Starting phenix.real_space_refine on Tue Aug 26 07:48:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q05_18050/08_2025/8q05_18050.map" } resolution = 2.77 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= 0.019 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 22026 2.51 5 N 6181 2.21 5 O 7429 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35836 Number of models: 1 Model: "" Number of chains: 20 Chain: "Z" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 105 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" 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: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "L" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "O" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "Q" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "W" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "X" 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: C, F, I, L, O, S, W, G, J, M, P, Q, T, X Time building chain proxies: 5.11, per 1000 atoms: 0.14 Number of scatterers: 35836 At special positions: 0 Unit cell: (146.944, 143.5, 128.576, 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 7429 8.00 N 6181 7.00 C 22026 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8076 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 40 sheets defined 44.6% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'Z' and resid 167 through 179 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 'C' and resid 49 through 57 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU C 390 " --> pdb=" O HIS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 433 Processing helix chain 'C' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' 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 'I' and resid 49 through 57 Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 122 Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 154 through 163 Processing helix chain 'I' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 233 Processing helix chain 'I' and resid 246 through 261 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 273 through 288 Processing helix chain 'I' and resid 298 through 303 Processing helix chain 'I' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU I 314 " --> pdb=" O HIS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 351 Processing helix chain 'I' and resid 383 through 385 No H-bonds generated for 'chain 'I' and resid 383 through 385' Processing helix chain 'I' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU I 390 " --> pdb=" O HIS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 433 Processing helix chain 'I' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU I 460 " --> pdb=" O ALA I 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL J 58 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' 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 'O' and resid 49 through 57 Processing helix chain 'O' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE O 108 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 122 Processing helix chain 'O' and resid 141 through 146 Processing helix chain 'O' and resid 154 through 163 Processing helix chain 'O' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY O 195 " --> pdb=" O GLU O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 233 Processing helix chain 'O' and resid 246 through 261 Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 273 through 288 Processing helix chain 'O' and resid 298 through 303 Processing helix chain 'O' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU O 314 " --> pdb=" O HIS O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 351 Processing helix chain 'O' and resid 383 through 385 No H-bonds generated for 'chain 'O' and resid 383 through 385' Processing helix chain 'O' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU O 390 " --> pdb=" O HIS O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 433 Processing helix chain 'O' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU O 460 " --> pdb=" O ALA O 456 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 Processing helix chain 'Q' and resid 48 through 50 No H-bonds generated for 'chain 'Q' and resid 48 through 50' Processing helix chain 'Q' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL Q 58 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 100 Processing helix chain 'S' and resid 49 through 57 Processing helix chain 'S' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE S 108 " --> pdb=" O LEU S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 122 Processing helix chain 'S' and resid 141 through 146 Processing helix chain 'S' and resid 154 through 163 Processing helix chain 'S' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY S 195 " --> pdb=" O GLU S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 233 Processing helix chain 'S' and resid 246 through 261 Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'S' and resid 273 through 288 Processing helix chain 'S' and resid 298 through 303 Processing helix chain 'S' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU S 314 " --> pdb=" O HIS S 310 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 351 Processing helix chain 'S' and resid 383 through 385 No H-bonds generated for 'chain 'S' and resid 383 through 385' Processing helix chain 'S' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU S 390 " --> pdb=" O HIS S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 433 Processing helix chain 'S' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY S 442 " --> pdb=" O ALA S 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP S 443 " --> pdb=" O ARG S 439 " (cutoff:3.500A) Processing helix chain 'S' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU S 460 " --> pdb=" O ALA S 456 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 36 Processing helix chain 'T' and resid 48 through 50 No H-bonds generated for 'chain 'T' and resid 48 through 50' Processing helix chain 'T' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL T 58 " --> pdb=" O GLU T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 100 Processing helix chain 'W' and resid 49 through 57 Processing helix chain 'W' and resid 104 through 108 removed outlier: 3.534A pdb=" N PHE W 108 " --> pdb=" O LEU W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 122 Processing helix chain 'W' and resid 141 through 146 Processing helix chain 'W' and resid 154 through 163 Processing helix chain 'W' and resid 181 through 195 removed outlier: 3.677A pdb=" N GLY W 195 " --> pdb=" O GLU W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 213 through 233 Processing helix chain 'W' and resid 246 through 261 Processing helix chain 'W' and resid 269 through 273 Processing helix chain 'W' and resid 273 through 288 Processing helix chain 'W' and resid 298 through 303 Processing helix chain 'W' and resid 310 through 322 removed outlier: 3.512A pdb=" N LEU W 314 " --> pdb=" O HIS W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 351 Processing helix chain 'W' and resid 383 through 385 No H-bonds generated for 'chain 'W' and resid 383 through 385' Processing helix chain 'W' and resid 386 through 395 removed outlier: 3.501A pdb=" N LEU W 390 " --> pdb=" O HIS W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 412 through 433 Processing helix chain 'W' and resid 436 through 450 removed outlier: 6.889A pdb=" N GLY W 442 " --> pdb=" O ALA W 438 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP W 443 " --> pdb=" O ARG W 439 " (cutoff:3.500A) Processing helix chain 'W' and resid 452 through 460 removed outlier: 3.570A pdb=" N GLU W 460 " --> pdb=" O ALA W 456 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 36 Processing helix chain 'X' and resid 48 through 50 No H-bonds generated for 'chain 'X' and resid 48 through 50' Processing helix chain 'X' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL X 58 " --> pdb=" O GLU X 55 " (cutoff:3.500A) Processing helix chain 'X' 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: 3.725A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (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 'C' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU C 170 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS C 201 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS C 172 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS C 294 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 291 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS C 327 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE C 293 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY C 329 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS C 325 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 377 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS C 327 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER C 379 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C 329 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE C 402 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'D' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE D 105 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP D 111 " --> pdb=" O GLN D 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN D 117 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB2, 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: 