Starting phenix.real_space_refine on Mon Aug 25 21:34:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vye_43658/08_2025/8vye_43658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vye_43658/08_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_43658/08_2025/8vye_43658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vye_43658/08_2025/8vye_43658.map" model { file = "/net/cci-nas-00/data/ceres_data/8vye_43658/08_2025/8vye_43658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vye_43658/08_2025/8vye_43658.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.064 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31140 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" 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: {'ARG:plan': 14, 'GLN:plan1': 12, 'HIS:plan': 2, 'PHE:plan': 16, 'GLU:plan': 25, 'ASN:plan1': 20, 'ASP:plan': 20, 'TYR:plan': 14, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 560 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: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 11, 'HIS:plan': 1, 'TRP:plan': 3, 'ASP:plan': 6} 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: {'TRP:plan': 2, 'GLN:plan1': 8, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 2} 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, 'GLU:plan': 4, 'TYR:plan': 8, 'PHE:plan': 4, 'TRP:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} 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: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 6, 'TRP:plan': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1} 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, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 4, 'ASP:plan': 7, 'HIS:plan': 1} 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: {'TYR:plan': 6, 'GLU:plan': 5, 'GLN:plan1': 8, 'ASP:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 176 Chain: "K" 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: E, O, F, P, G, Q, I, R, J, S, M, T, N, U Time building chain proxies: 10.08, per 1000 atoms: 0.32 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=51, symmetry=0 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 284 " - pdb=" SG CYS K 294 " distance=2.02 Simple disulfide: pdb=" SG CYS K 329 " - pdb=" SG CYS K 354 " distance=2.03 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 425 " distance=2.04 Simple disulfide: pdb=" SG CYS K 384 " - pdb=" SG CYS K 518 " distance=2.12 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 583 " distance=2.02 Simple disulfide: pdb=" SG CYS K 610 " - pdb=" SG CYS K 642 " distance=2.03 Simple disulfide: pdb=" SG CYS K 655 " - pdb=" SG CYS K 664 " distance=2.04 Simple disulfide: pdb=" SG CYS K 731 " - pdb=" SG CYS K 753 " distance=2.14 Simple disulfide: pdb=" SG CYS K 736 " - pdb=" SG CYS K 742 " distance=2.11 Simple disulfide: pdb=" SG CYS K1025 " - pdb=" SG CYS K1036 " distance=2.02 Simple disulfide: pdb=" SG CYS K1075 " - pdb=" SG CYS K1119 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 284 " - pdb=" SG CYS E 294 " distance=2.02 Simple disulfide: pdb=" SG CYS O 284 " - pdb=" SG CYS O 294 " distance=2.02 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 354 " distance=2.03 Simple disulfide: pdb=" SG CYS O 329 " - pdb=" SG CYS O 354 " distance=2.03 Simple disulfide: pdb=" SG CYS E 372 " - pdb=" SG CYS E 425 " distance=2.04 Simple disulfide: pdb=" SG CYS O 372 " - pdb=" SG CYS O 425 " distance=2.04 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 518 " distance=2.12 Simple disulfide: pdb=" SG CYS O 384 " - pdb=" SG CYS O 518 " distance=2.12 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 583 " distance=2.02 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 583 " distance=2.02 Simple disulfide: pdb=" SG CYS E 610 " - pdb=" SG CYS E 642 " distance=2.03 Simple disulfide: pdb=" SG CYS O 610 " - pdb=" SG CYS O 642 " distance=2.03 Simple disulfide: pdb=" SG CYS E 655 " - pdb=" SG CYS E 664 " distance=2.04 Simple disulfide: pdb=" SG CYS O 655 " - pdb=" SG CYS O 664 " distance=2.04 Simple disulfide: pdb=" SG CYS E 731 " - pdb=" SG CYS E 753 " distance=2.15 Simple disulfide: pdb=" SG CYS O 731 " - pdb=" SG CYS O 753 " distance=2.14 Simple disulfide: pdb=" SG CYS E 736 " - pdb=" SG CYS E 742 " distance=2.11 Simple disulfide: pdb=" SG CYS O 736 " - pdb=" SG CYS O 742 " distance=2.11 Simple disulfide: pdb=" SG CYS E1025 " - pdb=" SG CYS E1036 " distance=2.02 Simple disulfide: pdb=" SG CYS O1025 " - pdb=" SG CYS O1036 " distance=2.02 Simple disulfide: pdb=" SG CYS E1075 " - pdb=" SG CYS E1119 " distance=2.02 Simple disulfide: pdb=" SG CYS O1075 " - pdb=" SG CYS O1119 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.05 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.05 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: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.02 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: 9.36 Time building geometry restraints manager: 3.84 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: 16529 17.64 - 35.27: 334 35.27 - 52.91: 87 52.91 - 70.55: 42 70.55 - 88.19: 9 Dihedral angle restraints: 17001 sinusoidal: 5676 harmonic: 11325 Sorted by residual: dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 96 " pdb=" CB CYS P 