Starting phenix.real_space_refine on Sat Oct 31 12:48:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fgh_31581/10_2026/7fgh_31581.cif" } resolution = 2.18 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= 0.001 sd= 0.053 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 12 5.49 5 S 336 5.16 5 C 27180 2.51 5 N 7512 2.21 5 O 9480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44532 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 46.090 168.911 60.711 1.00 0.00 S ATOM 1076 SG CYS A 141 48.875 171.684 59.981 1.00 0.00 S ATOM 4566 SG CYS B 134 20.777 131.262 60.711 1.00 0.00 S ATOM 4618 SG CYS B 141 21.803 135.056 59.981 1.00 0.00 S ATOM 8108 SG CYS C 134 17.689 85.992 60.711 1.00 0.00 S ATOM 8160 SG CYS C 141 16.680 89.790 59.981 1.00 0.00 S ATOM 11650 SG CYS D 134 37.639 45.240 60.711 1.00 0.00 S ATOM 11702 SG CYS D 141 34.866 48.025 59.981 1.00 0.00 S ATOM 15192 SG CYS E 134 75.296 19.933 60.711 1.00 0.00 S ATOM 15244 SG CYS E 141 71.502 20.958 59.981 1.00 0.00 S ATOM 18734 SG CYS F 134 120.567 16.835 60.711 1.00 0.00 S ATOM 18786 SG CYS F 141 116.769 15.826 59.981 1.00 0.00 S ATOM 22276 SG CYS G 134 161.310 36.790 60.711 1.00 0.00 S ATOM 22328 SG CYS G 141 158.525 34.016 59.981 1.00 0.00 S ATOM 25818 SG CYS H 134 186.626 74.453 60.711 1.00 0.00 S ATOM 25870 SG CYS H 141 185.600 70.659 59.981 1.00 0.00 S ATOM 29360 SG CYS I 134 189.724 119.713 60.711 1.00 0.00 S ATOM 29412 SG CYS I 141 190.733 115.915 59.981 1.00 0.00 S ATOM 32902 SG CYS J 134 169.760 160.461 60.711 1.00 0.00 S ATOM 32954 SG CYS J 141 172.533 157.676 59.981 1.00 0.00 S ATOM 36444 SG CYS K 134 132.106 185.782 60.711 1.00 0.00 S ATOM 36496 SG CYS K 141 135.900 184.757 59.981 1.00 0.00 S ATOM 39986 SG CYS L 134 86.846 188.870 60.711 1.00 0.00 S ATOM 40038 SG CYS L 141 90.644 189.879 59.981 1.00 0.00 S Time building chain proxies: 6.38, per 1000 atoms: 0.14 Number of scatterers: 44532 At special positions: 0 Unit cell: (208.25, 207.4, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 336 16.00 P 12 15.00 O 9480 8.00 N 7512 7.00 C 27180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10344 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 35.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.636A pdb=" N MET B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.696A pdb=" N LEU B 346 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG C 41 " --> pdb=" O HIS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG D 41 " --> pdb=" O HIS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.630A pdb=" N ARG E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.636A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET E 184 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.696A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 474 Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 removed outlier: 3.630A pdb=" N ARG F 41 " --> pdb=" O HIS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 474 Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.229A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.636A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.696A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG G 399 " --> pdb=" O ALA G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 474 Processing helix chain 'H' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.636A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.696A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG H 399 " --> pdb=" O ALA H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 474 Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.229A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG I 41 " --> pdb=" O HIS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET I 184 " --> pdb=" O THR I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG I 399 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 474 Processing helix chain 'J' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG J 41 " --> pdb=" O HIS J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET J 184 " --> pdb=" O THR J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU J 346 " --> pdb=" O THR J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG J 399 " --> pdb=" O ALA J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 474 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG K 41 " --> pdb=" O HIS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.636A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 removed outlier: 3.550A pdb=" N ALA K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET K 184 " --> pdb=" O THR K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.696A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 474 Processing helix chain 'L' and resid 13 through 22 removed outlier: 4.228A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.629A pdb=" N ARG L 41 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.635A pdb=" N MET L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 removed outlier: 3.551A pdb=" N ALA L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.557A pdb=" N MET L 184 " --> pdb=" O THR L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.697A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 403 removed outlier: 3.530A pdb=" N ARG L 399 " --> pdb=" O ALA L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL A 4 " --> pdb=" O GLU A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 148 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL A 176 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR A 150 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE A 178 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL B 4 " --> pdb=" O GLU B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.360A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA B 148 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL B 176 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 150 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE B 178 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL C 4 " --> pdb=" O GLU C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.360A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 