3.725A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'G' and resid 3 through 4 Processing sheet with id=AB6, 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=AB7, first strand: chain 'I' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU I 170 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS I 201 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS I 172 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR I 200 " --> pdb=" O TYR I 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN I 241 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS I 238 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET I 266 " --> pdb=" O HIS I 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU I 240 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP I 268 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE I 265 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS I 294 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS I 267 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU I 291 " --> pdb=" O HIS I 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS I 327 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE I 293 " --> pdb=" O HIS I 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY I 329 " --> pdb=" O ILE I 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS I 325 " --> pdb=" O MET I 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL I 377 " --> pdb=" O HIS I 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS I 327 " --> pdb=" O VAL I 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER I 379 " --> pdb=" O HIS I 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY I 329 " --> pdb=" O SER I 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU I 169 " --> pdb=" O LEU I 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE I 402 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY I 171 " --> pdb=" O PHE I 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE J 105 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP J 111 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN J 117 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing sheet with id=AC3, 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: 3.725A pdb=" N ASP L 86 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU L 37 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU L 138 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA L 39 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing sheet with id=AC4, 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=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AC7, 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=AC8, first strand: chain 'O' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU O 170 " --> pdb=" O PHE O 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS O 201 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS O 172 " --> pdb=" O LYS O 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR O 200 " --> pdb=" O TYR O 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN O 241 " --> pdb=" O THR O 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS O 238 " --> pdb=" O ILE O 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET O 266 " --> pdb=" O HIS O 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU O 240 " --> pdb=" O MET O 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP O 268 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE O 265 " --> pdb=" O HIS O 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS O 294 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS O 267 " --> pdb=" O HIS O 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU O 291 " --> pdb=" O HIS O 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS O 327 " --> pdb=" O LEU O 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE O 293 " --> pdb=" O HIS O 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY O 329 " --> pdb=" O ILE O 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS O 325 " --> pdb=" O MET O 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL O 377 " --> pdb=" O HIS O 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS O 327 " --> pdb=" O VAL O 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER O 379 " --> pdb=" O HIS O 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY O 329 " --> pdb=" O SER O 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU O 169 " --> pdb=" O LEU O 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE O 402 " --> pdb=" O LEU O 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY O 171 " --> pdb=" O PHE O 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 353 through 354 Processing sheet with id=AD2, first strand: chain 'Q' and resid 3 through 4 Processing sheet with id=AD3, first strand: chain 'Q' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE Q 105 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP Q 111 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN Q 117 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS S 84 " --> pdb=" O ALA S 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA S 102 " --> pdb=" O CYS S 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP S 86 " --> pdb=" O TYR S 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU S 37 " --> pdb=" O LEU S 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU S 138 " --> pdb=" O LEU S 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA S 39 " --> pdb=" O GLU S 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU S 170 " --> pdb=" O PHE S 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS S 201 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS S 172 " --> pdb=" O LYS S 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR S 200 " --> pdb=" O TYR S 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN S 241 " --> pdb=" O THR S 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS S 238 " --> pdb=" O ILE S 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET S 266 " --> pdb=" O HIS S 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU S 240 " --> pdb=" O MET S 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP S 268 " --> pdb=" O LEU S 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE S 265 " --> pdb=" O HIS S 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS S 294 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS S 267 " --> pdb=" O HIS S 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU S 291 " --> pdb=" O HIS S 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS S 327 " --> pdb=" O LEU S 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE S 293 " --> pdb=" O HIS S 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY S 329 " --> pdb=" O ILE S 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS S 325 " --> pdb=" O MET S 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL S 377 " --> pdb=" O HIS S 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS S 327 " --> pdb=" O VAL S 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER S 379 " --> pdb=" O HIS S 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY S 329 " --> pdb=" O SER S 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN S 401 " --> pdb=" O PRO S 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA S 378 " --> pdb=" O GLN S 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU S 169 " --> pdb=" O LEU S 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE S 402 " --> pdb=" O LEU S 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY S 171 " --> pdb=" O PHE S 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'S' and resid 353 through 354 Processing sheet with id=AD7, first strand: chain 'T' and resid 3 through 4 Processing sheet with id=AD8, first strand: chain 'T' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE T 105 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP T 111 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN T 117 " --> pdb=" O ASP T 111 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 83 through 89 removed outlier: 5.937A pdb=" N CYS W 84 " --> pdb=" O ALA W 102 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA W 102 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP W 86 " --> pdb=" O TYR W 100 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU W 37 " --> pdb=" O LEU W 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU W 138 " --> pdb=" O LEU W 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA W 39 " --> pdb=" O GLU W 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 169 through 173 removed outlier: 6.462A pdb=" N LEU W 170 " --> pdb=" O PHE W 199 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS W 201 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS W 172 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR W 200 " --> pdb=" O TYR W 239 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN W 241 " --> pdb=" O THR W 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS W 238 " --> pdb=" O ILE W 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET W 266 " --> pdb=" O HIS W 238 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU W 240 " --> pdb=" O MET W 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP W 268 " --> pdb=" O LEU W 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE W 265 " --> pdb=" O HIS W 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS W 294 " --> pdb=" O ILE W 265 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS W 267 " --> pdb=" O HIS W 294 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU W 291 " --> pdb=" O HIS W 325 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS W 327 " --> pdb=" O LEU W 291 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE W 293 " --> pdb=" O HIS W 327 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY W 329 " --> pdb=" O ILE W 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS W 325 " --> pdb=" O MET W 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL W 377 " --> pdb=" O HIS W 325 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS W 327 " --> pdb=" O VAL W 377 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER W 379 " --> pdb=" O HIS W 327 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY W 329 " --> pdb=" O SER W 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN W 401 " --> pdb=" O PRO W 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA W 378 " --> pdb=" O GLN W 401 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU W 169 " --> pdb=" O LEU W 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE W 402 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY W 171 " --> pdb=" O PHE W 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'W' and resid 353 through 354 Processing sheet with id=AE3, first strand: chain 'X' and resid 3 through 4 Processing sheet with id=AE4, first strand: chain 'X' and resid 74 through 75 removed outlier: 6.289A pdb=" N ILE X 105 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP X 111 " --> pdb=" O GLN X 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN X 117 " --> pdb=" O ASP X 111 " (cutoff:3.500A) 1537 hydrogen bonds defined for protein. 4371 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: 7.33 Time building geometry restraints manager: 3.30 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: 8989 1.33 - 1.45: 7222 1.45 - 1.57: 19182 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 35681 Sorted by residual: bond pdb=" N VAL A 90 " pdb=" CA VAL A 90 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.93e+01 bond pdb=" N VAL S 90 " pdb=" CA VAL S 90 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.93e+01 bond pdb=" N VAL F 90 " pdb=" CA VAL F 90 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.93e+01 bond pdb=" N VAL L 90 " pdb=" CA VAL L 90 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.93e+01 bond pdb=" N VAL I 90 " pdb=" CA VAL I 90 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.93e+01 ... (remaining 35676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 38744 1.13 - 2.26: 6754 2.26 - 3.39: 2440 3.39 - 4.52: 393 4.52 - 5.65: 72 Bond angle restraints: 48403 Sorted by residual: 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 I 337 " pdb=" C GLY I 337 " pdb=" O GLY I 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 C 337 " pdb=" C GLY C 337 " pdb=" O GLY C 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 S 337 " pdb=" C GLY S 337 " pdb=" O GLY S 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 W 337 " pdb=" C GLY W 337 " pdb=" O GLY W 337 " ideal model delta sigma weight residual 122.29 118.14 4.15 8.10e-01 1.52e+00 2.63e+01 ... (remaining 48398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 18514 17.42 - 34.85: 1931 34.85 - 52.27: 425 52.27 - 69.69: 176 69.69 - 87.11: 40 Dihedral angle restraints: 21086 sinusoidal: 8395 harmonic: 12691 Sorted by residual: dihedral pdb=" CA LYS C 175 " pdb=" C LYS C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 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 S 175 " pdb=" C LYS S 175 " pdb=" N PRO S 176 " pdb=" CA PRO S 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 F 175 " pdb=" C LYS F 175 " pdb=" N PRO F 176 " pdb=" CA PRO F 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 21083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2771 0.042 - 0.084: 1195 0.084 - 0.126: 784 0.126 - 0.168: 258 0.168 - 0.210: 128 Chirality restraints: 5136 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 X 43 " pdb=" N GLU X 43 " pdb=" C GLU X 43 " pdb=" CB GLU X 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 5133 not shown) Planarity restraints: 6378 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 134 " 0.619 9.50e-02 1.11e+02 2.77e-01 4.70e+01 pdb=" NE ARG C 134 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 134 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 134 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 134 " 0.019 2.00e-02 2.50e+03 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10609 2.82 - 3.34: 34568 3.34 - 3.86: 68253 3.86 - 4.38: 82507 4.38 - 4.90: 132180 Nonbonded interactions: 328117 Sorted by model distance: nonbonded pdb=" O LEU A 105 " pdb=" O HOH A 501 " model vdw 2.302 3.040 nonbonded pdb=" O GLU W 231 " pdb=" O HOH W 501 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR T 5 " pdb=" O HOH T 201 " model vdw 2.303 3.040 nonbonded pdb=" O HOH M 213 " pdb=" O HOH M 218 " model vdw 2.307 3.040 nonbonded pdb=" O MET C 212 " pdb=" O HOH C 501 " model vdw 2.307 3.040 ... (remaining 328112 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'X' } 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: 0.130 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: 0.390 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 26.800 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 35681 Z= 0.603 Angle : 1.021 5.648 48403 Z= 0.752 Chirality : 0.069 0.210 5136 Planarity : 0.021 0.277 6378 Dihedral : 16.012 87.114 13010 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 15.08 % Favored : 84.92 % 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 aren not related in a simple way. whole: 0.52 (0.12), residues: 4374 helix: 1.62 (0.12), residues: 1644 sheet: -0.36 (0.19), residues: 680 loop : -0.40 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 187 TYR 0.015 0.002 TYR I 24 PHE 0.019 0.002 PHE Z 173 TRP 0.024 0.002 TRP L 385 HIS 0.004 0.001 HIS O 298 Details of bonding type rmsd covalent geometry : bond 0.00834 (35681) covalent geometry : angle 1.02122 (48403) hydrogen bonds : bond 0.14247 ( 1537) hydrogen bonds : angle 7.04701 ( 4371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 778 time to evaluate : 1.451 Fit side-chains TARDY: cannot create tardy model for: "THR D 14 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR X 14 " (corrupted residue). Skipping it. REVERT: A 45 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6966 (mm-40) REVERT: A 106 ASP cc_start: 0.8355 (m-30) cc_final: 0.8047 (m-30) REVERT: P 88 GLN cc_start: 0.7475 (tp40) cc_final: 0.6872 (tp40) REVERT: P 102 ASP cc_start: 0.7771 (m-30) cc_final: 0.7415 (m-30) REVERT: C 387 MET cc_start: 0.8176 (tpp) cc_final: 0.7976 (ttm) REVERT: D 27 SER cc_start: 0.8110 (t) cc_final: 0.7860 (p) REVERT: D 133 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7193 (mm-40) REVERT: F 41 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8558 (ttm-80) REVERT: F 203 ASP cc_start: 0.7360 (t70) cc_final: 0.7135 (t70) REVERT: F 255 GLU cc_start: 0.8500 (tp30) cc_final: 0.8184 (tm-30) REVERT: F 385 TRP cc_start: 0.7427 (p90) cc_final: 0.7164 (p90) REVERT: F 446 ARG cc_start: 0.6332 (mtt180) cc_final: 0.5773 (mmm160) REVERT: G 49 SER cc_start: 0.8760 (p) cc_final: 0.8269 (m) REVERT: G 92 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7604 (mm-30) REVERT: G 98 ARG cc_start: 0.7119 (mtm110) cc_final: 0.6437 (mtt180) REVERT: I 52 GLU cc_start: 0.7619 (tt0) cc_final: 0.7275 (mt-10) REVERT: I 177 LYS cc_start: 0.7091 (mtmt) cc_final: 0.6786 (tttm) REVERT: I 249 GLU cc_start: 0.8440 (tp30) cc_final: 0.8213 (tp30) REVERT: J 88 GLN cc_start: 0.7647 (tp40) cc_final: 0.7054 (tp-100) REVERT: L 96 GLN cc_start: 0.7877 (mt0) cc_final: 0.7485 (mt0) REVERT: L 123 ASN cc_start: 0.7866 (p0) cc_final: 0.7446 (p0) REVERT: L 252 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8790 (ttmt) REVERT: L 255 GLU cc_start: 0.8583 (tp30) cc_final: 0.8309 (tt0) REVERT: L 383 HIS cc_start: 0.6824 (m-70) cc_final: 0.6151 (m-70) REVERT: L 386 HIS cc_start: 0.6681 (m-70) cc_final: 0.6419 (m90) REVERT: L 413 ASN cc_start: 0.6898 (m-40) cc_final: 0.6571 (m-40) REVERT: L 454 GLU cc_start: 0.7029 (mp0) cc_final: 0.6707 (mp0) REVERT: M 9 ASN cc_start: 0.8190 (t0) cc_final: 0.7930 (t160) REVERT: M 32 TYR cc_start: 0.8870 (t80) cc_final: 0.8624 (t80) REVERT: O 22 LEU cc_start: 0.7929 (mm) cc_final: 0.7650 (mt) REVERT: O 128 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7207 (mmtp) REVERT: O 203 ASP cc_start: 0.7664 (t70) cc_final: 0.7457 (t70) REVERT: O 249 GLU cc_start: 0.8378 (tp30) cc_final: 0.8105 (tp30) REVERT: O 454 GLU cc_start: 0.6812 (mp0) cc_final: 0.6612 (mp0) REVERT: Q 119 SER cc_start: 0.8775 (t) cc_final: 0.8543 (m) REVERT: S 22 LEU cc_start: 0.7861 (mm) cc_final: 0.7630 (mt) REVERT: S 41 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8461 (ttm-80) REVERT: S 95 ASN cc_start: 0.4950 (t0) cc_final: 0.4631 (t0) REVERT: S 304 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8313 (mm110) REVERT: S 454 GLU cc_start: 0.6358 (mp0) cc_final: 0.6087 (pm20) REVERT: T 111 ASP cc_start: 0.8426 (t70) cc_final: 0.8215 (t70) REVERT: T 133 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8218 (mm-40) REVERT: W 338 GLU cc_start: 0.6674 (tp30) cc_final: 0.6463 (tp30) REVERT: W 375 MET cc_start: 0.9079 (ttm) cc_final: 0.8853 (ttp) REVERT: X 88 GLN cc_start: 0.7310 (tp40) cc_final: 0.6823 (mm-40) outliers