb=" O VAL K 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.883A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.663A pdb=" N TRP E 346 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN E 381 " --> pdb=" O THR E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 403 removed outlier: 3.910A pdb=" N ARG E 401 " --> pdb=" O ASP E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 415 Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.746A pdb=" N SER E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 Processing helix chain 'E' and resid 609 through 613 Processing helix chain 'E' and resid 730 through 737 Processing helix chain 'E' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU E 747 " --> pdb=" O SER E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 750 No H-bonds generated for 'chain 'E' and resid 748 through 750' Processing helix chain 'E' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP E 768 " --> pdb=" O ALA E 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 774 " --> pdb=" O ASN E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 819 Processing helix chain 'E' and resid 846 through 849 Processing helix chain 'E' and resid 859 through 878 Processing helix chain 'E' and resid 879 through 883 Processing helix chain 'E' and resid 890 through 901 Processing helix chain 'E' and resid 905 through 911 removed outlier: 4.209A pdb=" N LEU E 909 " --> pdb=" O THR E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE E 927 " --> pdb=" O ALA E 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN E 928 " --> pdb=" O ILE E 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP E 929 " --> pdb=" O GLY E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL E 944 " --> pdb=" O LYS E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 961 No H-bonds generated for 'chain 'E' and resid 959 through 961' Processing helix chain 'E' and resid 969 through 977 Processing helix chain 'E' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL E 984 " --> pdb=" O PRO E 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 988 " --> pdb=" O VAL E 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.882A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'O' and resid 287 through 296 Processing helix chain 'O' and resid 331 through 336 Processing helix chain 'O' and resid 342 through 346 removed outlier: 3.664A pdb=" N TRP O 346 " --> pdb=" O VAL O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 363 Processing helix chain 'O' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN O 381 " --> pdb=" O THR O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 403 removed outlier: 3.909A pdb=" N ARG O 401 " --> pdb=" O ASP O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'O' and resid 431 through 436 removed outlier: 3.747A pdb=" N SER O 436 " --> pdb=" O ASN O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 498 Processing helix chain 'O' and resid 609 through 613 Processing helix chain 'O' and resid 730 through 737 Processing helix chain 'O' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU O 747 " --> pdb=" O SER O 743 " (cutoff:3.500A) Processing helix chain 'O' and resid 748 through 750 No H-bonds generated for 'chain 'O' and resid 748 through 750' Processing helix chain 'O' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP O 768 " --> pdb=" O ALA O 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 774 " --> pdb=" O ASN O 770 " (cutoff:3.500A) Processing helix chain 'O' and resid 809 through 819 Processing helix chain 'O' and resid 846 through 849 Processing helix chain 'O' and resid 859 through 878 Processing helix chain 'O' and resid 879 through 883 Processing helix chain 'O' and resid 890 through 901 Processing helix chain 'O' and resid 905 through 911 removed outlier: 4.210A pdb=" N LEU O 909 " --> pdb=" O THR O 905 " (cutoff:3.500A) Processing helix chain 'O' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE O 927 " --> pdb=" O ALA O 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN O 928 " --> pdb=" O ILE O 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP O 929 " --> pdb=" O GLY O 925 " (cutoff:3.500A) Processing helix chain 'O' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL O 944 " --> pdb=" O LYS O 940 " (cutoff:3.500A) Processing helix chain 'O' and resid 959 through 961 No H-bonds generated for 'chain 'O' and resid 959 through 961' Processing helix chain 'O' and resid 969 through 977 Processing helix chain 'O' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL O 984 " --> pdb=" O PRO O 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG O 988 " --> pdb=" O VAL O 984 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.882A pdb=" N TYR R 32 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'S' and resid 30 through 32 No H-bonds generated for 'chain 'S' and resid 30 through 32' Processing helix chain 'T' and resid 65 through 67 No H-bonds generated for 'chain 'T' and resid 65 through 67' Processing helix chain 'T' and resid 88 through 92 Processing helix chain 'U' and resid 26 through 30 Processing helix chain 'U' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'K' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN K 61 " --> pdb=" O TYR K 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR K 262 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA K 257 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR K 95 " --> pdb=" O ALA K 257 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN K 188 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP K 280 " --> pdb=" O LYS K 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 84 through 85 current: chain 'K' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL K 126 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU K 169 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 11.400A pdb=" N ILE K 128 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR K 167 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL K 130 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN K 165 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU K 132 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA K 163 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 134 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL K 159 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASP K 138 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N PHE K 157 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 12.480A pdb=" N PHE K 140 " --> pdb=" O SER K 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER K 155 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY K 142 " --> pdb=" O MET K 153 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET K 153 " --> pdb=" O GLY K 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 152 through 172 current: chain 'K' and resid 250 through 252 Processing sheet with id=AA4, first strand: chain 'K' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL K 588 " --> pdb=" O THR K 308 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN K 310 " --> pdb=" O GLY K 586 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY K 586 " --> pdb=" O ASN K 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY K 587 " --> pdb=" O GLN K 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 317 through 318 removed outlier: 6.688A pdb=" N GLU K 317 " --> pdb=" O ASN K 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN K 535 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP K 567 " --> pdb=" O ILE K 580 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA K 568 " --> pdb=" O GLY K 559 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 347 through 351 Processing sheet with id=AA7, first strand: chain 'K' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS K 354 " --> pdb=" O CYS K 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 445 through 447 Processing sheet with id=AA9, first strand: chain 'K' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE K 663 " --> pdb=" O ILE K 659 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 695 through 697 removed outlier: 3.831A pdb=" N LYS O 783 " --> pdb=" O ASN K 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 704 through 721 current: chain 'K' and resid 1052 through 1071 removed outlier: 3.746A pdb=" N ALA K1071 " --> pdb=" O PHE K1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE K1088 " --> pdb=" O ALA K1071 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 726 through 729 removed outlier: 4.347A pdb=" N LYS K 726 " --> pdb=" O LEU K 854 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 781 through 783 removed outlier: 5.738A pdb=" N ILE K 781 " --> pdb=" O ASN E 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'K' and resid 1113 through 1118 removed outlier: 4.729A pdb=" N ALA K1080 " --> pdb=" O SER K1116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 60 current: chain 'B' and resid 111 through 112 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 53 through 54 current: chain 'C' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'A' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 10 through 12 current: chain 'A' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 60 current: chain 'A' and resid 114 through 115 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 46 through 50 removed outlier: 3.526A pdb=" N SER D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 55 current: chain 'D' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU H 108 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 11 current: chain 'L' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 47 current: chain 'L' and resid 94 through 97 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN E 61 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR E 262 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA E 257 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR E 95 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP E 280 " --> pdb=" O LYS E 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 85 current: chain 'E' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL E 126 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU E 169 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ILE E 128 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR E 167 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 130 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN E 165 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU E 132 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA E 163 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASP E 138 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 10.973A pdb=" N PHE E 157 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 12.480A pdb=" N PHE E 140 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER E 155 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY E 142 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET E 153 " --> pdb=" O GLY E 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 152 through 172 current: chain 'E' and resid 250 through 252 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL E 588 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN E 310 " --> pdb=" O GLY E 586 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY E 586 " --> pdb=" O ASN E 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY E 587 " --> pdb=" O GLN E 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.689A pdb=" N GLU E 317 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN E 535 " --> pdb=" O GLU E 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP E 567 " --> pdb=" O ILE E 580 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA E 568 " --> pdb=" O GLY E 559 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 351 Processing sheet with id=AD7, first strand: chain 'E' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS E 354 " --> pdb=" O CYS E 518 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 445 through 447 Processing sheet with id=AD9, first strand: chain 'E' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE E 663 " --> pdb=" O ILE E 659 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 704 through 721 current: chain 'E' and resid 1052 through 1071 removed outlier: 3.745A pdb=" N ALA E1071 " --> pdb=" O PHE E1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E1088 " --> pdb=" O ALA E1071 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 726 through 729 removed outlier: 4.347A pdb=" N LYS E 726 " --> pdb=" O LEU E 854 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 781 through 783 removed outlier: 5.738A pdb=" N ILE E 781 " --> pdb=" O ASN O 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 1113 through 1118 removed outlier: 4.730A pdb=" N ALA E1080 " --> pdb=" O SER E1116 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'F' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 12 current: chain 'F' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 