Starting phenix.real_space_refine on Thu Jun 26 20:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vye_43658/06_2025/8vye_43658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vye_43658/06_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_43658/06_2025/8vye_43658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vye_43658/06_2025/8vye_43658.map" model { file = "/net/cci-nas-00/data/ceres_data/8vye_43658/06_2025/8vye_43658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vye_43658/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 22.23, per 1000 atoms: 0.71 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: 7.77 Conformation dependent library (CDL) restraints added in 4.8 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: 5.57 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: 16.32 Time building geometry restraints manager: 9.16 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: 0.25 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: 8.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.410 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 82.320 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.250 ------------------------------------------------------------------------------- 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 : 3.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 1.1760 time to fit residues: 516.8559 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 : 3.477 ------------------------------------------------------------------------------- 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 = 0.199113 restraints weight = 38007.187| |-----------------------------------------------------------------------------| 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: 0.3528 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- 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 13.467 42759 Z= 0.282 Chirality : 0.047 0.406 4053 Planarity : 0.004 0.040 6237 Dihedral : 4.497 57.855 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 3.19365 ( 171) hydrogen bonds : bond 0.05286 ( 1333) hydrogen bonds : angle 5.63344 ( 3423) covalent geometry : bond 0.00223 (31683) covalent geometry : angle 0.52195 (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 : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: K 237 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7010 (mtm180) REVERT: K 733 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7198 (tmm) REVERT: K 745 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (mp) REVERT: K 976 ARG cc_start: 0.7193 (mtt90) cc_final: 0.6907 (ttm-80) REVERT: K 1003 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8645 (pp30) REVERT: K 1131 TYR cc_start: 0.7745 (t80) cc_final: 0.7251 (t80) REVERT: E 202 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.6968 (mmpt) REVERT: E 307 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: E 733 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7365 (tmm) REVERT: E 748 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: E 773 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8430 (mm-30) REVERT: O 202 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.6894 (mmpt) REVERT: O 237 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7434 (mtm180) REVERT: O 307 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: O 733 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7148 (tmm) REVERT: O 1131 TYR cc_start: 0.7766 (t80) cc_final: 0.7370 (t80) outliers start: 44 outliers final: 10 residues processed: 252 average time/residue: 1.2407 time to fit residues: 389.4720 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 : 3.412 ------------------------------------------------------------------------------- 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: 0.6980 chunk 337 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 chunk 501 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 390 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 537 ASN E 648 HIS O 121 ASN O 748 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.241632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.197932 restraints weight = 37689.774| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.74 r_work: 0.3573 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31740 Z= 0.184 Angle : 0.585 10.373 42759 Z= 0.296 Chirality : 0.051 0.432 4053 Planarity : 0.004 0.043 6237 Dihedral : 4.429 55.075 6486 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.79 % Allowed : 6.99 % Favored : 90.23 % 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: 1.20 (0.12), residues: 5094 helix: 1.69 (0.21), residues: 642 sheet: 0.94 (0.12), residues: 1791 loop : 0.61 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 879 HIS 0.007 0.001 HIS E 648 PHE 0.020 0.002 PHE E 816 TYR 0.020 0.002 TYR E 258 ARG 0.007 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 57) link_NAG-ASN : angle 2.73072 ( 171) hydrogen bonds : bond 0.06134 ( 1333) hydrogen bonds : angle 5.26072 ( 3423) covalent geometry : bond 0.00444 (31683) covalent geometry : angle 0.56051 (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 277 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 3.122 Fit side-chains REVERT: K 81 ASN cc_start: 0.7380 (m-40) cc_final: 0.6972 (m-40) REVERT: K 202 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7019 (mmpt) REVERT: K 733 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7300 (tmm) REVERT: K 745 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8409 (mp) REVERT: K 748 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: K 950 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: K 976 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6979 (ttm-80) REVERT: E 53 ASP cc_start: 0.7649 (t0) cc_final: 0.7439 (t0) REVERT: E 81 ASN cc_start: 0.7358 (m-40) cc_final: 0.7119 (m-40) REVERT: E 202 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7083 (mmpt) REVERT: E 229 LEU cc_start: 0.6680 (mt) cc_final: 0.6438 (mt) REVERT: E 307 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: E 733 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7420 (tmm) REVERT: E 748 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: O 237 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7471 (mtm180) REVERT: O 307 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: O 532 VAL cc_start: 0.8303 (p) cc_final: 0.8056 (m) REVERT: O 653 TYR cc_start: 0.8847 (m-80) cc_final: 0.8622 (m-80) REVERT: O 733 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7351 (tmm) REVERT: O 748 GLN cc_start: 0.8238 (mt0) cc_final: 0.7981 (mm-40) REVERT: O 950 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: O 1131 TYR cc_start: 0.7977 (t80) cc_final: 0.7595 (t80) outliers start: 59 outliers final: 24 residues processed: 248 average time/residue: 1.1107 time to fit residues: 340.9883 Evaluate side-chains 243 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS 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 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 748 GLN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 950 GLN 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 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 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 733 MET Chi-restraints excluded: chain O residue 950 GLN Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 1003 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 33 optimal weight: 9.9990 chunk 380 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 460 optimal weight: 50.0000 chunk 54 optimal weight: 0.8980 chunk 447 optimal weight: 10.0000 chunk 348 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.240254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194075 restraints weight = 37761.660| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.77 r_work: 0.3543 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31740 Z= 0.197 Angle : 0.595 10.582 42759 Z= 0.296 Chirality : 0.052 0.752 4053 Planarity : 0.004 0.043 6237 Dihedral : 4.484 54.720 6486 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.16 % Allowed : 7.27 % Favored : 89.57 % 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: 1.07 (0.12), residues: 5094 helix: 1.52 (0.20), residues: 645 sheet: 0.93 (0.12), residues: 1770 loop : 0.48 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 879 HIS 0.005 0.001 HIS E1051 PHE 0.020 0.002 PHE E 891 TYR 0.020 0.002 TYR E 258 ARG 0.007 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 57) link_NAG-ASN : angle 2.82661 ( 171) hydrogen bonds : bond 0.06154 ( 1333) hydrogen bonds : angle 5.10386 ( 3423) covalent geometry : bond 0.00477 (31683) covalent geometry : angle 0.56859 (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 284 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 3.283 Fit side-chains REVERT: K 81 ASN cc_start: 0.7389 (m-40) cc_final: 0.6972 (m-40) REVERT: K 202 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7101 (mmpt) REVERT: K 307 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8646 (tp40) REVERT: K 733 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: E 81 ASN cc_start: 0.7337 (m-40) cc_final: 0.7119 (m-40) REVERT: E 202 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7135 (mmpt) REVERT: E 307 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: E 745 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8519 (mp) REVERT: E 748 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: E 977 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7904 (mp) REVERT: O 81 ASN cc_start: 0.7380 (m-40) cc_final: 0.6655 (p0) REVERT: O 307 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: O 733 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7390 (tmm) REVERT: O 748 GLN cc_start: 0.8260 (mt0) cc_final: 0.8017 (mm-40) REVERT: O 849 ASN cc_start: 0.8220 (m-40) cc_final: 0.7943 (m-40) REVERT: O 950 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: O 953 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8148 (t0) outliers start: 67 outliers final: 33 residues processed: 253 average time/residue: 1.0643 time to fit residues: 336.0291 Evaluate side-chains 256 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL 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 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 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 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 745 LEU Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 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 950 GLN Chi-restraints excluded: chain O residue 953 ASN 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: 0.8980 chunk 66 optimal weight: 3.9990 chunk 348 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 382 optimal weight: 30.0000 chunk 394 optimal weight: 0.5980 chunk 503 optimal weight: 50.0000 chunk 365 optimal weight: 0.8980 chunk 286 optimal weight: 50.0000 chunk 310 optimal weight: 0.3980 chunk 179 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 GLN E1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.241541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195062 restraints weight = 37664.955| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.69 r_work: 0.3575 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31740 Z= 0.112 Angle : 0.520 10.728 42759 Z= 0.254 Chirality : 0.047 0.492 4053 Planarity : 0.004 0.039 6237 Dihedral : 4.257 54.825 6486 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.83 % Allowed : 7.51 % Favored : 89.66 % 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: 1.25 (0.12), residues: 5094 helix: 2.05 (0.21), residues: 621 