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.48 46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.50 46.50 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.54 46.46 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 16998 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: 2.40 - 2.90: 13256 2.90 - 3.40: 23987 3.40 - 3.90: 46201 3.90 - 4.40: 49822 4.40 - 4.90: 85288 Nonbonded interactions: 218554 Sorted by model distance: nonbonded pdb=" O THR O 95 " pdb=" OG1 THR O 95 " model vdw 2.401 3.040 nonbonded pdb=" O THR E 95 " pdb=" OG1 THR E 95 " model vdw 2.401 3.040 nonbonded pdb=" O THR K 95 " pdb=" OG1 THR K 95 " model vdw 2.401 3.040 nonbonded pdb=" OD2 ASP O 111 " pdb=" NZ LYS O 113 " model vdw 2.404 3.120 nonbonded pdb=" OD2 ASP E 111 " pdb=" NZ LYS E 113 " model vdw 2.404 3.120 ... (remaining 218549 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: 0.11 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'E' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'T' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'U' } 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: 9.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.060 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.600 ------------------------------------------------------------------------------- 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 0.114 31791 Z= 0.535 Angle : 1.324 8.229 42861 Z= 0.899 Chirality : 0.075 0.352 4053 Planarity : 0.005 0.022 6237 Dihedral : 8.857 88.187 10752 Min Nonbonded Distance : 2.401 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E1012 TYR 0.033 0.004 TYR K1060 PHE 0.019 0.003 PHE K 891 TRP 0.018 0.005 TRP K 879 HIS 0.002 0.001 HIS K 648 Details of bonding type rmsd covalent geometry : bond 0.00894 (31683) covalent geometry : angle 1.31041 (42588) SS BOND : bond 0.04073 ( 51) SS BOND : angle 3.21785 ( 102) hydrogen bonds : bond 0.18206 ( 1333) hydrogen bonds : angle 7.92002 ( 3423) link_NAG-ASN : bond 0.05538 ( 57) link_NAG-ASN : angle 2.41414 ( 171) *********************** 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 : 1.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.6152 time to fit residues: 267.6341 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 : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 4.9990 overall best weight: 1.4960 ------------------------------------------------------------------------------- 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 121 ASN E 648 HIS E 651 ASN E 894 GLN E 928 GLN O 30 ASN O 121 ASN O 648 HIS O 651 ASN O 748 GLN O 894 GLN O1118 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.241733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.198580 restraints weight = 37865.965| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.73 r_work: 0.3575 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31791 Z= 0.186 Angle : 0.639 14.171 42861 Z= 0.322 Chirality : 0.051 0.434 4053 Planarity : 0.005 0.039 6237 Dihedral : 4.749 57.263 6486 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.74 % Allowed : 5.24 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 5094 helix: 1.72 (0.21), residues: 615 sheet: 0.95 (0.12), residues: 1761 loop : 0.55 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 34 TYR 0.021 0.002 TYR E 258 PHE 0.017 0.002 PHE E1114 TRP 0.018 0.002 TRP O 879 HIS 0.010 0.002 HIS O 648 Details of bonding type rmsd covalent geometry : bond 0.00443 (31683) covalent geometry : angle 0.60255 (42588) SS BOND : bond 0.00286 ( 51) SS BOND : angle 1.03721 ( 102) hydrogen bonds : bond 0.06315 ( 1333) hydrogen bonds : angle 5.74438 ( 3423) link_NAG-ASN : bond 0.00528 ( 57) link_NAG-ASN : angle 3.34700 ( 171) *********************** 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 284 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7071 (mmpt) REVERT: K 237 ARG cc_start: 0.7745 (mtm180) cc_final: 0.7135 (mtm-85) REVERT: K 307 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (tp40) REVERT: K 733 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7234 (tmm) REVERT: K 745 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8366 (mp) REVERT: K 871 LEU cc_start: 0.9046 (mt) cc_final: 0.8839 (mm) REVERT: K 976 ARG cc_start: 0.7245 (mtt90) cc_final: 0.7008 (ttm-80) REVERT: K 1131 TYR cc_start: 0.7865 (t80) cc_final: 0.7420 (t80) REVERT: E 202 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7006 (mmpt) REVERT: E 307 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: E 733 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7462 (tmm) REVERT: E 748 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: E 977 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7956 (mp) REVERT: O 202 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.6961 (mmpt) REVERT: O 307 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: O 532 VAL cc_start: 0.7877 (m) cc_final: 0.7655 (p) REVERT: O 733 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: O 748 GLN cc_start: 0.8317 (mt0) cc_final: 0.8041 (mm-40) REVERT: O 976 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6837 (mtm-85) REVERT: O 1131 TYR cc_start: 0.7932 (t80) cc_final: 0.7555 (t80) outliers start: 58 outliers final: 26 residues processed: 258 average time/residue: 0.5455 time