147 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 148 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL C 176 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR C 150 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE C 178 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL D 4 " --> pdb=" O GLU D 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 147 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 148 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL D 176 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR D 150 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE D 178 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 303 through 307 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 removed outlier: 6.169A pdb=" N VAL E 4 " --> pdb=" O GLU E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.360A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 147 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA E 148 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL E 176 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR E 150 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE E 178 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL F 4 " --> pdb=" O GLU F 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 147 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA F 148 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL F 176 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR F 150 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE F 178 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 251 removed outlier: 7.015A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.167A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 147 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA G 148 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL G 176 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR G 150 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE G 178 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL H 4 " --> pdb=" O GLU H 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 133 through 134 removed outlier: 8.360A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL H 147 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA H 148 " --> pdb=" O TYR H 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL H 176 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR H 150 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE H 178 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 303 through 307 Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL I 4 " --> pdb=" O GLU I 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 147 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA I 148 " --> pdb=" O TYR I 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL I 176 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR I 150 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE I 178 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL J 4 " --> pdb=" O GLU J 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL J 147 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA J 148 " --> pdb=" O TYR J 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL J 176 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR J 150 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE J 178 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 303 through 307 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.361A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL K 147 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 148 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL K 176 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR K 150 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE K 178 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 6.168A pdb=" N VAL L 4 " --> pdb=" O GLU L 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.360A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL L 147 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA L 148 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL L 176 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR L 150 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N PHE L 178 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 246 through 251 removed outlier: 7.014A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 303 through 307 1812 hydrogen bonds defined for protein. 5112 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: 11.89 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6996 1.30 - 1.43: 11766 1.43 - 1.56: 24750 1.56 - 1.69: 36 1.69 - 1.82: 516 Bond restraints: 44064 Sorted by residual: bond pdb=" C4' G7M E1003 " pdb=" C3' G7M E1003 " ideal model delta sigma weight residual 1.521 1.289 0.232 1.50e-02 4.44e+03 2.39e+02 bond pdb=" C4' G7M I1003 " pdb=" C3' G7M I1003 " ideal model delta sigma weight residual 1.521 1.289 0.232 1.50e-02 4.44e+03 2.39e+02 bond pdb=" C4' G7M D1003 " pdb=" C3' G7M D1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 bond pdb=" C4' G7M A1003 " pdb=" C3' G7M A1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 bond pdb=" C4' G7M J1003 " pdb=" C3' G7M J1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 44059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 58583 3.04 - 6.09: 997 6.09 - 9.13: 144 9.13 - 12.18: 36 12.18 - 15.22: 12 Bond angle restraints: 59772 Sorted by residual: angle pdb=" C3' G7M I1003 " pdb=" C2' G7M I1003 " pdb=" C1' G7M I1003 " ideal model delta sigma weight residual 101.30 106.57 -5.27 1.00e+00 1.00e+00 2.78e+01 angle pdb=" C3' G7M H1003 " pdb=" C2' G7M H1003 " pdb=" C1' G7M H1003 " ideal model delta sigma weight residual 101.30 106.55 -5.25 1.00e+00 1.00e+00 2.75e+01 angle pdb=" C3' G7M E1003 " pdb=" C2' G7M E1003 " pdb=" C1' G7M E1003 " ideal model delta sigma weight residual 101.30 106.55 -5.25 1.00e+00 1.00e+00 2.75e+01 angle pdb=" C3' G7M F1003 " pdb=" C2' G7M F1003 " pdb=" C1' G7M F1003 " ideal model delta sigma weight residual 101.30 106.54 -5.24 1.00e+00 1.00e+00 2.75e+01 angle pdb=" C3' G7M K1003 " pdb=" C2' G7M K1003 " pdb=" C1' G7M K1003 " ideal model delta sigma