Starting phenix.real_space_refine on Sat Feb 7 16:07:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.map" model { file = "/net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q04_18049/02_2026/8q04_18049.cif" } resolution = 2.39 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 21960 2.51 5 N 6160 2.21 5 O 7647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35967 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3263 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "P" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1076 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "J" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "N" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "O" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: B, D, F, H, J, L, N, C, E, G, I, K, M, O Time building chain proxies: 4.61, per 1000 atoms: 0.13 Number of scatterers: 35967 At special positions: 0 Unit cell: (138.908, 138.908, 127.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 7647 8.00 N 6160 7.00 C 21960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8048 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 40 sheets defined 44.5% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL P 58 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 100 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU B 390 " --> pdb=" O HIS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL E 58 " --> pdb=" O GLU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 100 Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU F 390 " --> pdb=" O HIS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU F 460 " --> pdb=" O ALA F 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL G 58 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 100 Processing helix chain 'H' and resid 49 through 57 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU H 390 " --> pdb=" O HIS H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP H 443 " --> pdb=" O ARG H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU H 460 " --> pdb=" O ALA H 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL I 58 " --> pdb=" O GLU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 100 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 154 through 163 Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY J 195 " --> pdb=" O GLU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 246 through 261 Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 273 through 288 Processing helix chain 'J' and resid 298 through 303 Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU J 314 " --> pdb=" O HIS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 351 Processing helix chain 'J' and resid 383 through 385 No H-bonds generated for 'chain 'J' and resid 383 through 385' Processing helix chain 'J' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU J 390 " --> pdb=" O HIS J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 433 Processing helix chain 'J' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY J 442 " --> pdb=" O ALA J 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP J 443 " --> pdb=" O ARG J 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU J 460 " --> pdb=" O ALA J 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL K 58 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 100 Processing helix chain 'L' and resid 49 through 57 Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE L 108 " --> pdb=" O LEU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 122 Processing helix chain 'L' and resid 141 through 146 Processing helix chain 'L' and resid 154 through 163 Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY L 195 " --> pdb=" O GLU L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 246 through 261 Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 273 through 288 Processing helix chain 'L' and resid 298 through 303 Processing helix chain 'L' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU L 314 " --> pdb=" O HIS L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 351 Processing helix chain 'L' and resid 383 through 385 No H-bonds generated for 'chain 'L' and resid 383 through 385' Processing helix chain 'L' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU L 390 " --> pdb=" O HIS L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY L 442 " --> pdb=" O ALA L 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP L 443 " --> pdb=" O ARG L 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU L 460 " --> pdb=" O ALA L 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 48 through 50 No H-bonds generated for 'chain 'M' and resid 48 through 50' Processing helix chain 'M' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL M 58 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 100 Processing helix chain 'N' and resid 49 through 57 Processing helix chain 'N' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE N 108 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 122 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 154 through 163 Processing helix chain 'N' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY N 195 " --> pdb=" O GLU N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 233 Processing helix chain 'N' and resid 246 through 261 Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 273 through 288 Processing helix chain 'N' and resid 298 through 303 Processing helix chain 'N' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU N 314 " --> pdb=" O HIS N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 351 Processing helix chain 'N' and resid 383 through 385 No H-bonds generated for 'chain 'N' and resid 383 through 385' Processing helix chain 'N' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU N 390 " --> pdb=" O HIS N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 433 Processing helix chain 'N' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY N 442 " --> pdb=" O ALA N 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP N 443 " --> pdb=" O ARG N 439 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing helix chain 'O' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL O 58 " --> pdb=" O GLU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS A 294 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 291 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS A 327 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 293 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY A 329 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS A 325 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 377 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS A 327 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER A 379 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY A 329 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'P' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'P' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE P 105 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP P 111 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN P 117 " --> pdb=" O ASP P 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 172 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS B 294 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 291 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS B 327 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 293 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY B 329 