start: 0 outliers final: 3 residues processed: 778 average time/residue: 0.8968 time to fit residues: 816.9986 Evaluate side-chains 594 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 591 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 345 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 304 GLN A 401 GLN P 2 GLN P 94 GLN P 133 GLN C 153 HIS C 304 GLN D 2 GLN D 9 ASN F 153 HIS F 304 GLN F 401 GLN G 2 GLN G 8 ASN G 29 GLN G 94 GLN G 124 ASN I 153 HIS I 413 ASN J 2 GLN J 9 ASN J 61 GLN L 153 HIS M 2 GLN M 29 GLN M 94 GLN O 153 HIS O 304 GLN O 383 HIS Q 2 GLN Q 29 GLN Q 133 GLN S 153 HIS S 156 GLN S 207 ASN S 304 GLN S 401 GLN S 413 ASN T 29 GLN T 115 GLN W 153 HIS W 304 GLN W 401 GLN X 2 GLN X 29 GLN X 36 ASN X 133 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097594 restraints weight = 41578.835| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.73 r_work: 0.2863 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 35681 Z= 0.173 Angle : 0.554 6.467 48403 Z= 0.302 Chirality : 0.044 0.174 5136 Planarity : 0.005 0.054 6378 Dihedral : 4.505 59.862 4942 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.30 % Allowed : 15.75 % Favored : 81.95 % 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 aren not related in a simple way. whole: 1.02 (0.13), residues: 4374 helix: 2.25 (0.12), residues: 1668 sheet: -0.59 (0.18), residues: 760 loop : -0.11 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 339 TYR 0.018 0.002 TYR A 269 PHE 0.030 0.002 PHE O 345 TRP 0.015 0.001 TRP C 385 HIS 0.010 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00394 (35681) covalent geometry : angle 0.55435 (48403) hydrogen bonds : bond 0.04535 ( 1537) hydrogen bonds : angle 5.47322 ( 4371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 592 time to evaluate : 1.595 Fit side-chains TARDY: cannot create tardy model for: "THR D 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR T 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR X 14 " (corrupted residue). Skipping it. REVERT: Z 170 GLN cc_start: 0.7861 (mt0) cc_final: 0.7578 (mt0) REVERT: A 106 ASP cc_start: 0.8501 (m-30) cc_final: 0.8207 (m-30) REVERT: A 355 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: P 88 GLN cc_start: 0.7323 (tp40) cc_final: 0.6731 (tp40) REVERT: P 102 ASP cc_start: 0.8046 (m-30) cc_final: 0.7781 (m-30) REVERT: C 249 GLU cc_start: 0.8498 (tp30) cc_final: 0.8297 (mm-30) REVERT: C 255 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: C 339 ARG cc_start: 0.7329 (ttm170) cc_final: 0.6995 (ttm-80) REVERT: C 358 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8029 (mmm-85) REVERT: D 13 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 27 SER cc_start: 0.8326 (t) cc_final: 0.8107 (p) REVERT: D 94 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: D 133 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7177 (mm-40) REVERT: F 41 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8588 (ttm-80) REVERT: F 81 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6094 (pttt) REVERT: F 175 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7636 (mmpt) REVERT: F 203 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7378 (t0) REVERT: F 249 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: F 339 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7180 (ptm-80) REVERT: F 435 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6817 (mtt-85) REVERT: F 446 ARG cc_start: 0.6473 (mtt180) cc_final: 0.5830 (mmp-170) REVERT: G 49 SER cc_start: 0.8664 (p) cc_final: 0.8190 (m) REVERT: G 88 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7484 (tm130) REVERT: G 92 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7697 (mm-30) REVERT: G 98 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6295 (mtt180) REVERT: I 83 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7814 (ptm160) REVERT: I 249 GLU cc_start: 0.8477 (tp30) cc_final: 0.8269 (tp30) REVERT: I 302 ASP cc_start: 0.8292 (p0) cc_final: 0.8055 (p0) REVERT: J 29 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8279 (mp-120) REVERT: J 88 GLN cc_start: 0.7867 (tp40) cc_final: 0.7370 (tp-100) REVERT: L 255 GLU cc_start: 0.8819 (tp30) cc_final: 0.8401 (tt0) REVERT: L 383 HIS cc_start: 0.7003 (m-70) cc_final: 0.6284 (m-70) REVERT: L 386 HIS cc_start: 0.6865 (m-70) cc_final: 0.6539 (m90) REVERT: L 413 ASN cc_start: 0.6769 (m-40) cc_final: 0.6257 (m-40) REVERT: M 90 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7517 (mt) REVERT: O 22 LEU cc_start: 0.7957 (mm) cc_final: 0.7637 (mt) REVERT: O 128 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7487 (mmtp) REVERT: O 203 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7920 (t70) REVERT: O 305 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7704 (ttm-80) REVERT: Q 51 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: Q 66 LEU cc_start: 0.8628 (mt) cc_final: 0.8416 (mp) REVERT: Q 111 ASP cc_start: 0.8425 (t0) cc_final: 0.8202 (t0) REVERT: Q 113 VAL cc_start: 0.7988 (m) cc_final: 0.7668 (p) REVERT: S 22 LEU cc_start: 0.8031 (mm) cc_final: 0.7712 (mt) REVERT: S 41 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8512 (ttm-80) REVERT: S 268 ASP cc_start: 0.8691 (m-30) cc_final: 0.8472 (m-30) REVERT: S 339 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7178 (ttt180) REVERT: S 454 GLU cc_start: 0.6670 (mp0) cc_final: 0.6249 (pm20) REVERT: T 21 MET cc_start: 0.8256 (mtm) cc_final: 0.7739 (OUTLIER) REVERT: T 66 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7802 (mp) REVERT: W 340 GLU cc_start: 0.7865 (mp0) cc_final: 0.7648 (mp0) REVERT: W 375 MET cc_start: 0.9120 (ttm) cc_final: 0.8889 (ttp) REVERT: X 2 GLN cc_start: 0.5675 (OUTLIER) cc_final: 0.5260 (mt0) REVERT: X 66 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8041 (mp) REVERT: X 75 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8973 (tpt) outliers start: 83 outliers final: 32 residues processed: 631 average time/residue: 0.8938 time to fit residues: 661.5125 Evaluate side-chains 592 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 544 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 449 CYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J 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 51 GLU Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 339 ARG Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain X residue 2 GLN Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 75 MET Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 391 optimal weight: 2.9990 chunk 385 optimal weight: 8.9990 chunk 362 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 263 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 133 GLN D 9 ASN D 29 GLN G 29 GLN G 94 GLN M 88 GLN M 94 GLN O 383 HIS Q 115 GLN Q 133 GLN ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 29 GLN T 115 GLN W 401 GLN X 133 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097895 restraints weight = 41591.527| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.78 r_work: 0.2848 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35681 Z= 0.137 Angle : 0.509 5.634 48403 Z= 0.275 Chirality : 0.043 0.166 5136 Planarity : 0.004 0.039 6378 Dihedral : 4.329 18.414 4936 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.38 % Allowed : 15.94 % Favored : 81.67 % 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 aren not related in a simple way. whole: 1.11 (0.13), residues: 4374 helix: 2.42 (0.12), residues: 1676 sheet: -0.65 (0.18), residues: 760 loop : -0.12 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 435 TYR 0.014 0.001 TYR A 269 PHE 0.026 0.002 PHE S 345 TRP 0.016 0.001 TRP I 385 HIS 0.004 0.001 HIS F 386 Details of bonding type rmsd covalent geometry : bond 0.00312 (35681) covalent geometry : angle 0.50916 (48403) hydrogen bonds : bond 0.03963 ( 1537) hydrogen bonds : angle 5.15573 ( 4371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 563 time to evaluate : 1.425 Fit side-chains TARDY: cannot create tardy model for: "THR D 14 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR X 14 " (corrupted residue). Skipping it. REVERT: Z 170 GLN cc_start: 0.7841 (mt0) cc_final: 0.7520 (mt0) REVERT: A 106 ASP cc_start: 0.8537 (m-30) cc_final: 0.8251 (m-30) REVERT: A 302 ASP cc_start: 0.8314 (p0) cc_final: 0.7989 (p0) REVERT: A 355 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 435 ARG cc_start: 0.6407 (mmm-85) cc_final: 0.6204 (mmm-85) REVERT: P 88 GLN cc_start: 0.7318 (tp40) cc_final: 0.6822 (tp-100) REVERT: P 90 LEU cc_start: 0.8322 (tp) cc_final: 0.8110 (tm) REVERT: P 102 ASP cc_start: 0.7955 (m-30) cc_final: 0.7702 (m-30) REVERT: C 175 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7256 (mtmt) REVERT: C 249 GLU cc_start: 0.8484 (tp30) cc_final: 0.8278 (mm-30) REVERT: C 255 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: D 2 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.5475 (mt0) REVERT: D 27 SER cc_start: 0.8403 (t) cc_final: 0.8135 (p) REVERT: D 133 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7192 (mm-40) REVERT: F 41 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8643 (ttm-80) REVERT: F 128 LYS cc_start: 0.8244 (mptt) cc_final: 0.7711 (mmmm) REVERT: F 203 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7277 (t0) REVERT: F 249 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: F 255 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: F 339 