60 current: chain 'F' and resid 111 through 112 Processing sheet with id=AE7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 13 current: chain 'G' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 53 through 54 current: chain 'G' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 60 current: chain 'I' and resid 114 through 115 Processing sheet with id=AF2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 46 through 50 removed outlier: 3.526A pdb=" N SER J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 55 current: chain 'J' and resid 97 through 98 Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG M 40 " --> pdb=" O TRP M 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP M 49 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU M 108 " --> pdb=" O TRP M 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 11 current: chain 'N' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 47 current: chain 'N' and resid 94 through 97 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'O' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN O 61 " --> pdb=" O TYR O 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR O 262 " --> pdb=" O ASN O 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA O 257 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR O 95 " --> pdb=" O ALA O 257 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN O 188 " --> pdb=" O GLU O 96 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE O 201 " --> pdb=" O ASP O 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP O 228 " --> pdb=" O PHE O 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE O 203 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS O 207 " --> pdb=" O ALA O 222 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ALA O 222 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL O 36 " --> pdb=" O LEU O 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP O 280 " --> pdb=" O LYS O 271 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 84 through 85 current: chain 'O' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL O 126 " --> pdb=" O GLU O 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU O 169 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ILE O 128 " --> pdb=" O THR O 167 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR O 167 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL O 130 " --> pdb=" O ASN O 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN O 165 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU O 132 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA O 163 " --> pdb=" O GLU O 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN O 134 " --> pdb=" O SER O 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL O 159 " --> pdb=" O CYS O 136 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ASP O 138 " --> pdb=" O PHE O 157 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N PHE O 157 " --> pdb=" O ASP O 138 " (cutoff:3.500A) removed outlier: 12.479A pdb=" N PHE O 140 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER O 155 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY O 142 " --> pdb=" O MET O 153 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET O 153 " --> pdb=" O GLY O 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 152 through 172 current: chain 'O' and resid 250 through 252 Processing sheet with id=AG3, first strand: chain 'O' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL O 588 " --> pdb=" O THR O 308 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN O 310 " --> pdb=" O GLY O 586 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY O 586 " --> pdb=" O ASN O 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY O 587 " --> pdb=" O GLN O 606 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 317 through 318 removed outlier: 6.689A pdb=" N GLU O 317 " --> pdb=" O ASN O 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN O 535 " --> pdb=" O GLU O 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP O 567 " --> pdb=" O ILE O 580 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA O 568 " --> pdb=" O GLY O 559 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 347 through 351 Processing sheet with id=AG6, first strand: chain 'O' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS O 354 " --> pdb=" O CYS O 518 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 445 through 447 Processing sheet with id=AG8, first strand: chain 'O' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE O 663 " --> pdb=" O ILE O 659 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 704 through 721 current: chain 'O' and resid 1052 through 1071 removed outlier: 3.745A pdb=" N ALA O1071 " --> pdb=" O PHE O1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE O1088 " --> pdb=" O ALA O1071 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 726 through 729 removed outlier: 4.348A pdb=" N LYS O 726 " --> pdb=" O LEU O 854 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 1113 through 1118 removed outlier: 4.729A pdb=" N ALA O1080 " --> pdb=" O SER O1116 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AH4, first strand: chain 'P' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 11 through 12 current: chain 'P' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 58 through 60 current: chain 'P' and resid 111 through 112 Processing sheet with id=AH5, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'Q' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 13 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AH7, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 58 through 60 current: chain 'R' and resid 114 through 115 Processing sheet with id=AH9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'S' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 12 current: chain 'S' and resid 46 through 50 removed outlier: 3.525A pdb=" N SER S 54 " --> pdb=" O TYR S 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 54 through 55 current: chain 'S' and resid 97 through 98 Processing sheet with id=AI2, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'T' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG T 40 " --> pdb=" O TRP T 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP T 49 " --> pdb=" O ARG T 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU T 108 " --> pdb=" O TRP T 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 9 through 11 current: chain 'U' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 44 through 47 current: chain 'U' and resid 94 through 97 No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'U' and resid 18 through 23 1333 hydrogen bonds defined for protein. 