to fit residues: 172.3545 Evaluate side-chains 246 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 609 ASN 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 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 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 609 ASN 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 E residue 977 LEU 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 569 VAL 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 609 ASN Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 928 GLN Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 332 optimal weight: 40.0000 chunk 226 optimal weight: 0.8980 chunk 319 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 268 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 460 optimal weight: 2.9990 chunk 505 optimal weight: 50.0000 chunk 405 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 66 HIS K 537 ASN E 66 HIS O 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.239990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197312 restraints weight = 37482.627| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.69 r_work: 0.3554 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31791 Z= 0.223 Angle : 0.639 10.796 42861 Z= 0.322 Chirality : 0.053 0.464 4053 Planarity : 0.005 0.044 6237 Dihedral : 4.817 54.457 6486 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.59 % Allowed : 5.85 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.12), residues: 5094 helix: 1.35 (0.20), residues: 642 sheet: 0.82 (0.12), residues: 1791 loop : 0.47 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1100 TYR 0.022 0.002 TYR E 258 PHE 0.022 0.003 PHE E 891 TRP 0.012 0.002 TRP O 879 HIS 0.006 0.002 HIS K1051 Details of bonding type rmsd covalent geometry : bond 0.00541 (31683) covalent geometry : angle 0.61024 (42588) SS BOND : bond 0.00361 ( 51) SS BOND : angle 1.07393 ( 102) hydrogen bonds : bond 0.06713 ( 1333) hydrogen bonds : angle 5.31669 ( 3423) link_NAG-ASN : bond 0.00660 ( 57) link_NAG-ASN : angle 2.99270 ( 171) *********************** 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 295 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 219 time to evaluate : 1.182 Fit side-chains REVERT: K 81 ASN cc_start: 0.7542 (m-40) cc_final: 0.7214 (m-40) REVERT: K 237 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7065 (mtm-85) REVERT: K 307 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8583 (tp40) REVERT: K 733 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7321 (tmm) REVERT: E 52 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: E 81 ASN cc_start: 0.7427 (m-40) cc_final: 0.7210 (m-40) REVERT: E 229 LEU cc_start: 0.6653 (mt) cc_final: 0.6418 (mm) REVERT: E 237 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7314 (mtm180) REVERT: E 307 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: E 733 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: E 748 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: E 977 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7987 (mp) REVERT: E 998 GLN cc_start: 0.8655 (tt0) cc_final: 0.8406 (mt0) REVERT: O 81 ASN cc_start: 0.7403 (m-40) cc_final: 0.6695 (p0) REVERT: O 275 ASN cc_start: 0.7584 (m-40) cc_final: 0.7343 (m-40) REVERT: O 307 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: O 570 ARG cc_start: 0.6780 (ttm170) cc_final: 0.6497 (ttm-80) REVERT: O 733 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7351 (tmm) REVERT: O 849 ASN cc_start: 0.8258 (m-40) cc_final: 0.7904 (m-40) REVERT: O 976 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6895 (mtm-85) outliers start: 76 outliers final: 32 residues processed: 264 average time/residue: 0.4568 time to fit residues: 150.2300 Evaluate side-chains 249 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 532 VAL Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 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 52 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL 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 733 MET Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain O residue 62 VAL 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 977 LEU Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 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 413 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 357 optimal weight: 3.9990 chunk 143 optimal weight: 50.0000 chunk 445 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 275 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 320 optimal weight: 50.0000 chunk 353 optimal weight: 0.8980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 606 GLN E 634 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.240890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194620 restraints weight = 37373.140| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.79 r_work: 0.3555 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31791 Z= 0.136 Angle : 0.554 10.732 42861 Z= 0.274 Chirality : 0.049 0.737 4053 Planarity : 0.004 0.042 6237 Dihedral : 4.546 59.704 6486 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.88 % Allowed : 6.85 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.12), residues: 5094 helix: 1.71 (0.21), residues: 630 sheet: 