weight residual 101.30 106.54 -5.24 1.00e+00 1.00e+00 2.74e+01 ... (remaining 59767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23317 17.68 - 35.35: 2574 35.35 - 53.03: 521 53.03 - 70.70: 192 70.70 - 88.38: 60 Dihedral angle restraints: 26664 sinusoidal: 10716 harmonic: 15948 Sorted by residual: dihedral pdb=" CA GLU E 26 " pdb=" C GLU E 26 " pdb=" N VAL E 27 " pdb=" CA VAL E 27 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU C 26 " pdb=" C GLU C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU I 26 " pdb=" C GLU I 26 " pdb=" N VAL I 27 " pdb=" CA VAL I 27 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 26661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3641 0.040 - 0.081: 2022 0.081 - 0.121: 800 0.121 - 0.161: 260 0.161 - 0.202: 21 Chirality restraints: 6744 Sorted by residual: chirality pdb=" C1' G7M F1003 " pdb=" O4' G7M F1003 " pdb=" C2' G7M F1003 " pdb=" N9 G7M F1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1' G7M C1003 " pdb=" O4' G7M C1003 " pdb=" C2' G7M C1003 " pdb=" N9 G7M C1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1' G7M L1003 " pdb=" O4' G7M L1003 " pdb=" C2' G7M L1003 " pdb=" N9 G7M L1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 6741 not shown) Planarity restraints: 7512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 183 " 0.021 2.00e-02 2.50e+03 1.37e-02 3.30e+00 pdb=" CG PHE C 183 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 183 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 183 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 183 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 183 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 183 " 0.021 2.00e-02 2.50e+03 1.37e-02 3.28e+00 pdb=" CG PHE B 183 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 183 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 183 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 183 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 183 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 183 " -0.020 2.00e-02 2.50e+03 1.37e-02 3.27e+00 pdb=" CG PHE K 183 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE K 183 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE K 183 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE K 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 183 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 183 " -0.010 2.00e-02 2.50e+03 ... (remaining 7509 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 581 2.67 - 3.23: 39040 3.23 - 3.79: 66147 3.79 - 4.34: 96696 4.34 - 4.90: 152010 Nonbonded interactions: 354474 Sorted by model distance: nonbonded pdb=" OE1 GLU C 129 " pdb="ZN ZN C1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU I 129 " pdb="ZN ZN I1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU J 129 " pdb="ZN ZN J1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU D 129 " pdb="ZN ZN D1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU A 129 " pdb="ZN ZN A1001 " model vdw 2.118 2.230 ... (remaining 354469 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 46.340 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.130 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:9.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.010 0.232 44112 Z= 0.631 Angle : 1.039 15.220 59772 Z= 0.557 Chirality : 0.057 0.202 6744 Planarity : 0.006 0.045 7512 Dihedral : 16.496 88.378 16320 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.31 % Allowed : 12.82 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.11), residues: 5340 helix: 1.58 (0.13), residues: 1644 sheet: 0.60 (0.15), residues: 1020 loop : -1.69 (0.10), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 238 TYR 0.017 0.002 TYR C 150 PHE 0.028 0.003 PHE L 183 TRP 0.012 0.002 TRP H 175 HIS 0.006 0.002 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.55 (44064) covalent geometry : angle 1.03905 / 0.56 (59772) hydrogen bonds : bond 0.17852 / 12.08 ( 1812) hydrogen bonds : angle 5.80622 / 4.06 ( 5112) metal coordination : bond 0.00708 / 0.45 ( 36) Misc. bond : bond 0.18849 / 12.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 441 time to evaluate : 1.634 Fit side-chains outliers start: 60 outliers final: 12 residues processed: 465 average time/residue: 0.8518 time to fit residues: 476.3068 Evaluate side-chains 403 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 391 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN D 95 ASN G 95 ASN J 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103650 restraints weight = 45108.932| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.50 r_work: 0.3169 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44112 Z= 0.144 Angle : 0.584 5.103 59772 Z= 0.322 Chirality : 0.044 0.143 6744 Planarity : 0.005 0.039 7512 Dihedral : 7.177 55.944 6252 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.94 % Allowed : 12.55 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.12), residues: 5340 helix: 2.81 (0.13), residues: 1680 sheet: 0.33 (0.14), residues: 1224 loop : -1.67 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 238 TYR 0.015 0.001 TYR K 150 PHE 0.014 0.001 PHE H 264 TRP 0.008 0.001 TRP F 175 HIS 0.005 0.001 HIS F 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (44064) covalent geometry : angle 0.58415 / 0.32 (59772) hydrogen bonds : bond 0.05784 / 3.90 ( 1812) hydrogen bonds : angle 4.65763 / 3.21 ( 5112) metal coordination : bond 0.00288 / 0.19 ( 36) Misc. bond : bond 0.00093 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 408 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: B 30 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: B 54 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: B 85 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8127 (mmm-85) REVERT: C 30 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7321 (ttm-80) REVERT: C 364 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6678 (mt0) REVERT: D 54 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: E 30 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7455 (ttm-80) REVERT: E 123 MET cc_start: 0.7674 (mmp) cc_final: 0.7419 (mmp) REVERT: F 30 