sheet: 1.03 (0.12), residues: 1725 loop : 0.53 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 879 HIS 0.003 0.001 HIS E1051 PHE 0.015 0.001 PHE K1114 TYR 0.016 0.001 TYR E 653 ARG 0.007 0.000 ARG K 976 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 57) link_NAG-ASN : angle 2.82021 ( 171) hydrogen bonds : bond 0.05011 ( 1333) hydrogen bonds : angle 4.81687 ( 3423) covalent geometry : bond 0.00247 (31683) covalent geometry : angle 0.48918 (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 281 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 3.545 Fit side-chains REVERT: K 81 ASN cc_start: 0.7386 (m-40) cc_final: 0.6983 (m-40) REVERT: K 202 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7073 (mmpt) REVERT: K 584 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.6903 (p) REVERT: K 653 TYR cc_start: 0.8861 (m-80) cc_final: 0.8638 (m-80) REVERT: K 733 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7320 (tmm) REVERT: K 976 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.6815 (mtm-85) REVERT: K 998 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: E 202 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7090 (mmpt) REVERT: E 307 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: E 745 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8458 (mp) REVERT: E 748 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7434 (mm-40) REVERT: O 81 ASN cc_start: 0.7272 (m-40) cc_final: 0.6548 (p0) REVERT: O 237 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7356 (mtm180) REVERT: O 307 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: O 570 ARG cc_start: 0.6643 (ttm170) cc_final: 0.6355 (ttm-80) REVERT: O 653 TYR cc_start: 0.8828 (m-80) cc_final: 0.8615 (m-80) REVERT: O 733 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: O 849 ASN cc_start: 0.8158 (m-40) cc_final: 0.7957 (m-40) REVERT: O 953 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8082 (t0) REVERT: O 1131 TYR cc_start: 0.7984 (t80) cc_final: 0.7611 (t80) outliers start: 60 outliers final: 21 residues processed: 255 average time/residue: 1.0770 time to fit residues: 341.4941 Evaluate side-chains 242 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 3.570 ------------------------------------------------------------------------------- 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 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 K residue 998 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 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 745 LEU Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 1003 GLN 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 695 GLU Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 818 LYS Chi-restraints excluded: chain O residue 953 ASN 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 chunk 318 optimal weight: 0.0670 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: 40.0000 chunk 335 optimal weight: 50.0000 chunk 253 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 634 ASN E1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.239230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.202227 restraints weight = 37384.074| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.03 r_work: 0.4005 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31740 Z= 0.224 Angle : 0.622 10.743 42759 Z= 0.308 Chirality : 0.052 0.575 4053 Planarity : 0.004 0.045 6237 Dihedral : 4.546 54.018 6486 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.16 % Allowed : 7.22 % Favored : 89.61 % 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: 1.06 (0.12), residues: 5094 helix: 1.65 (0.20), residues: 636 sheet: 0.94 (0.12), residues: 1770 loop : 0.43 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 104 HIS 0.006 0.001 HIS K1051 PHE 0.022 0.002 PHE E 891 TYR 0.020 0.002 TYR O 258 ARG 0.008 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 57) link_NAG-ASN : angle 2.94235 ( 171) hydrogen bonds : bond 0.06396 ( 1333) hydrogen bonds : angle 4.97922 ( 3423) covalent geometry : bond 0.00549 (31683) covalent geometry : angle 0.59424 (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 284 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 3.270 Fit side-chains revert: symmetry clash REVERT: K 81 ASN cc_start: 0.6691 (m-40) cc_final: 0.6368 (m-40) REVERT: K 733 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7289 (tmm) REVERT: K 976 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7209 (mtm-85) REVERT: E 52 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 229 LEU cc_start: 0.6827 (mt) cc_final: 0.6507 (mt) REVERT: E 307 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: E 748 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7531 (mm-40) REVERT: O 81 ASN cc_start: 0.6791 (m-40) cc_final: 0.6591 (p0) REVERT: O 307 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: O 733 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7441 (tmm) REVERT: O 849 ASN cc_start: 0.7953 (m-40) cc_final: 0.7704 (m-40) outliers start: 67 outliers final: 37 residues processed: 256 average time/residue: 1.0284 time to fit residues: 330.6456 Evaluate side-chains 250 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 3.209 ------------------------------------------------------------------------------- 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 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 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 K residue 998 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL 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 784 THR 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 695 GLU 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 977 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 495 optimal weight: 0.0060 chunk 322 optimal weight: 0.0010 chunk 30 optimal