3423 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: 19.32 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9801 1.33 - 1.46: 6052 1.46 - 1.58: 15668 1.58 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 31683 Sorted by residual: bond pdb=" N VAL E 143 " pdb=" CA VAL E 143 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.65e+00 bond pdb=" CA PRO K 979 " pdb=" C PRO K 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.58e+00 bond pdb=" N VAL O 143 " pdb=" CA VAL O 143 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.55e+00 bond pdb=" CA PRO E 979 " pdb=" C PRO E 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.53e+00 bond pdb=" CA PRO O 979 " pdb=" C PRO O 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.42e+00 ... (remaining 31678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 36818 1.65 - 3.29: 4666 3.29 - 4.94: 524 4.94 - 6.58: 360 6.58 - 8.23: 220 Bond angle restraints: 42588 Sorted by residual: angle pdb=" C GLN U 6 " pdb=" N PRO U 7 " pdb=" CA PRO U 7 " ideal model delta sigma weight residual 119.66 126.75 -7.09 7.30e-01 1.88e+00 9.43e+01 angle pdb=" C GLN N 6 " pdb=" N PRO N 7 " pdb=" CA PRO N 7 " ideal model delta sigma weight residual 119.66 126.74 -7.08 7.30e-01 1.88e+00 9.41e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.72 -7.06 7.30e-01 1.88e+00 9.34e+01 angle pdb=" C LEU K 854 " pdb=" N PRO K 855 " pdb=" CA PRO K 855 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.05e+01 angle pdb=" C LEU E 854 " pdb=" N PRO E 855 " pdb=" CA PRO E 855 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.04e+01 ... (remaining 42583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16430 17.64 - 35.27: 304 35.27 - 52.91: 63 52.91 - 70.55: 42 70.55 - 88.19: 9 Dihedral angle restraints: 16848 sinusoidal: 5523 harmonic: 11325 Sorted by residual: dihedral pdb=" CA THR E 592 " pdb=" C THR E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA THR K 592 " pdb=" C THR K 592 " pdb=" N PRO K 593 " pdb=" CA PRO K 593 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA THR O 592 " pdb=" C THR O 592 " pdb=" N PRO O 593 " pdb=" CA PRO O 593 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 16845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3054 0.070 - 0.141: 711 0.141 - 0.211: 201 0.211 - 0.281: 54 0.281 - 0.352: 33 Chirality restraints: 4053 Sorted by residual: chirality pdb=" C2 NAG O1304 " pdb=" C1 NAG O1304 " pdb=" C3 NAG O1304 " pdb=" N2 NAG O1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2 NAG E1304 " pdb=" C1 NAG E1304 " pdb=" C3 NAG E1304 " pdb=" N2 NAG E1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C2 NAG K1304 " pdb=" C1 NAG K1304 " pdb=" C3 NAG K1304 " pdb=" N2 NAG K1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4050 not shown) Planarity restraints: 6294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 61 " 0.040 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN K 61 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN K 61 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 61 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG K1319 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 61 " -0.040 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN O 61 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN O 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN O 61 " 0.060 2.00e-02 2.50e+03 pdb=" C1 NAG O1319 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 61 " 0.040 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" CG ASN E 61 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 61 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 61 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG E1319 " 0.048 2.00e-02 2.50e+03 ... (remaining 6291 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 24908 3.17 - 3.75: 40651 3.75 - 4.32: 58907 4.32 - 4.90: 94181 Nonbonded interactions: 218707 Sorted by model distance: nonbonded pdb=" SG CYS O 531 " pdb=" SG CYS O 583 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS K 531 " pdb=" SG CYS K 583 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS E 531 " pdb=" SG CYS E 583 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS O 284 " pdb=" SG CYS O 294 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS E 284 " pdb=" SG CYS E 294 " model vdw 2.019 3.760 ... (remaining 218702 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: 0.29 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'T' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'U' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'Q' } 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: 8.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 81.220 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 0.084 31740 Z= 0.529 Angle : 1.317 8.229 42759 Z= 0.897 Chirality : 0.075 0.352 4053 Planarity : 0.005 0.022 6237 Dihedral : 8.857 88.187 10752 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 5094 helix: 0.36 (0.19), residues: 666 sheet: 1.12 (0.12), residues: 1644 loop : 0.29 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP K 879 HIS 0.002 0.001 HIS K 648 PHE 0.019 0.003 PHE K 891 TYR 0.033 0.004 TYR K1060 ARG 0.003 0.000 ARG E1012 Details of bonding type rmsd link_NAG-ASN : bond 0.05538 ( 57) link_NAG-ASN : angle 2.41414 ( 171) hydrogen bonds : bond 0.18206 ( 1333) hydrogen bonds : angle 7.92002 ( 3423) covalent geometry : bond 0.00894 (31683) covalent geometry : angle 1.31041 (42588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 3.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 1.1779 time to fit residues: 516.3259 Evaluate side-chains 195 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 0.5980 chunk 384 optimal weight: 40.0000 chunk 213 optimal weight: 50.0000 chunk 131 optimal weight: 0.0000 chunk 259 optimal weight: 0.7980 chunk 205 optimal weight: 40.0000 chunk 397 optimal weight: 0.8980 chunk 153 optimal weight: 0.0470 chunk 241 optimal weight: 0.7980 chunk 295 optimal weight: 0.0970 chunk 460 optimal weight: 50.0000 overall best weight: 0.