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS B 325 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 377 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS B 327 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER B 379 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY B 329 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE C 105 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP C 111 " --> pdb=" O GLN C 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN C 117 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU D 170 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS D 201 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS D 172 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS D 294 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 291 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS D 327 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 293 " --> pdb=" O HIS D 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY D 329 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS D 325 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 377 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS D 327 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER D 379 " --> pdb=" O HIS D 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY D 329 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN D 401 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 378 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY D 171 " --> pdb=" O PHE D 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB6, first strand: chain 'E' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE E 105 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP E 111 " --> pdb=" O GLN E 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN E 117 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS F 294 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 291 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS F 327 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE F 293 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY F 329 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS F 325 " --> pdb=" O MET F 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 377 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS F 327 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER F 379 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY F 329 " --> pdb=" O SER F 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 4 Processing sheet with id=AC2, first strand: chain 'G' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE G 105 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP G 111 " --> pdb=" O GLN G 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN G 117 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS H 172 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS H 294 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU H 291 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS H 327 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE H 293 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY H 329 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS H 325 " --> pdb=" O MET H 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL H 377 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS H 327 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER H 379 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY H 329 " --> pdb=" O SER H 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AC7, first strand: chain 'I' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE I 105 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP I 111 " --> pdb=" O GLN I 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN I 117 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP J 86 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA J 39 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU J 170 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS J 201 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS J 172 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS J 294 " --> pdb=" O ILE J 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU J 291 " --> pdb=" O HIS J 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS J 327 " --> pdb=" O LEU J 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE J 293 " --> pdb=" O HIS J 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY J 329 " --> pdb=" O ILE J 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS J 325 " --> pdb=" O MET J 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL J 377 " --> pdb=" O HIS J 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS J 327 " --> pdb=" O VAL J 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER J 379 " --> pdb=" O HIS J 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 329 " --> pdb=" O SER J 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE J 402 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY J 171 " --> pdb=" O PHE J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 353 through 354 Processing sheet with id=AD2, first strand: chain 'K' and resid 3 through 4 Processing sheet with id=AD3, first strand: chain 'K' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE K 105 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP K 111 " --> pdb=" O GLN K 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN K 117 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS L 84 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA L 102 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP L 86 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA L 39 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU L 170 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS L 201 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS L 172 " --> pdb=" O LYS L 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR L 200 " --> pdb=" O TYR L 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN L 241 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS L 238 " --> pdb=" O ILE L 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET L 266 " --> pdb=" O HIS L 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU L 240 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP L 268 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE L 265 " --> pdb=" O HIS L 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS L 294 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS L 267 " --> pdb=" O HIS L 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU L 291 " --> pdb=" O HIS L 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS L 327 " --> pdb=" O LEU L 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE L 293 " --> pdb=" O HIS L 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY L 329 " --> pdb=" O ILE L 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS L 325 " --> pdb=" O MET L 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL L 377 " --> pdb=" O HIS L 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS L 327 " --> pdb=" O VAL L 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER L 379 " --> pdb=" O HIS L 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY L 329 " --> pdb=" O SER L 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN L 401 " --> pdb=" O PRO L 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA L 378 " --> pdb=" O GLN L 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU L 169 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE L 402 