0.96 (0.12), residues: 1719 loop : 0.47 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O1100 TYR 0.016 0.002 TYR E 258 PHE 0.016 0.002 PHE K1114 TRP 0.009 0.001 TRP O 879 HIS 0.003 0.001 HIS E1051 Details of bonding type rmsd covalent geometry : bond 0.00314 (31683) covalent geometry : angle 0.52648 (42588) SS BOND : bond 0.00191 ( 51) SS BOND : angle 0.84091 ( 102) hydrogen bonds : bond 0.05489 ( 1333) hydrogen bonds : angle 5.02510 ( 3423) link_NAG-ASN : bond 0.00503 ( 57) link_NAG-ASN : angle 2.74054 ( 171) *********************** 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 276 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 1.127 Fit side-chains REVERT: K 81 ASN cc_start: 0.7382 (m-40) cc_final: 0.6985 (m-40) REVERT: K 202 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8135 (mtmt) REVERT: K 237 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7088 (mtm-85) REVERT: K 307 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8625 (tp40) REVERT: K 570 ARG cc_start: 0.6589 (ttm170) cc_final: 0.5759 (ttm170) REVERT: K 653 TYR cc_start: 0.8881 (m-80) cc_final: 0.8587 (m-80) REVERT: K 733 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7319 (tmm) REVERT: K 976 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.6901 (mtm-85) REVERT: K 998 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: E 53 ASP cc_start: 0.7604 (t0) cc_final: 0.7386 (t0) REVERT: E 81 ASN cc_start: 0.7375 (m-40) cc_final: 0.7173 (m-40) REVERT: E 237 ARG cc_start: 0.7541 (mtm180) cc_final: 0.7237 (mtm180) REVERT: E 307 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: E 998 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: O 81 ASN cc_start: 0.7273 (m-40) cc_final: 0.6514 (p0) REVERT: O 202 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.6941 (mmpt) REVERT: O 237 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7514 (mtm180) REVERT: O 307 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: O 532 VAL cc_start: 0.8163 (p) cc_final: 0.7932 (m) REVERT: O 570 ARG cc_start: 0.6683 (ttm170) cc_final: 0.6444 (ttm-80) REVERT: O 733 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7361 (tmm) REVERT: O 849 ASN cc_start: 0.8241 (m-40) cc_final: 0.7977 (m-40) REVERT: O 976 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6916 (mtm-85) outliers start: 61 outliers final: 33 residues processed: 248 average time/residue: 0.4974 time to fit residues: 151.6466 Evaluate side-chains 249 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 818 LYS 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 K residue 1003 GLN 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 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 871 LEU Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL 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 784 THR Chi-restraints excluded: chain O residue 818 LYS Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 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 173 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 164 optimal weight: 50.0000 chunk 460 optimal weight: 50.0000 chunk 402 optimal weight: 1.9990 chunk 449 optimal weight: 40.0000 chunk 431 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 421 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 919 GLN K1128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.239217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.202982 restraints weight = 37429.644| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.16 r_work: 0.4002 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31791 Z= 0.189 Angle : 0.608 12.330 42861 Z= 0.299 Chirality : 0.051 0.500 4053 Planarity : 0.004 0.044 6237 Dihedral : 4.640 59.880 6486 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.31 % Allowed : 7.22 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.12), residues: 5094 helix: 1.47 (0.20), residues: 660 sheet: 0.91 (0.12), residues: 1755 loop : 0.40 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O1100 TYR 0.022 0.002 TYR K1131 PHE 0.021 0.002 PHE E 891 TRP 0.009 0.002 TRP E 104 HIS 0.005 0.001 HIS E1051 Details of bonding type rmsd covalent geometry : bond 0.00457 (31683) covalent geometry : angle 0.57806 (42588) SS BOND : bond 0.00304 ( 51) SS BOND : angle 0.93094 ( 102) hydrogen bonds : bond 0.06097 ( 1333) hydrogen bonds : angle 5.00969 ( 3423) link_NAG-ASN : bond 0.00467 ( 57) link_NAG-ASN : angle 2.96047 ( 171) *********************** 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 282 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.864 Fit side-chains REVERT: K 307 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8557 (tp40) REVERT: K 570 ARG cc_start: 0.6872 (ttm170) cc_final: 0.6321 (ttm170) REVERT: K 733 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7316 (tmm) REVERT: K 976 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7215 (mtm-85) REVERT: K 998 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: E 52 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7458 (tm-30) REVERT: E 81 ASN cc_start: 0.6574 (m-40) cc_final: 0.6373 (p0) REVERT: E 307 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: E 748 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7478 (mm-40) REVERT: O 81 ASN cc_start: 0.6733 (m-40) cc_final: 0.6512 (p0) REVERT: O 307 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: O 532 VAL cc_start: 0.8457 (p) cc_final: 0.8111 (m) REVERT: O 733 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7387 (tmm) outliers start: 70 outliers final: 36 residues processed: 249 average time/residue: 0.5061 time to fit residues: 154.8253 Evaluate side-chains 246 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain 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 229 LEU 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 871 LEU Chi-restraints excluded: chain E residue 1003 GLN 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 744 ASN 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 1010 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 454 optimal weight: 50.0000 chunk 213 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 330 optimal weight: 40.0000 chunk 172 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 453 optimal weight: 0.0050 chunk 212 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.238040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.203292 restraints weight = 37132.389| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.04 r_work: 0.4003 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 31791 Z= 0.275 Angle : 0.680 11.238 42861 Z= 0.340 Chirality : 0.056 0.706 4053 Planarity : 0.005 0.049 6237 Dihedral : 4.939 53.706 6486 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.54 % Allowed : 7.46 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.12), residues: 5094 helix: 1.29 (0.20), residues: 636 sheet: 0.82 (0.12), residues: 1743 loop : 0.23 (0.12), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O1100 TYR 0.023 0.003 TYR K1131 PHE 0.025 0.003 PHE E 891 TRP 0.013 0.002 TRP E 104 HIS 0.006 0.001 HIS K1051 Details of bonding type rmsd covalent geometry : bond 0.00679 (31683) covalent geometry : angle 0.65304 (42588) SS BOND : bond 0.00469 ( 51) SS BOND : angle 1.10879 ( 102) hydrogen bonds : bond 0.06968 ( 1333) hydrogen bonds : angle 5.13319 ( 3423) link_NAG-ASN : bond 0.00558 ( 57) link_NAG-ASN : angle 2.99482 ( 171) *********************** 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 283 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: K 307 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8480 (tp40) REVERT: K 733 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7326 (tmm) REVERT: E 52 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 307 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: E 653 TYR cc_start: 0.8810 (m-80) cc_final: 0.8605 (m-80) REVERT: O 307 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: O 733 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7348 (tmm) outliers start: 75 outliers final: 44 residues processed: 255 average time/residue: 0.5387 time to fit residues: 169.0144 Evaluate side-chains 250 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 725 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 K residue 1126 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 229 LEU 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 784 THR Chi-restraints excluded: chain E residue 871 LEU 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 695 GLU Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 744 ASN 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 1010 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 426 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 241 optimal weight: 0.6980 chunk 144 optimal weight: 50.0000 chunk 264 optimal weight: 1.9990 chunk 386 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 418 optimal weight: 0.9990 chunk 466 optimal weight: 3.9990 chunk 337 optimal weight: 50.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4728 r_free = 0.4728 target = 0.239365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.204809 restraints weight = 37273.781| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.02 r_work: 0.4026 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31791 Z= 0.152 Angle : 0.568 13.696 42861 Z= 0.280 Chirality : 0.049 0.554 4053 Planarity : 0.004 0.050 6237 Dihedral : 4.615 56.976 6486 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.02 % Allowed : 8.50 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.12), residues: 5094 helix: 1.69 (0.20), residues: 636 sheet: 0.95 (0.13), residues: 1719 loop : 0.30 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 102 TYR 0.019 0.002 TYR K1131 PHE 0.017 0.002 PHE K1114 TRP 0.008 0.001 TRP E 104 HIS 0.003 0.001 HIS E1051 Details of bonding type rmsd covalent geometry : bond 0.00359 (31683) covalent geometry : angle 0.53839 (42588) SS BOND : bond 0.00224 ( 51) SS BOND : angle 0.87294 ( 102) hydrogen bonds : bond 0.05588 ( 1333) hydrogen bonds : angle 4.85330 ( 3423) link_NAG-ASN : bond 0.00470 ( 57) link_NAG-ASN : angle 2.85219 ( 171) *********************** 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 270 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 1.002 Fit side-chains REVERT: K 307 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8544 (tp40) REVERT: K 733 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7246 (tmm) REVERT: K 998 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: E 237 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7241 (mtm180) REVERT: E 307 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: O 307 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: O 733 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7389 (tmm) REVERT: O 909 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (tt) outliers start: 64 outliers final: 33 residues processed: 238 average time/residue: 0.5192 time to fit residues: 150.5301 Evaluate side-chains 236 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 818 LYS 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 229 LEU 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 712 THR Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR Chi-restraints excluded: chain O residue 818 LYS 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 1010 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 418 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 344 optimal weight: 0.0670 chunk 154 optimal weight: 50.0000 chunk 469 optimal weight: 50.0000 chunk 468 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 320 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 466 optimal weight: 3.9990 chunk 439 optimal weight: 1.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 919 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.238747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.204418 restraints weight = 37288.826| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.01 r_work: 0.4019 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31791 Z= 0.187 Angle : 0.608 14.992 42861 Z= 0.299 Chirality : 0.051 0.591 4053 Planarity : 0.004 0.064 6237 Dihedral : 4.663 55.213 6486 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 9.07 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.12), residues: 5094 helix: 1.62 (0.20), residues: 630 sheet: 1.00 (0.13), residues: 1716 loop : 0.28 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 102 TYR 0.027 0.002 TYR K1131 PHE 0.020 0.002 PHE E 891 TRP 0.010 0.002 TRP O 104 HIS 0.004 0.001 HIS K1051 Details of bonding type rmsd covalent geometry : bond 0.00453 (31683) covalent geometry : angle 0.57506 (42588) SS BOND : bond 0.00308 ( 51) SS BOND : angle 0.92443 ( 102) hydrogen bonds : bond 0.06047 ( 1333) hydrogen bonds : angle 4.87228 ( 3423) link_NAG-ASN : bond 0.00478 ( 57) link_NAG-ASN : angle 3.14989 ( 171) *********************** 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 257 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: K 102 ARG cc_start: 0.6994 (mmt90) cc_final: 0.6733 (mmp-170) REVERT: K 307 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8541 (tp40) REVERT: K 733 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7338 (tmm) REVERT: K 976 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7298 (mmm-85) REVERT: E 52 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 307 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: E 653 TYR cc_start: 0.8785 (m-80) cc_final: 0.8555 (m-80) REVERT: O 307 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: O 733 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7382 (tmm) outliers start: 60 outliers final: 38 residues processed: 227 average time/residue: 0.4796 time to fit residues: 135.4123 Evaluate side-chains 237 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 542 THR 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 229 LEU 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 784 THR Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 725 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 1010 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 467 optimal weight: 40.0000 chunk 494 optimal weight: 7.9990 chunk 453 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 136 optimal weight: 50.0000 chunk 66 optimal weight: 0.7980 chunk 433 optimal weight: 1.9990 chunk 496 optimal weight: 10.0000 chunk 486 optimal weight: 50.0000 chunk 374 optimal weight: 50.0000 chunk 341 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.4716 r_free = 0.4716 target = 0.237980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.203311 restraints weight = 37040.423| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.94 r_work: 0.4010 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31791 Z= 0.258 Angle : 0.675 16.648 42861 Z= 0.335 Chirality : 0.054 0.470 4053 Planarity : 0.005 0.091 6237 Dihedral : 4.932 53.371 6486 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.74 % Allowed : 9.16 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.12), residues: 5094 helix: 1.18 (0.20), residues: 657 sheet: 0.95 (0.13), residues: 1698 loop : 0.14 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1100 TYR 0.027 0.003 TYR K1131 PHE 0.025 0.003 PHE K 891 TRP 0.013 0.002 TRP O 104 HIS 0.006 0.001 HIS K1051 Details of bonding type rmsd covalent geometry : bond 0.00639 (31683) covalent geometry : angle 0.64402 (42588) SS BOND : bond 0.00437 ( 51) SS BOND : angle 1.02911 ( 102) hydrogen bonds : bond 0.06827 ( 1333) hydrogen bonds : angle 5.01843 ( 3423) link_NAG-ASN : bond 0.00551 ( 57) link_NAG-ASN : angle 3.18239 ( 171) *********************** 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 258 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: K 102 ARG cc_start: 0.7131 (mmt90) cc_final: 0.6778 (mmp-170) REVERT: K 307 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8566 (tp40) REVERT: K 733 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7417 (tmm) REVERT: K 976 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7357 (mmm-85) REVERT: E 52 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 307 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: E 653 TYR cc_start: 0.8834 (m-80) cc_final: 0.8598 (m-80) REVERT: O 307 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: O 733 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7424 (tmm) outliers start: 58 outliers final: 38 residues processed: 231 average time/residue: 0.5216 time to fit residues: 149.9037 Evaluate side-chains 238 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 542 THR 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 229 LEU 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 712 THR Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 871 LEU 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 608 VAL Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 725 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 1010 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 160 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 153 optimal weight: 0.0170 chunk 220 optimal weight: 7.9990 chunk 455 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 412 optimal weight: 0.8980 chunk 150 optimal weight: 50.0000 chunk 299 optimal weight: 50.0000 chunk 429 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.4736 r_free = 0.4736 target = 0.240276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.205474 restraints weight = 37312.045| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 1.95 r_work: 0.4045 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31791 Z= 0.106 Angle : 0.527 13.858 42861 Z= 0.259 Chirality : 0.047 0.428 4053 Planarity : 0.004 0.084 6237 Dihedral : 4.407 54.862 6486 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.42 % Allowed : 10.62 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.12), residues: 5094 helix: 1.81 (0.20), residues: 648 sheet: 1.14 (0.13), residues: 1695 loop : 0.33 (0.12), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 102 TYR 0.026 0.001 TYR K1131 PHE 0.016 0.001 PHE K1114 TRP 0.008 0.001 TRP O 879 HIS 0.003 0.001 HIS E1057 Details of bonding type rmsd covalent geometry : bond 0.00235 (31683) covalent geometry : angle 0.49746 (42588) SS BOND : bond 0.00142 ( 51) SS BOND : angle 0.78847 ( 102) hydrogen bonds : bond 0.04807 ( 1333) hydrogen bonds : angle 4.63028 ( 3423) link_NAG-ASN : bond 0.00478 ( 57) link_NAG-ASN : angle 2.75180 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: K 733 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: K 976 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7222 (mtm-85) REVERT: K 998 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: E 307 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: O 307 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: O 733 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7230 (tmm) REVERT: O 744 ASN cc_start: 0.8073 (m-40) cc_final: 0.7848 (t0) outliers start: 30 outliers final: 21 residues processed: 220 average time/residue: 0.5105 time to fit residues: 139.3814 Evaluate side-chains 217 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 725 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 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 229 LEU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 725 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 378 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 328 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 472 optimal weight: 0.9980 chunk 242 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 340 optimal weight: 1.9990 chunk 375 optimal weight: 0.1980 chunk 220 optimal weight: 0.9990 chunk 350 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.4735 r_free = 0.4735 target = 0.240836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.207305 restraints weight = 37521.899| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.90 r_work: 0.4036 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31791 Z= 0.106 Angle : 0.521 15.066 42861 Z= 0.253 Chirality : 0.047 0.437 4053 Planarity : 0.004 0.076 6237 Dihedral : 4.237 55.080 6486 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.37 % Allowed : 11.10 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.12), residues: 5094 helix: 2.04 (0.20), residues: 648 sheet: 1.26 (0.13), residues: 1701 loop : 0.43 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 102 TYR 0.025 0.001 TYR K1131 PHE 0.016 0.001 PHE E 32 TRP 0.008 0.001 TRP O 879 HIS 0.002 0.001 HIS E1057 Details of bonding type rmsd covalent geometry : bond 0.00236 (31683) covalent geometry : angle 0.49374 (42588) SS BOND : bond 0.00157 ( 51) SS BOND : angle 0.75393 ( 102) hydrogen bonds : bond 0.04667 ( 1333) hydrogen bonds : angle 4.50345 ( 3423) link_NAG-ASN : bond 0.00466 ( 57) link_NAG-ASN : angle 2.64297 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13433.84 seconds wall clock time: 227 minutes 59.64 seconds (13679.64 seconds total)