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 634 ASN K 648 HIS K 894 GLN K1118 ASN E 30 ASN E 121 ASN E 651 ASN E 894 GLN E 928 GLN O 30 ASN O 648 HIS O 651 ASN O 748 GLN O 894 GLN O1118 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.245364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.199114 restraints weight = 38006.677| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.80 r_work: 0.3642 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31740 Z= 0.115 Angle : 0.559 13.465 42759 Z= 0.282 Chirality : 0.047 0.406 4053 Planarity : 0.004 0.040 6237 Dihedral : 4.497 57.854 6486 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.08 % Allowed : 5.62 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.12), residues: 5094 helix: 2.27 (0.21), residues: 609 sheet: 0.96 (0.12), residues: 1725 loop : 0.66 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 879 HIS 0.008 0.001 HIS E 648 PHE 0.016 0.001 PHE K 192 TYR 0.015 0.001 TYR E 258 ARG 0.008 0.001 ARG K 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 57) link_NAG-ASN : angle 3.19353 ( 171) hydrogen bonds : bond 0.05286 ( 1333) hydrogen bonds : angle 5.63360 ( 3423) covalent geometry : bond 0.00223 (31683) covalent geometry : angle 0.52194 (42588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7743 (mtmt) REVERT: K 237 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7014 (mtm180) REVERT: K 733 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7197 (tmm) REVERT: K 745 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8235 (mp) REVERT: K 976 ARG cc_start: 0.7193 (mtt90) cc_final: 0.6908 (ttm-80) REVERT: K 1003 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8642 (pp30) REVERT: K 1131 TYR cc_start: 0.7745 (t80) cc_final: 0.7251 (t80) REVERT: E 202 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.6970 (mmpt) REVERT: E 307 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: E 733 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: E 748 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: E 773 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8421 (mm-30) REVERT: O 202 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.6895 (mmpt) REVERT: O 237 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7440 (mtm180) REVERT: O 307 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: O 733 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7147 (tmm) REVERT: O 1131 TYR cc_start: 0.7766 (t80) cc_final: 0.7369 (t80) outliers start: 44 outliers final: 10 residues processed: 252 average time/residue: 1.0881 time to fit residues: 339.6335 Evaluate side-chains 229 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 609 ASN Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 740 THR Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 1003 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 609 ASN Chi-restraints excluded: chain E residue 733 MET Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 609 ASN Chi-restraints excluded: chain O residue 733 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 424 optimal weight: 0.2980 chunk 337 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 chunk 501 optimal weight: 50.0000 chunk 242 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 390 optimal weight: 5.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 537 ASN O 121 ASN O 748 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.243244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.197559 restraints weight = 37904.022| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.79 r_work: 0.3600 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31740 Z= 0.121 Angle : 0.518 10.303 42759 Z= 0.261 Chirality : 0.047 0.415 4053 Planarity : 0.004 0.044 6237 Dihedral : 4.161 55.289 6486 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.17 % Allowed : 7.46 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 5094 helix: 2.11 (0.21), residues: 633 sheet: 1.04 (0.12), residues: 1734 loop : 0.67 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 879 HIS 0.005 0.001 HIS E 648 PHE 0.012 0.002 PHE O1114 TYR 0.016 0.002 TYR K1060 ARG 0.004 0.000 ARG E 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 57) link_NAG-ASN : angle 2.57280 ( 171) hydrogen bonds : bond 0.05254 ( 1333) hydrogen bonds : angle 5.09230 ( 3423) covalent geometry : bond 0.00271 (31683) covalent geometry : angle 0.49277 (42588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 3.423 Fit side-chains REVERT: K 202 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7047 (mmpt) REVERT: K 733 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7314 (tmm) REVERT: K 745 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8339 (mp) REVERT: K 748 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: E 53 ASP cc_start: 0.7563 (t0) cc_final: 0.7339 (t0) REVERT: E 202 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7075 (mmpt) REVERT: E 229 LEU cc_start: 0.6670 (mt) cc_final: 0.6460 (mt) REVERT: E 307 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: E 733 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7372 (tmm) REVERT: E 748 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: E 773 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8538 (mm-30) REVERT: O 202 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.6938 (mmpt) REVERT: O 229 LEU cc_start: 0.6432 (mp) cc_final: 0.6150 (mt) REVERT: O 237 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7422 (mtm180) REVERT: O 307 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: O 532 VAL cc_start: 0.8339 (p) cc_final: 0.8125 (m) REVERT: O 733 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: O 748 GLN cc_start: 0.8223 (mt0) cc_final: 0.7967 (mm-40) REVERT: O 1131 TYR cc_start: 0.7902 (t80) cc_final: 0.7551 (t80) outliers start: 46 outliers final: 17 residues processed: 250 average time/residue: 1.0517 time to fit residues: 326.5284 Evaluate side-chains 244 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 537 ASN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 748 GLN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 733 MET Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 33 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 460 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 394 optimal weight: 0.7980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 537 ASN E1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.241338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.195348 restraints weight = 37881.144| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.77 r_work: 0.3564 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31740 Z= 0.159 Angle : 0.552 10.450 42759 Z= 0.274 Chirality : 0.050 0.617 4053 Planarity : 0.004 0.040 6237 Dihedral : 4.245 54.865 6486 