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY L 171 " --> pdb=" O PHE L 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 353 through 354 Processing sheet with id=AD7, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AD8, first strand: chain 'M' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE M 105 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP M 111 " --> pdb=" O GLN M 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN M 117 " --> pdb=" O ASP M 111 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS N 84 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA N 102 " --> pdb=" O CYS N 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP N 86 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA N 39 " --> pdb=" O GLU N 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU N 170 " --> pdb=" O PHE N 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS N 201 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS N 172 " --> pdb=" O LYS N 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR N 200 " --> pdb=" O TYR N 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN N 241 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS N 238 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET N 266 " --> pdb=" O HIS N 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU N 240 " --> pdb=" O MET N 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP N 268 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE N 265 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS N 294 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS N 267 " --> pdb=" O HIS N 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU N 291 " --> pdb=" O HIS N 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS N 327 " --> pdb=" O LEU N 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE N 293 " --> pdb=" O HIS N 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY N 329 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS N 325 " --> pdb=" O MET N 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL N 377 " --> pdb=" O HIS N 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS N 327 " --> pdb=" O VAL N 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER N 379 " --> pdb=" O HIS N 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY N 329 " --> pdb=" O SER N 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN N 401 " --> pdb=" O PRO N 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA N 378 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU N 169 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE N 402 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY N 171 " --> pdb=" O PHE N 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'N' and resid 353 through 354 Processing sheet with id=AE3, first strand: chain 'O' and resid 3 through 4 Processing sheet with id=AE4, first strand: chain 'O' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE O 105 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP O 111 " --> pdb=" O GLN O 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN O 117 " --> pdb=" O ASP O 111 " (cutoff:3.500A) 1528 hydrogen bonds defined for protein. 4344 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: 8.13 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9000 1.33 - 1.45: 7176 1.45 - 1.57: 19104 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 35568 Sorted by residual: bond pdb=" N VAL K 123 " pdb=" CA VAL K 123 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" N VAL M 123 " pdb=" CA VAL M 123 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" N VAL E 123 " pdb=" CA VAL E 123 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" N VAL I 123 " pdb=" CA VAL I 123 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" N VAL G 123 " pdb=" CA VAL G 123 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.59e+01 ... (remaining 35563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 40752 1.36 - 2.72: 6096 2.72 - 4.08: 1264 4.08 - 5.44: 112 5.44 - 6.80: 24 Bond angle restraints: 48248 Sorted by residual: angle pdb=" CA GLY F 337 " pdb=" C GLY F 337 " pdb=" O GLY F 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA GLY A 337 " pdb=" C GLY A 337 " pdb=" O GLY A 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA GLY N 337 " pdb=" C GLY N 337 " pdb=" O GLY N 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA GLY J 337 " pdb=" C GLY J 337 " pdb=" O GLY J 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA GLY B 337 " pdb=" C GLY B 337 " pdb=" O GLY B 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 ... (remaining 48243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 18392 17.42 - 34.85: 1968 34.85 - 52.27: 432 52.27 - 69.69: 192 69.69 - 87.11: 40 Dihedral angle restraints: 21024 sinusoidal: 8376 harmonic: 12648 Sorted by residual: dihedral pdb=" CA LYS A 175 " pdb=" C LYS A 175 " pdb=" N PRO A 176 " pdb=" CA PRO A 176 " ideal model delta harmonic sigma weight residual 0.00 31.39 -31.39 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LYS B 175 " pdb=" C LYS B 175 " pdb=" N PRO B 176 " pdb=" CA PRO B 176 " ideal model delta harmonic sigma weight residual 0.00 31.39 -31.39 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LYS D 175 " pdb=" C LYS D 175 " pdb=" N PRO D 176 " pdb=" CA PRO D 176 " ideal model delta harmonic sigma weight residual 0.00 31.39 -31.39 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 21021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2800 0.042 - 0.084: 1176 0.084 - 0.126: 760 0.126 - 0.168: 256 0.168 - 0.210: 128 Chirality restraints: 5120 Sorted by residual: chirality pdb=" CA GLU P 43 " pdb=" N GLU P 43 " pdb=" C GLU P 43 " pdb=" CB GLU P 43 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU O 43 " pdb=" N GLU O 43 " pdb=" C GLU O 43 " pdb=" CB GLU O 43 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU M 43 " pdb=" N GLU M 43 " pdb=" C GLU M 43 " pdb=" CB GLU M 43 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5117 not shown) Planarity restraints: 6352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.619 9.50e-02 1.11e+02 2.77e-01 4.70e+01 pdb=" NE ARG B 134 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 134 " -0.619 9.50e-02 1.11e+02 2.77e-01 4.70e+01 pdb=" NE ARG F 134 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG F 134 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 134 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 134 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 134 " -0.619 9.50e-02 1.11e+02 2.77e-01 4.70e+01 pdb=" NE ARG A 134 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 134 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 134 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 134 " -0.019 2.00e-02 2.50e+03 ... (remaining 6349 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5760 2.76 - 3.30: 35717 3.30 - 3.83: 68505 3.83 - 4.37: 86498 4.37 - 4.90: 137397 Nonbonded interactions: 333877 Sorted by model distance: nonbonded pdb=" OH TYR F 80 " pdb=" O HOH F 501 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 80 " pdb=" O HOH A 501 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 80 " pdb=" O HOH B 501 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR N 80 " pdb=" O HOH N 501 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR D 80 " pdb=" O HOH D 501 " model vdw 2.229 3.040 ... (remaining 333872 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.260 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.008 0.037 35568 Z= 0.588 