weight: 50.0000 chunk 482 optimal weight: 50.0000 chunk 371 optimal weight: 0.9980 chunk 486 optimal weight: 40.0000 chunk 431 optimal weight: 0.5980 chunk 147 optimal weight: 50.0000 chunk 2 optimal weight: 0.8980 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 537 ASN ** 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 = 0.4747 r_free = 0.4747 target = 0.241572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.203646 restraints weight = 37521.789| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.06 r_work: 0.4090 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31740 Z= 0.098 Angle : 0.501 10.788 42759 Z= 0.245 Chirality : 0.046 0.362 4053 Planarity : 0.004 0.042 6237 Dihedral : 4.174 54.933 6486 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.03 % Allowed : 8.88 % Favored : 89.09 % 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: 1.28 (0.12), residues: 5094 helix: 2.02 (0.21), residues: 630 sheet: 1.02 (0.12), residues: 1782 loop : 0.57 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 879 HIS 0.002 0.000 HIS O 207 PHE 0.015 0.001 PHE K1114 TYR 0.017 0.001 TYR K1131 ARG 0.005 0.000 ARG O 988 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 57) link_NAG-ASN : angle 2.61420 ( 171) hydrogen bonds : bond 0.04598 ( 1333) hydrogen bonds : angle 4.61869 ( 3423) covalent geometry : bond 0.00204 (31683) covalent geometry : angle 0.47344 (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 261 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 3.116 Fit side-chains REVERT: K 237 ARG cc_start: 0.7181 (mtm180) cc_final: 0.6892 (mtm180) REVERT: K 307 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: K 733 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7246 (tmm) REVERT: K 976 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7113 (mtm-85) REVERT: E 52 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 229 LEU cc_start: 0.6766 (mt) cc_final: 0.6533 (mt) REVERT: E 307 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 724 MET cc_start: 0.8618 (mtm) cc_final: 0.8371 (mtp) REVERT: O 307 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: O 733 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7157 (tmm) outliers start: 43 outliers final: 21 residues processed: 237 average time/residue: 1.0250 time to fit residues: 304.4334 Evaluate side-chains 232 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 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 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 784 THR 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 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN 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 733 MET Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1003 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 234 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 457 optimal weight: 1.9990 chunk 415 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 300 optimal weight: 50.0000 chunk 163 optimal weight: 50.0000 chunk 145 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.239397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.201739 restraints weight = 37417.898| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 2.08 r_work: 0.3998 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31740 Z= 0.198 Angle : 0.595 12.592 42759 Z= 0.294 Chirality : 0.050 0.330 4053 Planarity : 0.004 0.043 6237 Dihedral : 4.436 53.724 6486 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 8.78 % Favored : 88.86 % 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: 1.15 (0.12), residues: 5094 helix: 1.79 (0.20), residues: 627 sheet: 1.00 (0.12), residues: 1767 loop : 0.47 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 104 HIS 0.006 0.001 HIS E1051 PHE 0.020 0.002 PHE E 891 TYR 0.023 0.002 TYR K1131 ARG 0.007 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 57) link_NAG-ASN : angle 2.75233 ( 171) hydrogen bonds : bond 0.06106 ( 1333) hydrogen bonds : angle 4.81248 ( 3423) covalent geometry : bond 0.00481 (31683) covalent geometry : angle 0.57037 (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: 50 poor density : 206 time to evaluate : 3.611 Fit side-chains revert: symmetry clash REVERT: K 307 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8338 (tp40) REVERT: K 733 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: K 976 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7236 (mtm-85) REVERT: E 52 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 307 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: O 307 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: O 733 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: O 909 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 50 outliers final: 27 residues processed: 232 average time/residue: 1.0305 time to fit residues: 303.7177 Evaluate side-chains 238 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR 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 784 THR 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 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 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 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 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 909 LEU Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN 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: 1.