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.64 % Allowed : 7.55 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.12), residues: 5094 helix: 1.90 (0.21), residues: 642 sheet: 1.06 (0.12), residues: 1761 loop : 0.62 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 879 HIS 0.006 0.001 HIS E 648 PHE 0.027 0.002 PHE K 536 TYR 0.018 0.002 TYR E 258 ARG 0.005 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 57) link_NAG-ASN : angle 2.61607 ( 171) hydrogen bonds : bond 0.05639 ( 1333) hydrogen bonds : angle 4.96232 ( 3423) covalent geometry : bond 0.00376 (31683) covalent geometry : angle 0.52796 (42588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 2.682 Fit side-chains REVERT: K 81 ASN cc_start: 0.7320 (m-40) cc_final: 0.6899 (m-40) REVERT: K 202 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7108 (mmpt) REVERT: K 237 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7561 (mtm180) REVERT: K 307 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: K 570 ARG cc_start: 0.6471 (ttm170) cc_final: 0.5632 (ttm170) REVERT: K 733 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7305 (tmm) REVERT: K 745 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (mp) REVERT: K 976 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.6860 (mtm-85) REVERT: E 53 ASP cc_start: 0.7621 (t0) cc_final: 0.7391 (t0) REVERT: E 81 ASN cc_start: 0.7269 (m-40) cc_final: 0.7052 (m-40) REVERT: E 202 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7123 (mmpt) REVERT: E 307 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: E 748 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: O 81 ASN cc_start: 0.7279 (m-40) cc_final: 0.6526 (p0) REVERT: O 202 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.6957 (mmpt) REVERT: O 237 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7435 (mtm180) REVERT: O 307 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: O 532 VAL cc_start: 0.8274 (p) cc_final: 0.8009 (m) REVERT: O 570 ARG cc_start: 0.6618 (ttm170) cc_final: 0.6321 (ttm-80) REVERT: O 733 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7337 (tmm) REVERT: O 748 GLN cc_start: 0.8252 (mt0) cc_final: 0.8019 (mm-40) REVERT: O 950 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: O 1131 TYR cc_start: 0.7988 (t80) cc_final: 0.7615 (t80) outliers start: 56 outliers final: 29 residues processed: 244 average time/residue: 1.0674 time to fit residues: 324.8164 Evaluate side-chains 250 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 950 GLN Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1003 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 414 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 382 optimal weight: 40.0000 chunk 394 optimal weight: 0.0970 chunk 503 optimal weight: 50.0000 chunk 365 optimal weight: 0.7980 chunk 286 optimal weight: 50.0000 chunk 310 optimal weight: 0.0000 chunk 179 optimal weight: 8.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 606 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.243449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.195335 restraints weight = 37786.529| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.82 r_work: 0.3599 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 31740 Z= 0.094 Angle : 0.487 12.429 42759 Z= 0.237 Chirality : 0.046 0.618 4053 Planarity : 0.004 0.036 6237 Dihedral : 4.020 54.885 6486 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.12 % Allowed : 8.07 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.12), residues: 5094 helix: 2.32 (0.21), residues: 624 sheet: 1.18 (0.13), residues: 1704 loop : 0.64 (0.12), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 879 HIS 0.004 0.001 HIS E 648 PHE 0.014 0.001 PHE E 65 TYR 0.016 0.001 TYR E 653 ARG 0.003 0.000 ARG K 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 57) link_NAG-ASN : angle 2.71285 ( 171) hydrogen bonds : bond 0.04489 ( 1333) hydrogen bonds : angle 4.66094 ( 3423) covalent geometry : bond 0.00194 (31683) covalent geometry : angle 0.45636 (42588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 3.152 Fit side-chains REVERT: K 52 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7018 (tm-30) REVERT: K 65 PHE cc_start: 0.8300 (m-80) cc_final: 0.7938 (m-80) REVERT: K 81 ASN cc_start: 0.7362 (m-40) cc_final: 0.6948 (m-40) REVERT: K 307 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: K 653 TYR cc_start: 0.8862 (m-80) cc_final: 0.8642 (m-80) REVERT: K 733 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: K 745 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8276 (mp) REVERT: E 53 ASP cc_start: 0.7536 (t0) cc_final: 0.7314 (t0) REVERT: E 202 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7084 (mmpt) REVERT: E 307 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: E 748 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: E 773 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8473 (mm-30) REVERT: O 81 ASN cc_start: 0.7209 (m-40) cc_final: 0.6435 (p0) REVERT: O 202 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.6921 (mmpt) REVERT: O 229 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6024 (mt) REVERT: O 237 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7347 (mtm180) REVERT: O 307 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: O 532 VAL cc_start: 0.8227 (p) cc_final: 0.7941 (m) REVERT: O 584 SER cc_start: 0.7351 (t) cc_final: 0.7018 (p) REVERT: O 733 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: O 1131 TYR cc_start: 0.7922 (t80) cc_final: 0.7540 (t80) outliers start: 45 outliers final: 14 residues processed: 247 average time/residue: 1.0607 time to fit residues: 326.1384 Evaluate side-chains 239 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 359 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 chunk 318 optimal weight: 50.0000 chunk 441 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 334 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 335 optimal weight: 50.0000 chunk 253 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 66 HIS K1128 ASN E 66 HIS E 634 ASN O 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.236910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201275 restraints weight = 37248.522| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.87 r_work: 0.3986 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.121 31740 Z= 0.464 Angle : 0.855 12.482 42759 Z= 0.433 Chirality : 0.066 0.544 4053 Planarity : 0.006 0.068 6237 Dihedral : 5.320 52.725 6486 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 