Angle : 1.007 6.801 48248 Z= 0.739 Chirality : 0.068 0.210 5120 Planarity : 0.021 0.277 6352 Dihedral : 16.209 87.114 12976 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.58 (0.12), residues: 4360 helix: 1.66 (0.12), residues: 1632 sheet: -0.33 (0.19), residues: 688 loop : -0.35 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 187 TYR 0.015 0.002 TYR A 24 PHE 0.016 0.002 PHE F 345 TRP 0.024 0.002 TRP A 385 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00819 (35568) covalent geometry : angle 1.00681 (48248) hydrogen bonds : bond 0.14320 ( 1528) hydrogen bonds : angle 7.02924 ( 4344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.230 Fit side-chains TARDY: cannot create tardy model for: "THR P 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR E 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR G 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR I 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR K 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR O 14 " (corrupted residue). Skipping it. REVERT: P 25 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7747 (mt-10) REVERT: P 92 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 25 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 92 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7968 (mm-30) REVERT: E 25 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7749 (mt-10) REVERT: E 92 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7971 (mm-30) REVERT: G 25 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7749 (mt-10) REVERT: G 92 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7971 (mm-30) REVERT: I 25 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7744 (mt-10) REVERT: I 92 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7971 (mm-30) REVERT: K 25 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7743 (mt-10) REVERT: K 92 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7974 (mm-30) REVERT: M 25 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7747 (mt-10) REVERT: M 92 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7970 (mm-30) REVERT: O 25 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7746 (mt-10) REVERT: O 92 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7974 (mm-30) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.8707 time to fit residues: 754.1899 Evaluate side-chains 600 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 0.0670 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 383 HIS A 413 ASN P 2 GLN P 9 ASN P 29 GLN B 304 GLN B 383 HIS B 413 ASN C 2 GLN C 9 ASN C 29 GLN D 304 GLN D 383 HIS D 413 ASN E 2 GLN E 9 ASN E 29 GLN F 304 GLN F 383 HIS F 413 ASN G 2 GLN G 9 ASN G 29 GLN H 304 GLN H 383 HIS H 413 ASN I 2 GLN I 9 ASN I 29 GLN J 304 GLN J 383 HIS J 413 ASN K 2 GLN K 9 ASN K 29 GLN L 304 GLN L 383 HIS L 413 ASN M 2 GLN M 9 ASN M 29 GLN N 304 GLN N 383 HIS N 413 ASN O 2 GLN O 9 ASN O 29 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105197 restraints weight = 37340.225| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.49 r_work: 0.2948 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35568 Z= 0.185 Angle : 0.581 6.150 48248 Z= 0.315 Chirality : 0.045 0.171 5120 Planarity : 0.005 0.062 6352 Dihedral : 4.566 18.671 4920 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 17.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.12), residues: 4360 helix: 2.06 (0.12), residues: 1664 sheet: -0.18 (0.20), residues: 672 loop : -0.18 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 305 TYR 0.015 0.002 TYR E 67 PHE 0.018 0.002 PHE A 311 TRP 0.014 0.002 TRP A 385 HIS 0.012 0.002 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00420 (35568) covalent geometry : angle 0.58081 (48248) hydrogen bonds : bond 0.04834 ( 1528) hydrogen bonds : angle 5.51840 ( 4344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 592 time to evaluate : 1.416 Fit side-chains REVERT: A 305 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.8015 (ttp-110) REVERT: A 339 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7343 (ttt-90) REVERT: A 358 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8266 (mmm-85) REVERT: P 2 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6074 (mt0) REVERT: P 25 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8058 (mt-10) REVERT: P 92 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 305 ARG cc_start: 0.8401 (ttt-90) cc_final: 0.8122 (ttp-110) REVERT: B 339 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7343 (ttt-90) REVERT: B 358 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8266 (mmm-85) REVERT: C 2 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6071 (mt0) REVERT: C 25 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 92 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8187 (mm-30) REVERT: D 305 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.8120 (ttp-110) REVERT: D 339 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7352 (ttt-90) REVERT: D 358 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: E 2 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6071 (mt0) REVERT: E 25 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8072 (mt-10) REVERT: F 305 ARG cc_start: 0.8404 (ttt-90) cc_final: 0.8129 (ttp-110) REVERT: F 339 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7352 (ttt-90) REVERT: F 358 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8259 (mmm-85) REVERT: G 2 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6075 (mt0) REVERT: G 25 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8057 (mt-10) REVERT: H 305 ARG cc_start: 0.8400 (ttt-90) cc_final: 0.8015 (ttp-110) REVERT: H 339 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7341 (ttt-90) REVERT: H 358 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8269 (mmm-85) REVERT: I 2 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6068 (mt0) REVERT: I 25 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8060 (mt-10) REVERT: J 305 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.8118 (ttp-110) REVERT: J 339 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7334 (ttt-90) REVERT: J 358 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: K 2 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6068 (mt0) REVERT: K 25 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8060 (mt-10) REVERT: L 305 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.7979 (ttp-110) REVERT: L 339 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7339 (ttt-90) REVERT: L 358 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8265 (mmm-85) REVERT: M 2 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6060 (mt0) REVERT: M 25 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8058 (mt-10) REVERT: M 94 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: N 305 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.8013 (ttp-110) REVERT: N 339 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7338 (ttt-90) REVERT: N 358 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8270 (mmm-85) REVERT: O 2 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6077 (mt0) REVERT: O 25 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8053 (mt-10) REVERT: O 94 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7438 (mp10) outliers start: 72 outliers final: 8 residues processed: 624 average time/residue: 0.9042 time to fit residues: 656.7969 Evaluate side-chains 546 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 528 