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7309 (ttm-80) REVERT: F 85 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (mmt90) REVERT: G 54 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: H 30 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7443 (ttm-80) REVERT: I 30 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7281 (ttm-80) REVERT: I 85 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (mmt90) REVERT: I 99 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7851 (mptt) REVERT: I 364 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6687 (mt0) REVERT: J 26 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: J 54 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: K 30 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7426 (ttm-80) REVERT: K 54 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: L 26 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: L 30 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: L 54 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6024 (mp0) REVERT: L 364 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6670 (mt0) outliers start: 135 outliers final: 36 residues processed: 502 average time/residue: 0.8538 time to fit residues: 512.7239 Evaluate side-chains 430 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 370 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [496, 41, 337, 203, 122, 398, 503, 52, 158, 225, 426] chunk 496 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 337 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 398 optimal weight: 0.5980 chunk 503 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 426 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106725 restraints weight = 45085.776| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.52 r_work: 0.3214 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44112 Z= 0.117 Angle : 0.520 6.486 59772 Z= 0.280 Chirality : 0.042 0.133 6744 Planarity : 0.005 0.044 7512 Dihedral : 6.642 53.163 6252 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.39 % Allowed : 13.21 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 5340 helix: 3.06 (0.14), residues: 1692 sheet: 0.48 (0.14), residues: 1224 loop : -1.60 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 238 TYR 0.011 0.001 TYR E 150 PHE 0.012 0.001 PHE I 264 TRP 0.006 0.001 TRP C 175 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (44064) covalent geometry : angle 0.51968 / 0.28 (59772) hydrogen bonds : bond 0.04597 / 3.11 ( 1812) hydrogen bonds : angle 4.33648 / 2.99 ( 5112) metal coordination : bond 0.00243 / 0.16 ( 36) Misc. bond : bond 0.00008 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 376 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 30 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7392 (ttm-80) REVERT: C 30 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7334 (ttm-80) REVERT: C 85 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (mmt90) REVERT: C 364 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6264 (mt0) REVERT: D 26 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: D 353 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: E 30 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7394 (ttm-80) REVERT: E 99 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7970 (mptm) REVERT: E 123 MET cc_start: 0.7698 (mmp) cc_final: 0.7433 (mmp) REVERT: F 30 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7308 (ttm-80) REVERT: F 85 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8333 (mmt90) REVERT: G 26 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: G 353 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: H 30 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7384 (ttm-80) REVERT: I 30 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7309 (ttm-80) REVERT: I 85 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8303 (mmt90) REVERT: I 99 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7783 (mptt) REVERT: I 364 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: J 26 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: J 353 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: K 30 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7397 (ttm-80) REVERT: L 30 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7309 (ttm-80) REVERT: L 85 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8284 (mmt90) REVERT: L 364 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6257 (mt0) outliers start: 110 outliers final: 30 residues processed: 464 average time/residue: 0.8186 time to fit residues: 460.6025 Evaluate side-chains 415 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [385, 105, 387, 70, 251, 195, 284, 247, 35, 304, 51] chunk 385 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 387 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098020 restraints weight = 44127.574| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.41 r_work: 0.3090 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 44112 Z= 0.310 Angle : 0.845 9.082 59772 Z= 0.473 Chirality : 0.055 0.172 6744 Planarity : 0.007 0.044 7512 Dihedral : 7.533 59.302 6248 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.65 % Allowed : 12.97 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.11), residues: 5340 helix: 2.52 (0.13), residues: 1692 sheet: 0.74 (0.16), residues: 876 loop : -1.62 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 252 TYR 0.022 0.003 TYR K 150 PHE 0.034 0.003 PHE A 183 TRP 0.012 0.002 TRP G 394 HIS 0.010 0.002 HIS F 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.31 (44064) covalent geometry : angle 0.84466 / 0.47 (59772) hydrogen bonds : bond 0.10244 / 6.87 ( 1812) hydrogen bonds : angle 5.09664 / 3.52 ( 5112) metal coordination : bond 0.00792 / 0.50 ( 36) Misc. bond : bond 0.00148 / 0.