7.46 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.12), residues: 5094 helix: 0.77 (0.20), residues: 627 sheet: 0.82 (0.12), residues: 1749 loop : 0.23 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP K 104 HIS 0.011 0.003 HIS K1051 PHE 0.036 0.005 PHE E 816 TYR 0.029 0.004 TYR E 258 ARG 0.014 0.002 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 57) link_NAG-ASN : angle 3.27246 ( 171) hydrogen bonds : bond 0.08504 ( 1333) hydrogen bonds : angle 5.42639 ( 3423) covalent geometry : bond 0.01153 (31683) covalent geometry : angle 0.83083 (42588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 3.150 Fit side-chains REVERT: K 307 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8386 (tp40) REVERT: K 733 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7394 (tmm) REVERT: E 52 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7558 (tm-30) REVERT: E 81 ASN cc_start: 0.6754 (m-40) cc_final: 0.6520 (p0) REVERT: E 307 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: O 307 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: O 733 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7394 (tmm) REVERT: O 849 ASN cc_start: 0.8035 (m-40) cc_final: 0.7610 (m110) REVERT: O 943 ASP cc_start: 0.8075 (m-30) cc_final: 0.7827 (m-30) outliers start: 77 outliers final: 34 residues processed: 265 average time/residue: 0.9430 time to fit residues: 318.0752 Evaluate side-chains 245 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 1036 CYS Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 1003 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 495 optimal weight: 50.0000 chunk 322 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 482 optimal weight: 50.0000 chunk 371 optimal weight: 6.9990 chunk 486 optimal weight: 5.9990 chunk 431 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 537 ASN O 606 GLN O1128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.237876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201071 restraints weight = 37180.745| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.99 r_work: 0.3989 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 31740 Z= 0.286 Angle : 0.699 13.184 42759 Z= 0.349 Chirality : 0.056 0.631 4053 Planarity : 0.005 0.058 6237 Dihedral : 5.058 54.507 6486 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.26 % Allowed : 8.31 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.12), residues: 5094 helix: 0.96 (0.20), residues: 633 sheet: 0.72 (0.12), residues: 1749 loop : 0.19 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 104 HIS 0.007 0.002 HIS E 648 PHE 0.027 0.003 PHE E 65 TYR 0.034 0.003 TYR K1131 ARG 0.009 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 57) link_NAG-ASN : angle 3.43637 ( 171) hydrogen bonds : bond 0.06993 ( 1333) hydrogen bonds : angle 5.13996 ( 3423) covalent geometry : bond 0.00706 (31683) covalent geometry : angle 0.66551 (42588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 217 time to evaluate : 3.179 Fit side-chains REVERT: K 237 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7414 (mtm180) REVERT: K 307 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (tp40) REVERT: K 733 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7427 (tmm) REVERT: K 976 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7327 (mtm-85) REVERT: E 52 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 229 LEU cc_start: 0.6852 (mt) cc_final: 0.6511 (mt) REVERT: E 307 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: O 202 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8125 (mtmt) REVERT: O 307 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: O 733 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7403 (tmm) REVERT: O 849 ASN cc_start: 0.8140 (m-40) cc_final: 0.7780 (m110) REVERT: O 943 ASP cc_start: 0.8059 (m-30) cc_final: 0.7818 (m-30) outliers start: 69 outliers final: 39 residues processed: 260 average time/residue: 1.0071 time to fit residues: 328.6781 Evaluate side-chains 246 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 354 CYS Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 953 ASN Chi-restraints excluded: chain E residue 1036 CYS Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 354 CYS Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1003 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 234 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 457 optimal weight: 0.0270 chunk 415 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 chunk 163 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 995 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.240474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.203818 restraints weight = 37656.239| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.95 r_work: 0.4015 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31740 Z= 0.112 Angle : 0.534 11.287 42759 Z= 0.261 Chirality : 0.047 0.488 4053 Planarity : 0.004 0.057 6237 Dihedral : 4.472 57.690 6486 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.08 % Allowed : 9.82 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 5094 helix: 1.90 (0.20), residues: 615 sheet: 0.88 (0.12), residues: 1737 loop : 0.36 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 879 HIS 0.003 0.001 HIS E 648 PHE 0.016 0.001 PHE K1114 TYR 0.026 0.001 TYR K1131 ARG 0.003 0.001 ARG O 976 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 57) link_NAG-ASN : angle 2.85865 ( 171) hydrogen bonds : bond 0.04965 ( 1333) hydrogen bonds : angle 4.74738 ( 3423) covalent geometry : bond 0.00251 (31683) covalent geometry : angle 0.50340 (42588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 3.533 Fit side-chains REVERT: K 653 TYR cc_start: 0.8780 (m-80) cc_final: 0.8535 (m-80) REVERT: K 733 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7413 (tmm) REVERT: K 976 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7245 (mmm-85) REVERT: E 52 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7595 (tm-30) REVERT: E 81 ASN cc_start: 0.6163 (m-40) cc_final: 0.5933 (p0) REVERT: E 229 LEU cc_start: 0.6828 (mt) cc_final: 0.6562 (mt) REVERT: E 307 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: E 724 MET cc_start: 0.8667 (mtm) cc_final: 0.8351 (mtp) REVERT: O 307 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: O 733 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7416 (tmm) outliers start: 44 outliers final: 20 residues processed: 234 average time/residue: 1.0105 time to fit residues: 