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7156 (ptm-80) REVERT: F 435 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6904 (mtt-85) REVERT: F 446 ARG cc_start: 0.6692 (mtt180) cc_final: 0.5947 (mmp-170) REVERT: G 49 SER cc_start: 0.8693 (p) cc_final: 0.8224 (m) REVERT: G 88 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7458 (tm130) REVERT: G 92 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7778 (mm-30) REVERT: G 98 ARG cc_start: 0.7061 (mtm110) cc_final: 0.6324 (mtt180) REVERT: I 83 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7857 (ptm160) REVERT: I 302 ASP cc_start: 0.8280 (p0) cc_final: 0.8049 (p0) REVERT: I 331 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7125 (t) REVERT: J 16 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8699 (p) REVERT: J 88 GLN cc_start: 0.7766 (tp40) cc_final: 0.7299 (tp-100) REVERT: L 175 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8044 (mttp) REVERT: L 255 GLU cc_start: 0.8802 (tp30) cc_final: 0.8419 (tt0) REVERT: L 383 HIS cc_start: 0.7007 (m-70) cc_final: 0.6334 (m-70) REVERT: L 386 HIS cc_start: 0.6826 (m-70) cc_final: 0.6486 (m90) REVERT: L 413 ASN cc_start: 0.6825 (m-40) cc_final: 0.6321 (m-40) REVERT: L 454 GLU cc_start: 0.7082 (mp0) cc_final: 0.6690 (mp0) REVERT: M 90 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7538 (mt) REVERT: O 22 LEU cc_start: 0.7954 (mm) cc_final: 0.7569 (mt) REVERT: O 128 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7407 (mmtp) REVERT: O 203 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7874 (t70) REVERT: O 305 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7825 (ttm-80) REVERT: O 340 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7524 (mt-10) REVERT: Q 2 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: Q 51 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: Q 66 LEU cc_start: 0.8629 (mt) cc_final: 0.8408 (mp) REVERT: Q 90 LEU cc_start: 0.7976 (tp) cc_final: 0.7712 (tm) REVERT: Q 111 ASP cc_start: 0.8501 (t0) cc_final: 0.8263 (t0) REVERT: Q 113 VAL cc_start: 0.8234 (m) cc_final: 0.7910 (p) REVERT: S 22 LEU cc_start: 0.8129 (mm) cc_final: 0.7788 (mt) REVERT: S 41 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8492 (ttm-80) REVERT: S 95 ASN cc_start: 0.5415 (t0) cc_final: 0.4754 (t0) REVERT: S 268 ASP cc_start: 0.8633 (m-30) cc_final: 0.8427 (m-30) REVERT: T 21 MET cc_start: 0.8283 (mtm) cc_final: 0.7815 (mtp) REVERT: T 66 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7794 (mp) REVERT: T 113 VAL cc_start: 0.8191 (m) cc_final: 0.7834 (p) REVERT: T 130 ARG cc_start: 0.5640 (mmp-170) cc_final: 0.5131 (mmm160) REVERT: T 133 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8289 (mm-40) REVERT: W 440 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5418 (mp0) REVERT: X 66 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7952 (mp) REVERT: X 133 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6809 (mm110) outliers start: 86 outliers final: 24 residues processed: 607 average time/residue: 0.8613 time to fit residues: 615.2862 Evaluate side-chains 582 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 540 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 449 CYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 349 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 chunk 354 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 325 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS P 94 GLN P 133 GLN D 29 GLN G 29 GLN G 94 GLN L 207 ASN M 94 GLN O 205 ASN O 383 HIS Q 115 GLN Q 133 GLN S 413 ASN T 29 GLN W 401 GLN X 88 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.095728 restraints weight = 41173.829| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.70 r_work: 0.2842 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35681 Z= 0.165 Angle : 0.532 5.747 48403 Z= 0.287 Chirality : 0.044 0.176 5136 Planarity : 0.005 0.041 6378 Dihedral : 4.437 18.908 4936 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 15.55 % Favored : 81.87 % 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 aren not related in a simple way. whole: 0.97 (0.12), residues: 4374 helix: 2.34 (0.12), residues: 1668 sheet: -0.66 (0.18), residues: 760 loop : -0.26 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 435 TYR 0.016 0.002 TYR A 269 PHE 0.025 0.002 PHE S 345 TRP 0.022 0.001 TRP I 385 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00383 (35681) covalent geometry : angle 0.53246 (48403) hydrogen bonds : bond 0.04115 ( 1537) hydrogen bonds : angle 5.10939 ( 4371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 537 time to evaluate : 1.509 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8377 (m-30) cc_final: 0.8099 (m-30) REVERT: A 302 ASP cc_start: 0.8366 (p0) cc_final: 0.8017 (p0) REVERT: A 355 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: P 75 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8615 (ttm) REVERT: P 88 GLN cc_start: 0.7301 (tp40) cc_final: 0.6789 (tp40) REVERT: P 102 ASP cc_start: 0.8058 (m-30) cc_final: 0.7820 (m-30) REVERT: P 133 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7623 (mm-40) REVERT: C 249 GLU cc_start: 0.8508 (tp30) cc_final: 0.8284 (mm-30) REVERT: C 339 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6966 (ttp80) REVERT: D 27 SER cc_start: 0.8419 (t) cc_final: 0.8164 (p) REVERT: D 91 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7163 (mpp80) REVERT: D 133 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7179 (mm-40) REVERT: F 41 ARG cc_start: 0.8947 (ttm110) cc_final: 0.8615 (ttm-80) REVERT: F 81 LYS cc_start: 0.6425 (pttt) cc_final: 0.6024 (pttt) REVERT: F 128 LYS cc_start: 0.8239 (mptt) cc_final: 0.7757 (mmmm) REVERT: F 175 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7664 (mmpt) REVERT: F 203 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7573 (t0) REVERT: F 248 GLU cc_start: 0.8393 (mp0) cc_final: 0.8184 (mp0) REVERT: F 249 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: F 255 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: F 336 GLU cc_start: 0.5518 (mm-30) cc_final: 0.5247 (mm-30) REVERT: F 385 TRP cc_start: 0.7275 (p90) cc_final: 0.7026 (p90) REVERT: F 435 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6954 (mtt-85) REVERT: F 446 ARG cc_start: 0.6692 (mtt180) cc_final: 0.5899 (mmp-170) REVERT: G 29 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8636 (mp-120) REVERT: G 49 SER cc_start: 0.8695 (p) cc_final: 0.8217 (m) REVERT: G 88 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7460 (tm130) REVERT: G 98 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6340 (mtt180) REVERT: I 83 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: I 302 ASP cc_start: 0.8338 (p0) cc_final: 0.8111 (p0) REVERT: I 331 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7147 (t) REVERT: J 16 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8762 (p) REVERT: J 88 GLN cc_start: 0.7816 (tp40) cc_final: 0.7282 (tp-100) REVERT: L 33 ASP cc_start: 0.7957 (m-30) cc_final: 0.7718 (p0) REVERT: L 175 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8032 (mttp) REVERT: L 255 GLU cc_start: 0.8759 (tp30) cc_final: 0.8401 (tt0) REVERT: L 383 HIS cc_start: 0.7019 (m-70) cc_final: 0.6335 (m-70) REVERT: L 386 HIS cc_start: 0.6802 (m-70) cc_final: 0.6499 (m-70) REVERT: L 413 ASN cc_start: 0.6685 (m-40) cc_final: 0.6215 (m-40) REVERT: M 90 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7581 (mt) REVERT: O 22 LEU cc_start: 0.7904 (mm) cc_final: 0.7502 (mt) REVERT: O 128 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7418 (mmtp) REVERT: O 203 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7921 (t70) REVERT: O 340 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7421 (mt-10) REVERT: Q 51 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: Q 66 LEU cc_start: 0.8721 (mt) cc_final: 0.8295 (mp) REVERT: Q 90 LEU cc_start: 0.7994 (tp) cc_final: 0.7569 (tm) REVERT: Q 111 ASP cc_start: 0.8450 (t0) cc_final: 0.8190 (t0) REVERT: Q 113 VAL cc_start: 0.8385 (m) cc_final: 0.8108 (p) REVERT: S 22 LEU cc_start: 0.8095 (mm) cc_final: 0.7783 (mt) REVERT: S 41 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8497 (ttm-80) REVERT: S 95 ASN cc_start: 0.5506 (t0) cc_final: 0.4773 (t0) REVERT: S 268 ASP cc_start: 0.8661 (m-30) cc_final: 0.8451 (m-30) REVERT: T 66 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7818 (mp) REVERT: T 113 VAL cc_start: 0.8270 (m) cc_final: 0.7993 (p) REVERT: T 130 ARG cc_start: 0.5575 (mmp-170) cc_final: 0.5084 (mmm160) REVERT: T 133 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8288 (mm-40) REVERT: W 128 LYS cc_start: 0.8354 (mptt) cc_final: 0.7800 (mppt) REVERT: W 358 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7531 (ttm-80) REVERT: W 440 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: X 66 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8105 (mp) outliers start: 93 outliers final: 33 residues processed: 588 average time/residue: 0.8850 time to fit residues: 610.9252 Evaluate side-chains 573 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 522 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 401 GLN D 29 GLN G 94 GLN L 207 ASN M 88 GLN M 94 GLN O 383 HIS Q 133 GLN ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 29 GLN T 115 GLN W 401 GLN X 88 GLN X 133 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.095645 restraints weight = 41364.604| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.70 