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain P residue 2 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 2 GLN Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 204 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS P 29 GLN B 383 HIS C 29 GLN D 383 HIS E 29 GLN F 383 HIS G 29 GLN H 383 HIS I 29 GLN J 383 HIS K 29 GLN L 383 HIS M 29 GLN N 383 HIS O 29 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102519 restraints weight = 37315.886| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.53 r_work: 0.2910 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 35568 Z= 0.287 Angle : 0.659 5.472 48248 Z= 0.357 Chirality : 0.050 0.191 5120 Planarity : 0.006 0.075 6352 Dihedral : 4.930 19.964 4920 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 14.67 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.72 (0.12), residues: 4360 helix: 1.72 (0.12), residues: 1656 sheet: -0.09 (0.20), residues: 672 loop : -0.31 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 187 TYR 0.018 0.003 TYR L 269 PHE 0.022 0.003 PHE C 12 TRP 0.012 0.002 TRP A 385 HIS 0.013 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00665 (35568) covalent geometry : angle 0.65910 (48248) hydrogen bonds : bond 0.05488 ( 1528) hydrogen bonds : angle 5.55050 ( 4344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 512 time to evaluate : 1.400 Fit side-chains REVERT: A 305 ARG cc_start: 0.8433 (ttt-90) cc_final: 0.8053 (ttp-110) REVERT: P 94 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: B 305 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.8133 (ttp-110) REVERT: C 94 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: D 305 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.8135 (ttp-110) REVERT: E 94 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: F 305 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.8154 (ttp-110) REVERT: G 94 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: H 305 ARG cc_start: 0.8440 (ttt-90) cc_final: 0.8054 (ttp-110) REVERT: I 94 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: J 305 ARG cc_start: 0.8427 (ttt-90) cc_final: 0.8144 (ttp-110) REVERT: K 94 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: L 305 ARG cc_start: 0.8439 (ttt-90) cc_final: 0.8048 (ttp-110) REVERT: M 94 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: N 305 ARG cc_start: 0.8432 (ttt-90) cc_final: 0.8051 (ttp-110) REVERT: O 94 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7248 (mp10) outliers start: 88 outliers final: 32 residues processed: 560 average time/residue: 0.8924 time to fit residues: 584.0504 Evaluate side-chains 540 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 500 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 GLN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 304 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105455 restraints weight = 37128.290| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.56 r_work: 0.2931 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35568 Z= 0.129 Angle : 0.510 4.748 48248 Z= 0.279 Chirality : 0.042 0.162 5120 Planarity : 0.004 0.041 6352 Dihedral : 4.641 18.663 4920 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.97 % Allowed : 15.58 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4360 helix: 2.15 (0.12), residues: 1664 sheet: -0.16 (0.19), residues: 688 loop : -0.26 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 305 TYR 0.012 0.001 TYR A 269 PHE 0.023 0.002 PHE N 345 TRP 0.012 0.001 TRP B 385 HIS 0.007 0.001 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00287 (35568) covalent geometry : angle 0.50985 (48248) hydrogen bonds : bond 0.04018 ( 1528) hydrogen bonds : angle 5.15348 ( 4344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 535 time to evaluate : 1.393 Fit side-chains REVERT: A 303 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8125 (ttt90) REVERT: A 305 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.7988 (ttp-110) REVERT: P 25 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8044 (mt-10) REVERT: P 92 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8168 (mm-30) REVERT: P 94 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: B 303 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8124 (ttt90) REVERT: B 305 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.8080 (ttp-110) REVERT: C 25 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8045 (mt-10) REVERT: C 92 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 94 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: D 83 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8632 (ptm160) REVERT: D 303 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8115 (ttt90) REVERT: D 305 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.8086 (ttp-110) REVERT: E 25 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: E 92 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8231 (mm-30) REVERT: F 83 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8631 (ptm160) REVERT: F 303 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8125 (ttt90) REVERT: F 305 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.8101 (ttp-110) REVERT: G 25 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: G 92 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8220 (mm-30) REVERT: H 83 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8634 (ptm160) REVERT: H 303 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8127 (ttt90) REVERT: H 305 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.7987 (ttp-110) REVERT: I 25 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8046 (mt-10) REVERT: I 92 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8224 (mm-30) REVERT: J 83 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8633 (ptm160) REVERT: J 303 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8100 (ttt90) REVERT: J 305 ARG cc_start: 0.8378 (ttt-90) cc_final: 0.8093 (ttp-110) REVERT: K 25 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8030 (mt-10) REVERT: K 92 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8230 (mm-30) REVERT: L 83 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8647 (ptm160) REVERT: L 303 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8090 (ttt90) REVERT: L 305 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.7980 (ttp-110) REVERT: M 25 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8023 (mt-10) REVERT: M 90 LEU cc_start: 0.8275 (mt) cc_final: 0.7805 (tp) REVERT: M 94 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: N 303 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8115 (ttt90) REVERT: N 305 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.7984 (ttp-110) REVERT: O 25 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8035 (mt-10) REVERT: O 90 LEU cc_start: 0.8256 (mt) cc_final: 0.7778 (tp) REVERT: O 92 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8182 (mm-30) REVERT: O 94 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7414 (mp10) outliers start: 71 outliers final: 25 residues processed: 567 average time/residue: 0.8510 time to fit residues: 562.5290 Evaluate side-chains 556 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 512 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 83 ARG Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 271 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 97 optimal weight: 30.0000 chunk 381 optimal weight: 10.0000 chunk 371 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 56 