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 372 time to evaluate : 1.584 Fit side-chains REVERT: A 26 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: B 30 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (ttm-80) REVERT: B 84 MET cc_start: 0.8167 (mmm) cc_final: 0.7737 (mmt) REVERT: B 99 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8001 (mptt) REVERT: C 30 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7512 (ttm-80) REVERT: C 85 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8000 (mmm-85) REVERT: D 26 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: D 353 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: E 30 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7462 (ttm-80) REVERT: E 84 MET cc_start: 0.8168 (mmm) cc_final: 0.7674 (mmt) REVERT: E 99 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8023 (mptm) REVERT: F 30 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7324 (ttm-80) REVERT: G 26 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: G 353 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: H 30 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7448 (ttm-80) REVERT: H 84 MET cc_start: 0.8193 (mmm) cc_final: 0.7753 (mmt) REVERT: H 99 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8026 (mptt) REVERT: I 30 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7504 (ttm-80) REVERT: J 26 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: J 353 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: K 30 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7455 (ttm-80) REVERT: K 84 MET cc_start: 0.8163 (mmm) cc_final: 0.7729 (mmt) REVERT: K 99 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8001 (mptt) REVERT: L 26 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: L 30 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7508 (ttm-80) REVERT: L 85 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7993 (mmm-85) outliers start: 122 outliers final: 47 residues processed: 454 average time/residue: 0.8499 time to fit residues: 464.4840 Evaluate side-chains 438 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 369 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [425, 77, 188, 330, 15, 460, 502, 368, 38, 199, 259] chunk 425 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 460 optimal weight: 8.9990 chunk 502 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099704 restraints weight = 44266.726| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.41 r_work: 0.3117 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44112 Z= 0.226 Angle : 0.715 9.416 59772 Z= 0.399 Chirality : 0.049 0.157 6744 Planarity : 0.006 0.041 7512 Dihedral : 7.392 59.718 6248 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.42 % Allowed : 13.58 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.11), residues: 5340 helix: 2.64 (0.13), residues: 1692 sheet: 0.42 (0.15), residues: 984 loop : -1.57 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 238 TYR 0.018 0.002 TYR K 150 PHE 0.027 0.002 PHE A 183 TRP 0.011 0.002 TRP L 175 HIS 0.007 0.002 HIS I 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (44064) covalent geometry : angle 0.71539 / 0.40 (59772) hydrogen bonds : bond 0.08274 / 5.56 ( 1812) hydrogen bonds : angle 4.91422 / 3.39 ( 5112) metal coordination : bond 0.00573 / 0.37 ( 36) Misc. bond : bond 0.00084 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 377 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: A 353 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: B 5 TYR cc_start: 0.8425 (m-80) cc_final: 0.7841 (m-80) REVERT: B 30 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7463 (ttm-80) REVERT: C 26 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: C 30 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: C 85 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8362 (mmt90) REVERT: C 364 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6647 (mt0) REVERT: D 26 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: D 353 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: E 30 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7447 (ttm-80) REVERT: E 84 MET cc_start: 0.8088 (mmm) cc_final: 0.7669 (mmt) REVERT: F 26 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: F 30 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7311 (ttm-80) REVERT: G 26 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: G 353 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: H 30 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7432 (ttm-80) REVERT: I 26 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: I 30 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7308 (ttm-80) REVERT: I 364 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6640 (mt0) REVERT: J 26 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: J 353 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: K 30 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7511 (ttm-80) REVERT: L 26 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: L 30 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7329 (ttm-80) REVERT: L 85 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8344 (mmt90) REVERT: L 364 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6637 (mt0) outliers start: 111 outliers final: 41 residues processed: 460 average time/residue: 0.8300 time to fit residues: 462.6484 Evaluate side-chains 442 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 364 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [375, 530, 201, 81, 383, 354, 134, 466, 40, 407, 83] chunk 375 optimal weight: 4.9990 chunk 530 optimal weight: 4.9990 chunk 201 optimal weight: 0.0870 chunk 81 optimal weight: 0.3980 chunk 383 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 466 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 407 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 2.