r_work: 0.2833 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35681 Z= 0.163 Angle : 0.523 5.771 48403 Z= 0.282 Chirality : 0.043 0.230 5136 Planarity : 0.004 0.040 6378 Dihedral : 4.445 21.182 4936 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.55 % Allowed : 15.69 % Favored : 81.76 % 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 aren not related in a simple way. whole: 0.95 (0.12), residues: 4374 helix: 2.28 (0.12), residues: 1676 sheet: -0.64 (0.18), residues: 760 loop : -0.25 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 114 TYR 0.014 0.002 TYR A 269 PHE 0.027 0.002 PHE S 345 TRP 0.022 0.001 TRP I 385 HIS 0.005 0.001 HIS S 238 Details of bonding type rmsd covalent geometry : bond 0.00379 (35681) covalent geometry : angle 0.52323 (48403) hydrogen bonds : bond 0.03991 ( 1537) hydrogen bonds : angle 5.08211 ( 4371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 533 time to evaluate : 1.500 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8376 (m-30) cc_final: 0.8096 (m-30) REVERT: A 302 ASP cc_start: 0.8381 (p0) cc_final: 0.8021 (p0) REVERT: A 355 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: P 88 GLN cc_start: 0.7314 (tp40) cc_final: 0.6842 (tp40) REVERT: P 90 LEU cc_start: 0.8342 (tp) cc_final: 0.8126 (tm) REVERT: P 102 ASP cc_start: 0.8060 (m-30) cc_final: 0.7807 (m-30) REVERT: P 133 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7665 (mm-40) REVERT: C 249 GLU cc_start: 0.8504 (tp30) cc_final: 0.8276 (mm-30) REVERT: D 27 SER cc_start: 0.8442 (t) cc_final: 0.8169 (p) REVERT: D 91 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7331 (mpp80) REVERT: D 133 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7173 (mm-40) REVERT: F 128 LYS cc_start: 0.8200 (mptt) cc_final: 0.7800 (mmmm) REVERT: F 175 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7543 (mmpt) REVERT: F 203 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7681 (t0) REVERT: F 248 GLU cc_start: 0.8366 (mp0) cc_final: 0.8145 (mp0) REVERT: F 249 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: F 255 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: F 303 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7411 (ttt180) REVERT: F 336 GLU cc_start: 0.5506 (mm-30) cc_final: 0.5078 (mm-30) REVERT: F 435 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6985 (mtt-85) REVERT: F 446 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5959 (mmp-170) REVERT: G 49 SER cc_start: 0.8693 (p) cc_final: 0.8179 (m) REVERT: G 88 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7468 (tm-30) REVERT: G 98 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6359 (mtt180) REVERT: G 114 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7783 (mtm180) REVERT: I 83 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: I 302 ASP cc_start: 0.8362 (p0) cc_final: 0.8140 (p0) REVERT: I 305 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7705 (ptm160) REVERT: I 331 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7152 (t) REVERT: J 16 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (p) REVERT: J 21 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8065 (ttp) REVERT: J 88 GLN cc_start: 0.7802 (tp40) cc_final: 0.7241 (tp-100) REVERT: L 33 ASP cc_start: 0.8017 (m-30) cc_final: 0.7772 (p0) REVERT: L 175 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: L 255 GLU cc_start: 0.8788 (tp30) cc_final: 0.8416 (tt0) REVERT: L 383 HIS cc_start: 0.7045 (m-70) cc_final: 0.6349 (m-70) REVERT: L 386 HIS cc_start: 0.6801 (m-70) cc_final: 0.6481 (m-70) REVERT: L 413 ASN cc_start: 0.6531 (m-40) cc_final: 0.6188 (m-40) REVERT: M 90 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7639 (mt) REVERT: O 22 LEU cc_start: 0.7906 (mm) cc_final: 0.7490 (mt) REVERT: O 128 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7490 (mmtp) REVERT: O 203 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7877 (t70) REVERT: O 340 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7396 (mt-10) REVERT: Q 51 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: Q 66 LEU cc_start: 0.8716 (mt) cc_final: 0.8342 (mp) REVERT: Q 90 LEU cc_start: 0.8006 (tp) cc_final: 0.7648 (tm) REVERT: Q 111 ASP cc_start: 0.8434 (t0) cc_final: 0.8144 (t0) REVERT: Q 113 VAL cc_start: 0.8396 (m) cc_final: 0.8026 (p) REVERT: S 22 LEU cc_start: 0.8120 (mm) cc_final: 0.7799 (mt) REVERT: S 41 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8506 (ttm-80) REVERT: T 66 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7823 (mp) REVERT: T 113 VAL cc_start: 0.8323 (m) cc_final: 0.8079 (p) REVERT: T 130 ARG cc_start: 0.5680 (mmp-170) cc_final: 0.5133 (mmm160) REVERT: W 128 LYS cc_start: 0.8357 (mptt) cc_final: 0.7790 (mppt) REVERT: W 130 LEU cc_start: 0.8335 (mt) cc_final: 0.8107 (mt) REVERT: W 303 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7359 (ttt180) REVERT: W 440 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5490 (mp0) REVERT: X 66 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8051 (mp) REVERT: X 133 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6849 (mm110) outliers start: 92 outliers final: 41 residues processed: 583 average time/residue: 0.8901 time to fit residues: 608.7978 Evaluate side-chains 574 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 514 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 243 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 348 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 234 optimal weight: 0.0770 chunk 236 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 94 GLN D 29 GLN G 29 GLN G 94 GLN M 94 GLN O 383 HIS Q 115 GLN Q 133 GLN S 207 ASN S 413 ASN T 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.096115 restraints weight = 41160.976| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.70 r_work: 0.2842 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35681 Z= 0.140 Angle : 0.509 7.937 48403 Z= 0.274 Chirality : 0.043 0.184 5136 Planarity : 0.004 0.041 6378 Dihedral : 4.379 19.879 4936 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.41 % Allowed : 16.05 % Favored : 81.54 % 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 aren not related in a simple way. whole: 1.02 (0.12), residues: 4374 helix: 2.38 (0.12), residues: 1676 sheet: -0.64 (0.18), residues: 760 loop : -0.24 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 435 TYR 0.014 0.001 TYR A 269 PHE 0.026 0.002 PHE W 345 TRP 0.022 0.001 TRP I 385 HIS 0.003 0.001 HIS L 386 Details of bonding type rmsd covalent geometry : bond 0.00323 (35681) covalent geometry : angle 0.50915 (48403) hydrogen bonds : bond 0.03772 ( 1537) hydrogen bonds : angle 5.00816 ( 4371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 539 time to evaluate : 1.509 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8339 (m-30) cc_final: 0.8056 (m-30) REVERT: A 302 ASP cc_start: 0.8314 (p0) cc_final: 0.7957 (p0) REVERT: A 355 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: P 88 GLN cc_start: 0.7299 (tp40) cc_final: 0.6818 (tp40) REVERT: P 102 ASP cc_start: 0.8058 (m-30) cc_final: 0.7808 (m-30) REVERT: P 133 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7690 (mm-40) REVERT: C 249 GLU cc_start: 0.8498 (tp30) cc_final: 0.8273 (mm-30) REVERT: C 339 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6968 (ttp80) REVERT: C 387 MET cc_start: 0.8079 (tpp) cc_final: 0.7853 (ttm) REVERT: D 27 SER cc_start: 0.8442 (t) cc_final: 0.8162 (p) REVERT: D 91 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7288 (mpp80) REVERT: D 133 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7168 (mm-40) REVERT: F 41 ARG cc_start: 0.8952 (ttm110) cc_final: 0.8623 (ttm-80) REVERT: F 175 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7547 (mmpt) REVERT: F 203 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7671 (t0) REVERT: F 248 GLU cc_start: 0.8350 (mp0) cc_final: 0.8133 (mp0) REVERT: F 249 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: F 255 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: F 303 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7485 (ttt180) REVERT: F 336 GLU cc_start: 0.5545 (mm-30) cc_final: 0.5142 (mm-30) REVERT: F 435 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7079 (mtt-85) REVERT: F 446 ARG cc_start: 0.6798 (mtt180) cc_final: 0.5951 (mmp-170) REVERT: G 29 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8609 (mp-120) REVERT: G 49 SER cc_start: 0.8701 (p) cc_final: 0.8129 (m) REVERT: G 88 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7397 (tm130) REVERT: G 98 ARG cc_start: 0.7119 (mtm110) cc_final: 0.6366 (mtt180) REVERT: G 132 TYR cc_start: 0.7560 (p90) cc_final: 0.7228 (p90) REVERT: I 83 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: I 302 ASP cc_start: 0.8341 (p0) cc_final: 0.8141 (p0) REVERT: I 305 ARG cc_start: 0.7995 (ptm-80) cc_final: 0.7750 (ptm160) REVERT: I 331 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7145 (t) REVERT: I 355 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7588 (tm-30) REVERT: J 21 MET cc_start: 0.8491 (mtp) cc_final: 0.8032 (ttp) REVERT: J 29 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8655 (mp-120) REVERT: J 88 GLN cc_start: 0.7809 (tp40) cc_final: 0.7251 (tp-100) REVERT: L 33 ASP cc_start: 0.8010 (m-30) cc_final: 0.7762 (p0) REVERT: L 175 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8011 (mttp) REVERT: L 255 GLU cc_start: 0.8773 (tp30) cc_final: 0.8416 (tt0) REVERT: L 383 HIS cc_start: 0.7067 (m-70) cc_final: 0.6375 (m-70) REVERT: L 386 HIS cc_start: 0.6799 (m-70) cc_final: 0.6570 (m-70) REVERT: O 22 LEU cc_start: 0.7913 (mm) cc_final: 0.7491 (mt) REVERT: O 128 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7448 (mmtp) REVERT: O 203 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7844 (t70) REVERT: O 340 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7402 (mt-10) REVERT: Q 51 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: Q 66 LEU cc_start: 0.8721 (mt) cc_final: 0.8375 (mp) REVERT: Q 90 LEU cc_start: 0.8099 (tp) cc_final: 0.7676 (tm) REVERT: Q 111 ASP cc_start: 0.8427 (t0) cc_final: 0.8127 (t0) REVERT: Q 113 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8008 (p) REVERT: S 22 LEU cc_start: 0.8116 (mm) cc_final: 0.7784 (mt) REVERT: S 41 ARG cc_start: 0.8797 (ttm110) cc_final: 0.8513 (ttm-80) REVERT: S 95 ASN cc_start: 0.5615 (t0) cc_final: 0.4935 (t0) REVERT: S 440 GLU cc_start: 0.5445 (mt-10) cc_final: 0.4406 (mm-30) REVERT: T 66 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7790 (mp) REVERT: T 113 VAL cc_start: 0.8341 (m) cc_final: 0.8112 (p) REVERT: T 130 ARG cc_start: 0.5665 (mmp-170) cc_final: 0.5138 (mmm160) REVERT: W 128 LYS cc_start: 0.8338 (mptt) cc_final: 0.7774 (mppt) REVERT: W 130 LEU cc_start: 0.8333 (mt) cc_final: 0.8109 (mt) REVERT: W 303 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7322 (ttt180) REVERT: W 358 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7604 (ttm-80) REVERT: W 440 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5481 (mp0) REVERT: X 66 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7988 (mp) outliers start: 87 outliers final: 36 residues processed: 586 average time/residue: 0.8933 time to fit residues: 613.7785 Evaluate side-chains 576 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 521 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 2 optimal weight: 6.9990 chunk 264 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 171 optimal weight: 0.2980 chunk 261 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 GLN J 8 ASN M 94 GLN O 383 HIS Q 133 GLN S 413 ASN T 29 GLN X 88 GLN X 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.097796 restraints weight = 41279.893| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.71 r_work: 0.2867 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35681 Z= 0.101 Angle : 0.474 7.756 48403 Z= 0.255 Chirality : 0.041 0.185 5136 Planarity : 0.004 0.040 6378 Dihedral : 4.173 18.722 4936 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.83 % Allowed : 16.83 % Favored : 81.34 % 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 aren not related in a simple way. whole: 1.20 (0.13), residues: 4374 helix: 2.61 (0.12), residues: 1676 sheet: -0.61 (0.18), residues: 760 loop : -0.19 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 114 TYR 0.012 0.001 TYR G 67 PHE 0.027 0.001 PHE W 345 TRP 0.025 0.001 TRP I 385 HIS 0.003 0.001 HIS W 325 Details of bonding type rmsd covalent geometry : bond 0.00224 (35681) covalent geometry : angle 0.47358 (48403) hydrogen bonds : bond 0.03286 ( 1537) hydrogen bonds : angle 4.84049 ( 4371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 549 time to evaluate : 1.231 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8485 (m-30) cc_final: 0.8193 (m-30) REVERT: A 302 ASP cc_start: 0.8358 (p0) cc_final: 0.8024 (p0) REVERT: P 16 SER cc_start: 0.8776 (t) cc_final: 0.8426 (p) REVERT: P 21 MET cc_start: 0.8663 (mtm) cc_final: 0.8157 (ttp) REVERT: P 84 THR cc_start: 0.7685 (p) cc_final: 0.7456 (t) REVERT: P 88 GLN cc_start: 0.7333 (tp40) cc_final: 0.6828 (tp-100) REVERT: P 90 LEU cc_start: 0.8311 (tp) cc_final: 0.8081 (tm) REVERT: P 102 ASP cc_start: 0.7974 (m-30) cc_final: 0.7722 (m-30) REVERT: P 133 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7566 (mm-40) REVERT: C 107 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8157 (mp) REVERT: C 127 PHE cc_start: 0.8185 (m-10) cc_final: 0.7666 (m-10) REVERT: C 248 GLU cc_start: 0.8568 (mp0) cc_final: 0.8168 (mp0) REVERT: C 339 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7088 (ttt90) REVERT: C 387 MET cc_start: 0.8093 (tpp) cc_final: 0.7869 (ttm) REVERT: D 27 SER cc_start: 0.8419 (t) cc_final: 0.8136 (p) REVERT: D 91 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7293 (mpp80) REVERT: D 133 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7271 (mm-40) REVERT: F 26 THR cc_start: 0.8249 (m) cc_final: 0.7739 (p) REVERT: F 41 ARG cc_start: 0.8932 (ttm110) cc_final: 0.8607 (ttm-80) REVERT: F 175 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7504 (mmtp) REVERT: F 203 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7591 (t0) REVERT: F 249 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: F 255 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: F 303 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7453 (ttt180) REVERT: F 336 GLU cc_start: 0.5568 (mm-30) cc_final: 0.5184 (mm-30) REVERT: F 387 MET cc_start: 0.8442 (tpp) cc_final: 0.7892 (mtt) REVERT: F 435 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7130 (mtt-85) REVERT: F 446 ARG cc_start: 0.6791 (mtt180) cc_final: 0.5940 (mmp-170) REVERT: G 49 SER cc_start: 0.8692 (p) cc_final: 0.8079 (m) REVERT: G 88 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 114 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7817 (mtm180) REVERT: G 132 TYR cc_start: 0.7458 (p90) cc_final: 0.7120 (p90) REVERT: I 305 ARG cc_start: 0.7992 (ptm-80) cc_final: 0.7740 (ptm160) REVERT: I 331 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7036 (t) REVERT: I 360 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7734 (mtm110) REVERT: J 21 MET cc_start: 0.8453 (mtp) cc_final: 0.7980 (ttp) REVERT: J 29 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8559 (mp-120) REVERT: J 88 GLN cc_start: 0.7794 (tp40) cc_final: 0.7236 (tp-100) REVERT: L 33 ASP cc_start: 0.8023 (m-30) cc_final: 0.7765 (p0) REVERT: L 158 GLU cc_start: 0.8565 (tt0) cc_final: 0.7988 (pt0) REVERT: L 255 GLU cc_start: 0.8759 (tp30) cc_final: 0.8427 (tt0) REVERT: L 303 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8545 (tmt170) REVERT: L 383 HIS cc_start: 0.7047 (m-70) cc_final: 0.6356 (m-70) REVERT: L 386 HIS cc_start: 0.6793 (m-70) cc_final: 0.6559 (m-70) REVERT: O 22 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7491 (mt) REVERT: O 128 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7478 (mmtp) REVERT: O 203 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7793 (t70) REVERT: O 339 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7313 (tpp80) REVERT: O 340 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7400 (mt-10) REVERT: Q 49 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8631 (m) REVERT: Q 51 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: Q 66 LEU cc_start: 0.8721 (mt) cc_final: 0.8357 (mp) REVERT: Q 90 LEU cc_start: 0.8004 (tp) cc_final: 0.7699 (tm) REVERT: Q 111 ASP cc_start: 0.8377 (t0) cc_final: 0.8141 (t0) REVERT: Q 113 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8001 (p) REVERT: S 22 LEU cc_start: 0.8115 (mm) cc_final: 0.7779 (mt) REVERT: S 41 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8438 (ttm-80) REVERT: S 303 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (tmt170) REVERT: S 358 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: S 413 ASN cc_start: 0.7003 (m-40) cc_final: 0.6297 (m-40) REVERT: S 440 GLU cc_start: 0.5449 (mt-10) cc_final: 0.4460 (mm-30) REVERT: T 113 VAL cc_start: 0.8264 (m) cc_final: 0.8036 (p) REVERT: T 130 ARG cc_start: 0.5699 (mmp-170) cc_final: 0.5166 (mmm160) REVERT: W 128 LYS cc_start: 0.8331 (mptt) cc_final: 0.7767 (mppt) REVERT: W 130 LEU cc_start: 0.8301 (mt) cc_final: 0.8081 (mt) REVERT: W 303 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7223 (ttt180) REVERT: W 358 ARG cc_start: 0.8149 (mtp-110) cc_final: 0.7667 (ttm-80) REVERT: X 133 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6714 (mm110) outliers start: 66 outliers final: 25 residues processed: 582 average time/residue: 0.7714 time to fit residues: 526.0105 Evaluate side-chains 570 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 527 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 ARG Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 202 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 243 optimal weight: 5.9990 chunk 436 optimal weight: 8.9990 chunk 403 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 276 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 94 GLN D 29 GLN G 29 GLN G 94 GLN M 94 GLN O 383 HIS Q 115 GLN Q 133 GLN ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097290 restraints weight = 41283.712| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.70 r_work: 0.2856 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35681 Z= 0.118 Angle : 0.494 9.679 48403 Z= 0.265 Chirality : 0.042 0.166 5136 Planarity : 0.004 0.040 6378 Dihedral : 4.202 18.822 4936 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 17.05 % Favored : 81.09 % 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 aren not related in a simple way. whole: 1.17 (0.13), residues: 4374 helix: 2.58 (0.12), residues: 1676 sheet: -0.60 (0.18), residues: 760 loop : -0.20 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 435 TYR 0.011 0.001 TYR C 269 PHE 0.027 0.002 PHE W 345 TRP 0.026 0.001 TRP I 385 HIS 0.003 