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 overall best weight: 4.1926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105269 restraints weight = 37124.308| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.45 r_work: 0.2949 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35568 Z= 0.151 Angle : 0.530 4.814 48248 Z= 0.288 Chirality : 0.043 0.166 5120 Planarity : 0.005 0.043 6352 Dihedral : 4.639 18.732 4920 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 16.22 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4360 helix: 2.13 (0.12), residues: 1664 sheet: -0.11 (0.20), residues: 688 loop : -0.27 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 130 TYR 0.012 0.002 TYR D 269 PHE 0.024 0.002 PHE L 345 TRP 0.012 0.001 TRP D 385 HIS 0.008 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00344 (35568) covalent geometry : angle 0.52959 (48248) hydrogen bonds : bond 0.04157 ( 1528) hydrogen bonds : angle 5.12634 ( 4344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 510 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8627 (ptm160) REVERT: A 303 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7580 (ttt180) REVERT: A 305 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8000 (ttp-110) REVERT: B 175 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8207 (mttp) REVERT: B 303 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7587 (ttt180) REVERT: B 305 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.8081 (ttp-110) REVERT: D 83 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8620 (ptm160) REVERT: D 175 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8196 (mttp) REVERT: D 305 ARG cc_start: 0.8355 (ttt-90) cc_final: 0.8083 (ttp-110) REVERT: E 92 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8194 (mm-30) REVERT: F 83 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8620 (ptm160) REVERT: F 305 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.8103 (ttp-110) REVERT: G 92 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8180 (mm-30) REVERT: H 83 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (ptm160) REVERT: H 175 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8198 (mttp) REVERT: H 303 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7574 (ttt180) REVERT: H 305 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.8004 (ttp-110) REVERT: I 92 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8184 (mm-30) REVERT: J 83 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8620 (ptm160) REVERT: J 175 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8206 (mttp) REVERT: J 305 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.8100 (ttp-110) REVERT: K 92 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8187 (mm-30) REVERT: L 83 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8631 (ptm160) REVERT: L 305 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.7997 (ttp-110) REVERT: M 94 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: N 83 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8629 (ptm160) REVERT: N 303 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: N 305 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.8002 (ttp-110) REVERT: O 92 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8175 (mm-30) REVERT: O 94 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7398 (mp10) outliers start: 66 outliers final: 29 residues processed: 542 average time/residue: 0.7564 time to fit residues: 481.9558 Evaluate side-chains 541 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 499 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 83 ARG Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 83 ARG Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 324 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 363 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 405 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN B 383 HIS C 29 GLN D 383 HIS E 29 GLN G 29 GLN H 383 HIS I 29 GLN K 29 GLN M 29 GLN N 383 HIS O 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103486 restraints weight = 37085.459| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.49 r_work: 0.2922 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35568 Z= 0.224 Angle : 0.595 5.111 48248 Z= 0.322 Chirality : 0.047 0.174 5120 Planarity : 0.005 0.052 6352 Dihedral : 4.873 19.147 4920 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.64 % Allowed : 15.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.75 (0.12), residues: 4360 helix: 1.83 (0.12), residues: 1664 sheet: -0.25 (0.18), residues: 768 loop : -0.29 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 217 TYR 0.016 0.002 TYR L 269 PHE 0.023 0.003 PHE J 345 TRP 0.013 0.002 TRP D 385 HIS 0.010 0.002 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00518 (35568) covalent geometry : angle 0.59513 (48248) hydrogen bonds : bond 0.04851 ( 1528) hydrogen bonds : angle 5.30353 ( 4344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 515 time to evaluate : 1.377 Fit side-chains REVERT: A 83 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8619 (ptm160) REVERT: A 303 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7621 (ttt180) REVERT: A 305 ARG cc_start: 0.8412 (ttt-90) cc_final: 0.8027 (ttp-110) REVERT: P 25 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: P 94 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: B 303 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.7640 (ttt180) REVERT: B 305 ARG cc_start: 0.8349 (ttt-90) cc_final: 0.8096 (ttp-110) REVERT: C 25 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: C 94 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: D 83 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8618 (ptm160) REVERT: D 303 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7620 (ttt180) REVERT: D 305 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8098 (ttp-110) REVERT: E 25 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: E 94 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: F 83 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8623 (ptm160) REVERT: F 303 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: F 305 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8113 (ttp-110) REVERT: G 25 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: G 94 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: H 83 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8616 (ptm160) REVERT: H 303 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7611 (ttt180) REVERT: H 305 ARG cc_start: 0.8429 (ttt-90) cc_final: 0.8034 (ttp-110) REVERT: I 25 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: I 94 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: J 83 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8616 (ptm160) REVERT: J 303 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7595 (ttt180) REVERT: J 305 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.8102 (ttp-110) REVERT: K 25 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: L 83 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (ptm160) REVERT: L 303 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7595 (ttt180) REVERT: L 305 ARG cc_start: 0.8427 (ttt-90) cc_final: 0.8032 (ttp-110) REVERT: M 25 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: M 94 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: N 83 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8621 (ptm160) REVERT: N 303 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7610 (ttt180) REVERT: N 305 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.8028 (ttp-110) REVERT: O 25 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: O 92 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8171 (mm-30) REVERT: O 94 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7347 (mp10) outliers start: 95 outliers final: 32 residues processed: 555 average time/residue: 0.7859 time to fit residues: 513.1508 Evaluate side-chains 561 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 499 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 42 MET Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 83 ARG Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 83 ARG Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 427 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 321 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105677 restraints weight = 37320.620| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.54 r_work: 0.2941 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35568 Z= 0.128 Angle : 0.510 4.672 48248 Z= 0.278 Chirality : 0.042 0.161 5120 Planarity : 0.004 0.042 6352 Dihedral : 4.633 18.811 4920 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.58 % Allowed : 16.92 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.12), residues: 4360 helix: 2.17 (0.12), residues: 1664 sheet: -0.00 (0.20), residues: 688 loop : -0.30 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 305 TYR 0.012 0.001 TYR E 67 PHE 0.024 0.002 PHE L 345 TRP 0.014 0.001 TRP B 385 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00288 (35568) covalent geometry : angle 0.50978 (48248) hydrogen bonds : bond 0.03875 ( 1528) hydrogen bonds : angle 5.06317 ( 4344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 498 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.8029 (ttp-110) REVERT: P 25 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: P 90 LEU cc_start: 0.8222 (mt) cc_final: 0.8008 (tp) REVERT: B 305 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.8100 (ttp-110) REVERT: C 25 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: C 90 LEU cc_start: 0.8226 (mt) cc_final: 0.8007 (tp) REVERT: D 305 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.8096 (ttp-110) REVERT: E 25 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: F 305 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8107 (ttp-110) REVERT: G 25 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: H 305 ARG cc_start: 0.8450 (ttt-90) cc_final: 0.8041 (ttp-110) REVERT: I 25 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: J 305 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8105 (ttp-110) REVERT: K 25 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: K 94 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: L 305 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8035 (ttp-110) REVERT: M 25 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: M 90 LEU cc_start: 0.8246 (mt) cc_final: 0.7796 (tp) REVERT: M 94 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: N 305 ARG cc_start: 0.8440 (ttt-90) cc_final: 0.8067 (ttp-110) REVERT: O 25 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: O 90 LEU cc_start: 0.8185 (mt) cc_final: 0.7774 (tp) REVERT: O 92 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8163 (mm-30) REVERT: O 94 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7321 (mp10) outliers start: 57 outliers final: 25 residues processed: 522 average time/residue: 0.8264 time to fit residues: 505.2258 Evaluate side-chains 532 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 496 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain K residue 94 GLN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 129 optimal weight: 8.9990 chunk 438 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 316 optimal weight: 0.1980 chunk 166 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103892 restraints weight = 37088.260| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.49 r_work: 0.2933 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35568 Z= 0.194 Angle : 0.571 4.965 48248 Z= 0.310 Chirality : 0.045 0.172 5120 Planarity : 0.005 0.046 6352 Dihedral : 4.790 19.091 4920 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.58 % Allowed : 16.83 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.12), residues: 4360 helix: 1.93 (0.12), residues: 1664 sheet: -0.25 (0.18), residues: 768 loop : -0.27 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 130 TYR 0.014 0.002 TYR N 269 PHE 0.026 0.002 PHE A 345 TRP 0.017 0.001 TRP D 385 HIS 0.009 0.002 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00448 (35568) covalent geometry : angle 0.57137 (48248) hydrogen bonds : bond 0.04536 ( 1528) hydrogen bonds : angle 5.20091 ( 4344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 1.290 Fit side-chains REVERT: A 303 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7684 (ttt180) REVERT: A 305 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.8035 (ttp-110) REVERT: P 25 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: P 94 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: B 303 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.7686 (ttt180) REVERT: B 305 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.8094 (ttp-110) REVERT: C 25 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: C 94 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: D 303 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7688 (ttt180) REVERT: D 305 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.8089 (ttp-110) REVERT: E 25 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: E 94 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: F 303 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7686 (ttt180) REVERT: F 305 ARG cc_start: 0.8355 (ttt-90) cc_final: 0.8106 (ttp-110) REVERT: G 25 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: G 94 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: H 303 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7665 (ttt180) REVERT: H 305 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8038 (ttp-110) REVERT: I 25 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: I 94 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: J 303 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7659 (ttt180) REVERT: J 305 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.8090 (ttp-110) REVERT: K 25 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: L 303 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7656 (ttt180) REVERT: L 305 ARG cc_start: 0.8415 (ttt-90) cc_final: 0.8028 (ttp-110) REVERT: M 25 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: N 303 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7673 (ttt180) REVERT: N 305 ARG cc_start: 0.8415 (ttt-90) cc_final: 0.8035 (ttp-110) REVERT: O 25 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: O 94 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7264 (mp10) outliers start: 57 outliers final: 25 residues processed: 520 average time/residue: 0.8014 time to fit residues: 488.3919 Evaluate side-chains 538 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 491 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 94 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 274 optimal weight: 20.0000 chunk 346 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 286 optimal weight: 0.0670 chunk 305 optimal weight: 10.0000 chunk 422 optimal weight: 40.