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 40.0000 chunk 11 optimal weight: 0.9980 chunk 447 optimal weight: 0.0470 chunk 142 optimal weight: 0.0970 chunk 331 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.241214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.204270 restraints weight = 37390.222| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.02 r_work: 0.4036 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31740 Z= 0.102 Angle : 0.503 10.900 42759 Z= 0.245 Chirality : 0.046 0.294 4053 Planarity : 0.004 0.047 6237 Dihedral : 4.136 54.440 6486 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.03 % Allowed : 9.35 % Favored : 88.62 % 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: 1.30 (0.12), residues: 5094 helix: 2.15 (0.20), residues: 624 sheet: 1.09 (0.13), residues: 1749 loop : 0.52 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 879 HIS 0.002 0.001 HIS E1057 PHE 0.016 0.001 PHE K1114 TYR 0.024 0.001 TYR K1131 ARG 0.006 0.001 ARG O 988 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 57) link_NAG-ASN : angle 2.46702 ( 171) hydrogen bonds : bond 0.04720 ( 1333) hydrogen bonds : angle 4.55837 ( 3423) covalent geometry : bond 0.00220 (31683) covalent geometry : angle 0.47881 (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 257 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 2.926 Fit side-chains REVERT: K 307 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: K 976 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7156 (mtm-85) REVERT: E 52 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7446 (tm-30) REVERT: E 118 LEU cc_start: 0.8155 (tt) cc_final: 0.7954 (tp) REVERT: E 307 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: O 307 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: O 733 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7265 (tmm) outliers start: 43 outliers final: 26 residues processed: 232 average time/residue: 1.3757 time to fit residues: 400.9948 Evaluate side-chains 230 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 784 THR 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 62 VAL 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 712 THR Chi-restraints excluded: chain E residue 784 THR 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 542 THR 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 784 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 225 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 437 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 37 optimal weight: 50.0000 chunk 232 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 155 optimal weight: 50.0000 chunk 59 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.239646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.203835 restraints weight = 37406.670| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 1.89 r_work: 0.4022 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31740 Z= 0.179 Angle : 0.573 14.180 42759 Z= 0.282 Chirality : 0.049 0.318 4053 Planarity : 0.004 0.060 6237 Dihedral : 4.335 53.611 6486 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.65 % Allowed : 9.77 % Favored : 88.57 % 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: 1.21 (0.12), residues: 5094 helix: 1.83 (0.20), residues: 642 sheet: 1.03 (0.13), residues: 1764 loop : 0.52 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 879 HIS 0.005 0.001 HIS E1051 PHE 0.019 0.002 PHE E 891 TYR 0.024 0.002 TYR K1131 ARG 0.006 0.001 ARG O1100 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 57) link_NAG-ASN : angle 2.61513 ( 171) hydrogen bonds : bond 0.05831 ( 1333) hydrogen bonds : angle 4.69875 ( 3423) covalent geometry : bond 0.00432 (31683) covalent geometry : angle 0.54950 (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 243 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 3.247 Fit side-chains revert: symmetry clash REVERT: K 307 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8367 (tp40) REVERT: K 976 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7271 (mtm-85) REVERT: E 52 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 307 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: O 307 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: O 733 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7498 (tmm) outliers start: 35 outliers final: 27 residues processed: 223 average time/residue: 1.0822 time to fit residues: 309.5312 Evaluate side-chains 235 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 354 CYS Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 784 THR 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 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 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 542 THR 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 608 VAL Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 419 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 107 optimal weight: 0.0980 chunk 41 optimal weight: 40.0000 chunk 25 optimal weight: 0.9990 chunk 489 optimal weight: 30.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.239764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.203682 restraints weight = 37175.850| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.91 r_work: 0.4032 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31740 Z= 0.164 Angle : 0.556 13.100 42759 Z= 0.274 Chirality : 0.049 0.308 4053 Planarity : 0.004 0.083 6237 Dihedral : 4.332 52.926 6486 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.89 % Allowed : 9.73 % Favored : 88.39 % 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: 1.19 (0.12), residues: 5094 helix: 1.79 (0.20), residues: 645 sheet: 1.10 (0.13), residues: 1713 loop : 0.45 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 104 HIS 0.004 0.001 HIS E1051 PHE 0.019 0.002 PHE E 891 TYR 0.024 0.002 TYR K1131 ARG 0.007 0.001 ARG O 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 57) link_NAG-ASN : angle 2.53656 ( 171) hydrogen bonds : bond 0.05551 ( 1333) hydrogen bonds : angle 4.63068 ( 3423) covalent geometry : bond 0.00394 (31683) covalent geometry : angle 0.53340 (42588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28807.79 seconds wall clock time: 491 minutes 21.23 seconds (29481.23 seconds total)