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100683 restraints weight = 44295.123| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.52 r_work: 0.3119 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44112 Z= 0.194 Angle : 0.660 8.892 59772 Z= 0.367 Chirality : 0.047 0.153 6744 Planarity : 0.005 0.041 7512 Dihedral : 7.242 57.461 6241 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.20 % Allowed : 13.99 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.11), residues: 5340 helix: 2.79 (0.14), residues: 1692 sheet: 0.32 (0.14), residues: 1104 loop : -1.56 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 238 TYR 0.017 0.002 TYR H 150 PHE 0.023 0.002 PHE G 183 TRP 0.010 0.001 TRP I 175 HIS 0.006 0.001 HIS F 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (44064) covalent geometry : angle 0.65989 / 0.37 (59772) hydrogen bonds : bond 0.07455 / 5.01 ( 1812) hydrogen bonds : angle 4.79654 / 3.31 ( 5112) metal coordination : bond 0.00462 / 0.29 ( 36) Misc. bond : bond 0.00052 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 377 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 353 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 30 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7501 (ttm-80) REVERT: B 84 MET cc_start: 0.8069 (mmm) cc_final: 0.7698 (mmt) REVERT: B 99 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7994 (mptt) REVERT: B 229 ARG cc_start: 0.3336 (OUTLIER) cc_final: 0.3053 (mtt180) REVERT: C 26 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: C 30 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7380 (ttm-80) REVERT: C 85 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8359 (mmt90) REVERT: C 364 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: D 26 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: D 353 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: E 30 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7510 (ttm-80) REVERT: F 30 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7362 (ttm-80) REVERT: G 26 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: G 353 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: H 30 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7474 (ttm-80) REVERT: H 84 MET cc_start: 0.8119 (mmm) cc_final: 0.7702 (mmt) REVERT: H 99 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7987 (mptt) REVERT: I 30 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7390 (ttm-80) REVERT: I 364 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: J 26 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: J 353 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: K 30 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7525 (ttm-80) REVERT: K 84 MET cc_start: 0.8079 (mmm) cc_final: 0.7701 (mmt) REVERT: K 99 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7984 (mptt) REVERT: K 229 ARG cc_start: 0.3300 (OUTLIER) cc_final: 0.2960 (mtt180) REVERT: K 232 LYS cc_start: 0.8297 (pttp) cc_final: 0.8082 (tttm) REVERT: L 26 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: L 30 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7351 (ttm-80) REVERT: L 85 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8342 (mmt90) REVERT: L 364 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6555 (mt0) outliers start: 101 outliers final: 49 residues processed: 452 average time/residue: 0.8067 time to fit residues: 443.0908 Evaluate side-chains 446 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 369 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [145, 360, 229, 28, 428, 353, 238, 348, 95, 96, 452] chunk 145 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 428 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 95 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 452 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103464 restraints weight = 44337.521| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.52 r_work: 0.3157 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44112 Z= 0.152 Angle : 0.587 8.074 59772 Z= 0.323 Chirality : 0.045 0.147 6744 Planarity : 0.005 0.039 7512 Dihedral : 7.038 55.461 6240 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.83 % Allowed : 14.45 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 5340 helix: 3.03 (0.14), residues: 1692 sheet: 0.40 (0.15), residues: 1104 loop : -1.54 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.014 0.001 TYR A 150 PHE 0.017 0.002 PHE J 183 TRP 0.009 0.001 TRP C 175 HIS 0.005 0.001 HIS K 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (44064) covalent geometry : angle 0.58721 / 0.32 (59772) hydrogen bonds : bond 0.06083 / 4.09 ( 1812) hydrogen bonds : angle 4.59261 / 3.17 ( 5112) metal coordination : bond 0.00328 / 0.21 ( 36) Misc. bond : bond 0.00031 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 372 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: A 345 ILE cc_start: 0.8473 (mm) cc_final: 0.8200 (tp) REVERT: A 353 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 30 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7431 (ttm-80) REVERT: C 26 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: C 30 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7412 (ttm-80) REVERT: C 85 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8358 (mmt90) REVERT: D 26 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: D 353 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: E 30 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7427 (ttm-80) REVERT: F 30 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7366 (ttm-80) REVERT: G 26 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: G 353 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: H 30 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7421 (ttm-80) REVERT: H 84 MET cc_start: 0.8045 (mmm) cc_final: 0.7662 (mmt) REVERT: I 26 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: I 30 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7387 (ttm-80) REVERT: J 26 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: J 345 ILE cc_start: 0.8481 (mm) cc_final: 0.8210 (tp) REVERT: J 353 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: K 30 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7423 (ttm-80) REVERT: K 84 MET cc_start: 0.8001 (mmm) cc_final: 0.7677 (mmt) REVERT: K 229 ARG cc_start: 0.3494 (OUTLIER) cc_final: 0.3102 (mtt180) REVERT: L 26 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: L 30 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7385 (ttm-80) REVERT: L 85 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8343 (mmt90) outliers start: 84 outliers final: 45 residues processed: 439 average time/residue: 0.7984 time to fit residues: 424.4962 Evaluate side-chains 436 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 369 