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106311 restraints weight = 37162.123| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.54 r_work: 0.2950 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35568 Z= 0.119 Angle : 0.504 4.693 48248 Z= 0.274 Chirality : 0.042 0.157 5120 Planarity : 0.004 0.042 6352 Dihedral : 4.555 18.608 4920 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.89 % Allowed : 16.36 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4360 helix: 2.22 (0.12), residues: 1664 sheet: -0.00 (0.20), residues: 688 loop : -0.26 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 130 TYR 0.011 0.001 TYR K 67 PHE 0.024 0.002 PHE A 345 TRP 0.017 0.001 TRP D 385 HIS 0.006 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00270 (35568) covalent geometry : angle 0.50374 (48248) hydrogen bonds : bond 0.03692 ( 1528) hydrogen bonds : angle 4.98192 ( 4344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 507 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.8050 (ttp-110) REVERT: P 25 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: P 90 LEU cc_start: 0.8248 (mt) cc_final: 0.8024 (tp) REVERT: B 305 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8092 (ttp-110) REVERT: C 25 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: C 90 LEU cc_start: 0.8254 (mt) cc_final: 0.8025 (tp) REVERT: D 83 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8627 (ptm160) REVERT: D 303 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: D 305 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.8098 (ttp-110) REVERT: E 25 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: E 90 LEU cc_start: 0.8237 (mt) cc_final: 0.8000 (tp) REVERT: F 305 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.8108 (ttp-110) REVERT: G 25 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: G 90 LEU cc_start: 0.8233 (mt) cc_final: 0.8000 (tp) REVERT: H 305 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.8045 (ttp-110) REVERT: I 25 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: I 90 LEU cc_start: 0.8244 (mt) cc_final: 0.8009 (tp) REVERT: J 83 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8628 (ptm160) REVERT: J 303 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: J 305 ARG cc_start: 0.8348 (ttt-90) cc_final: 0.8093 (ttp-110) REVERT: K 25 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: L 305 ARG cc_start: 0.8416 (ttt-90) cc_final: 0.8063 (ttp-110) REVERT: M 25 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: N 83 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8626 (ptm160) REVERT: N 305 ARG cc_start: 0.8392 (ttt-90) cc_final: 0.8054 (ttp-110) REVERT: O 25 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: O 90 LEU cc_start: 0.8228 (mt) cc_final: 0.8003 (tp) outliers start: 68 outliers final: 27 residues processed: 539 average time/residue: 0.7793 time to fit residues: 494.3952 Evaluate side-chains 534 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 494 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 83 ARG Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 430 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 394 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN B 383 HIS C 29 GLN E 29 GLN G 29 GLN H 383 HIS I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104155 restraints weight = 37125.919| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.50 r_work: 0.2932 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 35568 Z= 0.197 Angle : 0.572 4.958 48248 Z= 0.310 Chirality : 0.045 0.171 5120 Planarity : 0.005 0.048 6352 Dihedral : 4.759 18.955 4920 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.19 % Allowed : 16.92 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.85 (0.12), residues: 4360 helix: 1.96 (0.12), residues: 1664 sheet: -0.21 (0.19), residues: 768 loop : -0.28 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 130 TYR 0.014 0.002 TYR A 269 PHE 0.025 0.002 PHE J 345 TRP 0.022 0.002 TRP H 385 HIS 0.009 0.001 HIS D 153 Details of bonding type rmsd covalent geometry : bond 0.00454 (35568) covalent geometry : angle 0.57208 (48248) hydrogen bonds : bond 0.04540 ( 1528) hydrogen bonds : angle 5.19439 ( 4344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 479 time to evaluate : 1.449 Fit side-chains REVERT: A 83 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8633 (ptm160) REVERT: A 305 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8031 (ttp-110) REVERT: P 25 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: B 303 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7576 (ttt180) REVERT: B 305 ARG cc_start: 0.8335 (ttt-90) cc_final: 0.8095 (ttp-110) REVERT: C 25 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: D 303 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7600 (ttt180) REVERT: D 305 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.8094 (ttp-110) REVERT: E 25 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: E 90 LEU cc_start: 0.8250 (mt) cc_final: 0.8047 (tp) REVERT: F 303 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7598 (ttt180) REVERT: F 305 ARG cc_start: 0.8360 (ttt-90) cc_final: 0.8107 (ttp-110) REVERT: G 25 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: G 90 LEU cc_start: 0.8245 (mt) cc_final: 0.8042 (tp) REVERT: H 305 ARG cc_start: 0.8413 (ttt-90) cc_final: 0.8023 (ttp-110) REVERT: I 25 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: J 303 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7574 (ttt180) REVERT: J 305 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.8096 (ttp-110) REVERT: K 25 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: L 305 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8024 (ttp-110) REVERT: M 25 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: N 303 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7572 (ttt180) REVERT: N 305 ARG cc_start: 0.8423 (ttt-90) cc_final: 0.8042 (ttp-110) REVERT: O 25 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7818 (mt-10) outliers start: 43 outliers final: 25 residues processed: 503 average time/residue: 0.8631 time to fit residues: 508.1229 Evaluate side-chains 519 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 480 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 158 optimal weight: 0.7980 chunk 370 optimal weight: 30.0000 chunk 427 optimal weight: 30.0000 chunk 210 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 29 GLN C 29 GLN E 29 GLN G 29 GLN I 29 GLN K 29 GLN M 29 GLN O 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103895 restraints weight = 36959.431| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.54 r_work: 0.2937 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35568 Z= 0.173 Angle : 0.558 4.815 48248 Z= 0.303 Chirality : 0.044 0.167 5120 Planarity : 0.005 0.041 6352 Dihedral : 4.746 18.864 4920 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.31 % Allowed : 16.94 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.12), residues: 4360 helix: 1.96 (0.12), residues: 1664 sheet: -0.23 (0.19), residues: 768 loop : -0.27 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 130 TYR 0.013 0.002 TYR A 269 PHE 0.025 0.002 PHE A 345 TRP 0.025 0.002 TRP B 385 HIS 0.009 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00398 (35568) covalent geometry : angle 0.55823 (48248) hydrogen bonds : bond 0.04319 ( 1528) hydrogen bonds : angle 5.17468 ( 4344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14094.56 seconds wall clock time: 240 minutes 35.74 seconds (14435.74 seconds total)