298.1887 Evaluate side-chains 221 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 1036 CYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 1003 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 chunk 447 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 chunk 331 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 173 optimal weight: 0.4980 chunk 345 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 919 GLN E 207 HIS E1128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.237254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201111 restraints weight = 37070.342| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.90 r_work: 0.3713 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 31740 Z= 0.346 Angle : 0.752 18.512 42759 Z= 0.376 Chirality : 0.059 0.593 4053 Planarity : 0.005 0.075 6237 Dihedral : 5.187 55.291 6486 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.22 % Allowed : 10.10 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5094 helix: 1.03 (0.20), residues: 645 sheet: 0.74 (0.12), residues: 1743 loop : 0.12 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP O 104 HIS 0.008 0.002 HIS E 648 PHE 0.028 0.004 PHE E 816 TYR 0.032 0.003 TYR K1131 ARG 0.011 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 57) link_NAG-ASN : angle 3.54664 ( 171) hydrogen bonds : bond 0.07531 ( 1333) hydrogen bonds : angle 5.14069 ( 3423) covalent geometry : bond 0.00861 (31683) covalent geometry : angle 0.71958 (42588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 3.306 Fit side-chains revert: symmetry clash REVERT: K 237 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7618 (mtm180) REVERT: K 307 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8503 (tp40) REVERT: K 718 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: K 733 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: E 52 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 118 LEU cc_start: 0.8370 (tt) cc_final: 0.8098 (tp) REVERT: E 135 PHE cc_start: 0.7584 (m-80) cc_final: 0.7261 (m-80) REVERT: E 307 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: E 977 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7875 (mp) REVERT: O 307 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: O 733 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7343 (tmm) outliers start: 47 outliers final: 29 residues processed: 231 average time/residue: 0.9634 time to fit residues: 282.7770 Evaluate side-chains 235 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 718 GLU Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 354 CYS Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 953 ASN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1036 CYS Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR Chi-restraints excluded: chain O residue 1003 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 225 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 437 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 232 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 201 optimal weight: 30.0000 chunk 155 optimal weight: 50.0000 chunk 59 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 995 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.240422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.203327 restraints weight = 37586.561| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.96 r_work: 0.4014 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31740 Z= 0.113 Angle : 0.541 15.550 42759 Z= 0.264 Chirality : 0.047 0.484 4053 Planarity : 0.004 0.090 6237 Dihedral : 4.540 59.082 6486 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.61 % Allowed : 10.81 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 5094 helix: 1.72 (0.20), residues: 642 sheet: 0.89 (0.13), residues: 1731 loop : 0.35 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 879 HIS 0.003 0.001 HIS E 648 PHE 0.017 0.001 PHE K1114 TYR 0.028 0.001 TYR O 170 ARG 0.003 0.001 ARG K 976 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 57) link_NAG-ASN : angle 3.01230 ( 171) hydrogen bonds : bond 0.04928 ( 1333) hydrogen bonds : angle 4.67583 ( 3423) covalent geometry : bond 0.00252 (31683) covalent geometry : angle 0.50731 (42588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 733 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7471 (tmm) REVERT: K 976 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7310 (mtm-85) REVERT: E 52 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7572 (tm-30) REVERT: E 307 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: E 724 MET cc_start: 0.8684 (mtm) cc_final: 0.8372 (mtp) REVERT: O 307 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: O 733 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7458 (tmm) REVERT: O 976 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7144 (mmm-85) outliers start: 34 outliers final: 23 residues processed: 221 average time/residue: 1.0373 time to fit residues: 294.1254 Evaluate side-chains 227 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 1036 CYS Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 1003 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 419 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 107 optimal weight: 0.0270 chunk 41 optimal weight: 50.0000 chunk 25 optimal weight: 0.7980 chunk 489 optimal weight: 40.0000 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.239095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.202433 restraints weight = 37151.556| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.92 r_work: 0.4018 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31740 Z= 0.183 Angle : 0.593 14.600 42759 Z= 0.293 Chirality : 0.050 0.471 4053 Planarity : 0.004 0.085 6237 Dihedral : 4.643 59.765 6486 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.70 % Allowed : 10.95 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 5094 helix: 1.61 (0.20), residues: 648 sheet: 0.86 (0.13), residues: 1740 loop : 0.35 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 104 HIS 0.005 0.001 HIS E1051 PHE 0.019 0.002 PHE E 891 TYR 0.031 0.002 TYR K1131 ARG 0.006 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 57) link_NAG-ASN : angle 3.01292 ( 171) hydrogen bonds : bond 0.05895 ( 1333) hydrogen bonds : angle 4.73773 ( 3423) covalent geometry : bond 0.00443 (31683) covalent geometry : angle 0.56313 (42588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27364.52 seconds wall clock time: 470 minutes 12.98 seconds (28212.98 seconds total)