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 229 ARG Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 229 ARG Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [377, 91, 421, 519, 244, 412, 349, 483, 411, 502, 456] chunk 377 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 421 optimal weight: 3.9990 chunk 519 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 349 optimal weight: 6.9990 chunk 483 optimal weight: 1.9990 chunk 411 optimal weight: 4.9990 chunk 502 optimal weight: 9.9990 chunk 456 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099119 restraints weight = 44239.652| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.41 r_work: 0.3112 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 44112 Z= 0.254 Angle : 0.753 8.961 59772 Z= 0.420 Chirality : 0.051 0.165 6744 Planarity : 0.006 0.041 7512 Dihedral : 7.398 59.141 6240 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.44 % Allowed : 14.10 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.11), residues: 5340 helix: 2.69 (0.13), residues: 1692 sheet: 0.73 (0.16), residues: 876 loop : -1.60 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 221 TYR 0.020 0.002 TYR A 150 PHE 0.029 0.003 PHE D 183 TRP 0.010 0.002 TRP I 175 HIS 0.007 0.002 HIS L 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.25 (44064) covalent geometry : angle 0.75287 / 0.42 (59772) hydrogen bonds : bond 0.09023 / 6.06 ( 1812) hydrogen bonds : angle 4.94056 / 3.41 ( 5112) metal coordination : bond 0.00627 / 0.40 ( 36) Misc. bond : bond 0.00081 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 375 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: A 353 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: B 30 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7543 (ttm-80) REVERT: B 84 MET cc_start: 0.8110 (mmm) cc_final: 0.7681 (mmt) REVERT: B 99 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8039 (mptt) REVERT: C 26 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: C 30 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: C 85 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8358 (mmt90) REVERT: D 26 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: D 353 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: E 30 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7541 (ttm-80) REVERT: E 84 MET cc_start: 0.8102 (mmm) cc_final: 0.7647 (mmt) REVERT: F 30 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7317 (ttm-80) REVERT: G 26 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: G 353 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: H 30 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7522 (ttm-80) REVERT: H 84 MET cc_start: 0.8111 (mmm) cc_final: 0.7645 (mmt) REVERT: H 99 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8039 (mptt) REVERT: I 26 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: I 30 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7370 (ttm-80) REVERT: J 26 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: J 353 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: K 30 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7513 (ttm-80) REVERT: K 84 MET cc_start: 0.8125 (mmm) cc_final: 0.7705 (mmt) REVERT: K 99 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8035 (mptt) REVERT: K 229 ARG cc_start: 0.3560 (OUTLIER) cc_final: 0.2763 (ttt90) REVERT: L 26 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: L 30 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7355 (ttm-80) REVERT: L 85 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (mmt90) outliers start: 112 outliers final: 59 residues processed: 460 average time/residue: 0.8035 time to fit residues: 447.7840 Evaluate side-chains 456 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 372 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 229 ARG Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 229 ARG Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [189, 134, 194, 323, 387, 475, 281, 159, 502, 174, 47] chunk 189 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 387 optimal weight: 8.9990 chunk 475 optimal weight: 0.0970 chunk 281 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 502 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102436 restraints weight = 44384.706| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.49 r_work: 0.3142 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44112 Z= 0.162 Angle : 0.609 8.640 59772 Z= 0.335 Chirality : 0.045 0.147 6744 Planarity : 0.005 0.039 7512 Dihedral : 7.118 55.749 6240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.13 % Allowed : 14.51 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 5340 helix: 2.91 (0.14), residues: 1692 sheet: 0.53 (0.15), residues: 984 loop : -1.48 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 238 TYR 0.015 0.001 TYR H 150 PHE 0.018 0.002 PHE D 183 TRP 0.009 0.001 TRP G 175 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (44064) covalent geometry : angle 0.60861 / 0.33 (59772) hydrogen bonds : bond 0.06452 / 4.34 ( 1812) hydrogen bonds : angle 4.65405 / 3.21 ( 5112) metal coordination : bond 0.00363 / 0.23 ( 36) Misc. bond : bond 0.00035 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 385 time to evaluate : 1.852 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 345 ILE cc_start: 0.8486 (mm) cc_final: 0.8210 (tp) REVERT: A 353 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: B 30 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7472 (ttm-80) REVERT: B 84 MET cc_start: 0.8047 (mmm) cc_final: 0.7723 (mmt) REVERT: B 99 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7995 (mptt) REVERT: C 26 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 30 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7464 (ttm-80) REVERT: C 85 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8351 (mmt90) REVERT: D 26 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: D 353 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: E 30 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7481 (ttm-80) REVERT: E 84 MET cc_start: 0.8030 (mmm) cc_final: 0.7673 (mmt) REVERT: F 30 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: G 26 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: G 353 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: H 30 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7481 (ttm-80) REVERT: H 84 MET cc_start: 0.8069 (mmm) cc_final: 0.7689 (mmt) REVERT: I 26 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: I 30 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7426 (ttm-80) REVERT: J 26 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: J 345 ILE cc_start: 0.8496 (mm) cc_final: 0.8222 (tp) REVERT: J 353 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: K 30 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7461 (ttm-80) REVERT: K 99 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: L 26 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: L 30 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7460 (ttm-80) REVERT: L 85 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (mmt90) outliers start: 98 outliers final: 54 residues processed: 461 average time/residue: 0.7942 time to fit residues: 446.0019 Evaluate side-chains 457 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 380 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [311, 67, 293, 42, 444, 390, 360, 99, 460, 379, 12] chunk 311 optimal weight: 0.0970 chunk 67 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 444 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 460 optimal weight: 3.9990 chunk 379 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 341 GLN I 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099380 restraints weight = 44183.966| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.41 r_work: 0.3112 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44112 Z= 0.244 Angle : 0.742 8.974 59772 Z= 0.413 Chirality : 0.050 0.164 6744 Planarity : 0.006 0.040 7512 Dihedral : 7.395 59.401 6240 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.18 % Allowed : 14.58 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.11), residues: 5340 helix: 2.71 (0.13), residues: 1692 sheet: 0.72 (0.16), residues: 876 loop : -1.61 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 238 TYR 0.020 0.002 TYR D 150 PHE 0.029 0.003 PHE D 183 TRP 0.011 0.002 TRP I 175 HIS 0.007 0.002 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (44064) covalent geometry : angle 0.74246 / 0.41 (59772) hydrogen bonds : bond 0.08855 / 5.94 ( 1812) hydrogen bonds : angle 4.91896 / 3.40 ( 5112) metal coordination : bond 0.00599 / 0.38 ( 36) Misc. bond : bond 0.00073 / 0.05 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 374 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: A 353 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: B 30 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7607 (ttm-80) REVERT: B 84 MET cc_start: 0.8094 (mmm) cc_final: 0.7635 (mmt) REVERT: B 99 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8031 (mptt) REVERT: C 26 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: C 30 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7411 (ttm-80) REVERT: C 85 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8345 (mmt90) REVERT: D 26 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: D 353 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: E 30 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7548 (ttm-80) REVERT: E 84 MET cc_start: 0.8092 (mmm) cc_final: 0.7684 (mmt) REVERT: F 30 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7338 (ttm-80) REVERT: G 26 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: G 353 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: H 30 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7528 (ttm-80) REVERT: H 84 MET cc_start: 0.8140 (mmm) cc_final: 0.7644 (mmt) REVERT: H 99 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8029 (mptt) REVERT: I 26 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: I 30 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7425 (ttm-80) REVERT: J 26 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: J 353 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: K 30 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7574 (ttm-80) REVERT: K 84 MET cc_start: 0.8115 (mmm) cc_final: 0.7699 (mmt) REVERT: K 99 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8025 (mptt) REVERT: L 26 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: L 30 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7403 (ttm-80) REVERT: L 85 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8341 (mmt90) outliers start: 100 outliers final: 62 residues processed: 451 average time/residue: 0.8057 time to fit residues: 441.4685 Evaluate side-chains 461 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 375 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 232 LYS Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: [537, 233, 304, 72, 388, 317, 93, 40, 75, 151, 445] chunk 537 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 317 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 445 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101692 restraints weight = 44708.368| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.53 r_work: 0.3137 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44112 Z= 0.178 Angle : 0.638 8.874 59772 Z= 0.352 Chirality : 0.046 0.150 6744 Planarity : 0.005 0.041 7512 Dihedral : 7.197 56.923 6240 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.09 % Allowed : 14.66 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.11), residues: 5340 helix: 2.88 (0.14), residues: 1692 sheet: 0.77 (0.16), residues: 876 loop : -1.56 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 238 TYR 0.017 0.002 TYR H 150 PHE 0.020 0.002 PHE A 183 TRP 0.009 0.001 TRP C 175 HIS 0.005 0.001 HIS L 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (44064) covalent geometry : angle 0.63825 / 0.35 (59772) hydrogen bonds : bond 0.06987 / 4.70 ( 1812) hydrogen bonds : angle 4.71666 / 3.26 ( 5112) metal coordination : bond 0.00411 / 0.26 ( 36) Misc. bond : bond 0.00039 / 0.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19712.67 seconds wall clock time: 334 minutes 41.70 seconds (20081.70 seconds total)