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00270 (35681) covalent geometry : angle 0.49439 (48403) hydrogen bonds : bond 0.03447 ( 1537) hydrogen bonds : angle 4.86502 ( 4371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 527 time to evaluate : 1.309 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8497 (m-30) cc_final: 0.8201 (m-30) REVERT: A 302 ASP cc_start: 0.8272 (p0) cc_final: 0.7958 (p0) REVERT: A 340 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7428 (mt-10) REVERT: A 443 ASP cc_start: 0.5809 (m-30) cc_final: 0.5432 (t0) REVERT: P 16 SER cc_start: 0.8792 (t) cc_final: 0.8429 (p) REVERT: P 84 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7461 (t) REVERT: P 88 GLN cc_start: 0.7343 (tp40) cc_final: 0.6769 (tp40) REVERT: P 102 ASP cc_start: 0.8010 (m-30) cc_final: 0.7762 (m-30) REVERT: P 133 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7606 (mm-40) REVERT: C 339 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7094 (ttt90) REVERT: C 387 MET cc_start: 0.8137 (tpp) cc_final: 0.7879 (ttm) REVERT: D 27 SER cc_start: 0.8417 (t) cc_final: 0.8131 (p) REVERT: D 91 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7334 (mpp80) REVERT: D 133 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7081 (mm-40) REVERT: F 26 THR cc_start: 0.8254 (m) cc_final: 0.7741 (p) REVERT: F 41 ARG cc_start: 0.8947 (ttm110) cc_final: 0.8625 (ttm-80) REVERT: F 175 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7473 (mmtp) REVERT: F 203 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7594 (t0) REVERT: F 248 GLU cc_start: 0.8374 (mp0) cc_final: 0.8065 (mp0) REVERT: F 249 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: F 255 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: F 303 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7477 (ttt180) REVERT: F 336 GLU cc_start: 0.5554 (mm-30) cc_final: 0.5177 (mm-30) REVERT: F 387 MET cc_start: 0.8486 (tpp) cc_final: 0.7880 (mtt) REVERT: F 446 ARG cc_start: 0.6819 (mtt180) cc_final: 0.5959 (mmp-170) REVERT: G 49 SER cc_start: 0.8723 (p) cc_final: 0.8073 (m) REVERT: G 88 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7396 (tm-30) REVERT: G 114 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7749 (mtm180) REVERT: G 132 TYR cc_start: 0.7394 (p90) cc_final: 0.7047 (p90) REVERT: I 106 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: I 302 ASP cc_start: 0.8425 (p0) cc_final: 0.8064 (p0) REVERT: I 305 ARG cc_start: 0.7978 (ptm-80) cc_final: 0.7708 (ptm160) REVERT: I 331 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.7046 (t) REVERT: I 355 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7570 (tm-30) REVERT: J 29 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8540 (mp-120) REVERT: J 88 GLN cc_start: 0.7816 (tp40) cc_final: 0.7264 (tp-100) REVERT: L 33 ASP cc_start: 0.8006 (m-30) cc_final: 0.7753 (p0) REVERT: L 158 GLU cc_start: 0.8588 (tt0) cc_final: 0.8017 (pt0) REVERT: L 255 GLU cc_start: 0.8755 (tp30) cc_final: 0.8429 (tt0) REVERT: L 303 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8531 (tmt170) REVERT: L 383 HIS cc_start: 0.7072 (m-70) cc_final: 0.6396 (m-70) REVERT: L 386 HIS cc_start: 0.6803 (m-70) cc_final: 0.6561 (m-70) REVERT: O 22 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7497 (mt) REVERT: O 128 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7507 (mmtp) REVERT: O 203 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7782 (t70) REVERT: O 339 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7327 (tpp80) REVERT: O 340 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7388 (mt-10) REVERT: Q 49 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8650 (m) REVERT: Q 66 LEU cc_start: 0.8676 (mt) cc_final: 0.8313 (mp) REVERT: Q 90 LEU cc_start: 0.8017 (tp) cc_final: 0.7592 (tm) REVERT: Q 113 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7990 (t) REVERT: S 22 LEU cc_start: 0.8119 (mm) cc_final: 0.7779 (mt) REVERT: S 41 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8432 (ttm-80) REVERT: S 358 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7609 (mmm-85) REVERT: S 413 ASN cc_start: 0.6952 (m-40) cc_final: 0.6280 (m-40) REVERT: S 440 GLU cc_start: 0.5443 (mt-10) cc_final: 0.4461 (mm-30) REVERT: T 113 VAL cc_start: 0.8283 (m) cc_final: 0.8036 (p) REVERT: T 130 ARG cc_start: 0.5628 (mmp-170) cc_final: 0.5120 (mmm160) REVERT: W 128 LYS cc_start: 0.8307 (mptt) cc_final: 0.7757 (mppt) REVERT: W 130 LEU cc_start: 0.8306 (mt) cc_final: 0.8078 (mt) REVERT: W 303 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7274 (ttt180) REVERT: W 358 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7696 (ttm-80) REVERT: W 440 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5806 (mp0) REVERT: X 133 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6720 (mm110) outliers start: 67 outliers final: 31 residues processed: 561 average time/residue: 0.7326 time to fit residues: 482.8544 Evaluate side-chains 568 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 520 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain S residue 42 MET Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 24 optimal weight: 6.9990 chunk 437 optimal weight: 9.9990 chunk 378 optimal weight: 0.0770 chunk 381 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 396 optimal weight: 0.0570 chunk 213 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 142 optimal weight: 0.0970 overall best weight: 2.2458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN G 29 GLN G 94 GLN ** L 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN O 383 HIS T 29 GLN X 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098111 restraints weight = 41100.116| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.70 r_work: 0.2871 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 35681 Z= 0.107 Angle : 0.480 5.173 48403 Z= 0.258 Chirality : 0.041 0.166 5136 Planarity : 0.004 0.041 6378 Dihedral : 4.135 18.531 4936 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.58 % Allowed : 17.52 % Favored : 80.90 % 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 aren not related in a simple way. whole: 1.22 (0.13), residues: 4374 helix: 2.63 (0.12), residues: 1676 sheet: -0.59 (0.18), residues: 760 loop : -0.19 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 435 TYR 0.010 0.001 TYR G 67 PHE 0.028 0.001 PHE W 345 TRP 0.027 0.001 TRP I 385 HIS 0.002 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00242 (35681) covalent geometry : angle 0.47958 (48403) hydrogen bonds : bond 0.03284 ( 1537) hydrogen bonds : angle 4.81835 ( 4371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 544 time to evaluate : 1.372 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8496 (m-30) cc_final: 0.8205 (m-30) REVERT: A 302 ASP cc_start: 0.8345 (p0) cc_final: 0.8023 (p0) REVERT: A 340 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7411 (mt-10) REVERT: A 443 ASP cc_start: 0.5802 (m-30) cc_final: 0.5428 (t0) REVERT: P 16 SER cc_start: 0.8778 (t) cc_final: 0.8432 (p) REVERT: P 84 THR cc_start: 0.7761 (p) cc_final: 0.7545 (t) REVERT: P 88 GLN cc_start: 0.7342 (tp40) cc_final: 0.7018 (tp40) REVERT: P 90 LEU cc_start: 0.8341 (tp) cc_final: 0.8114 (tm) REVERT: P 102 ASP cc_start: 0.7903 (m-30) cc_final: 0.7675 (m-30) REVERT: P 133 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7705 (mm-40) REVERT: C 107 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8133 (mp) REVERT: C 339 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7100 (ttt90) REVERT: C 387 MET cc_start: 0.8132 (tpp) cc_final: 0.7861 (ttm) REVERT: D 27 SER cc_start: 0.8402 (t) cc_final: 0.8096 (p) REVERT: D 91 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7277 (mpp80) REVERT: D 133 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7144 (mm-40) REVERT: F 26 THR cc_start: 0.8260 (m) cc_final: 0.7767 (p) REVERT: F 41 ARG cc_start: 0.8939 (ttm110) cc_final: 0.8697 (ttm-80) REVERT: F 203 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7586 (t0) REVERT: F 249 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: F 255 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: F 303 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7476 (ttt180) REVERT: F 336 GLU cc_start: 0.5654 (mm-30) cc_final: 0.5283 (mm-30) REVERT: F 387 MET cc_start: 0.8488 (tpp) cc_final: 0.7870 (mtt) REVERT: F 446 ARG cc_start: 0.6789 (mtt180) cc_final: 0.5908 (mmm160) REVERT: G 88 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7276 (tm-30) REVERT: G 98 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6493 (mtt180) REVERT: G 114 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7749 (mtm180) REVERT: G 132 TYR cc_start: 0.7361 (p90) cc_final: 0.7020 (p90) REVERT: I 106 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: I 302 ASP cc_start: 0.8364 (p0) cc_final: 0.8146 (p0) REVERT: I 305 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7689 (ptm160) REVERT: I 331 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7039 (t) REVERT: I 355 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7584 (tm-30) REVERT: J 21 MET cc_start: 0.8565 (mtp) cc_final: 0.8070 (ttp) REVERT: J 29 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8588 (mp-120) REVERT: J 88 GLN cc_start: 0.7807 (tp40) cc_final: 0.7258 (tp-100) REVERT: L 33 ASP cc_start: 0.7999 (m-30) cc_final: 0.7747 (p0) REVERT: L 158 GLU cc_start: 0.8580 (tt0) cc_final: 0.8015 (pt0) REVERT: L 255 GLU cc_start: 0.8750 (tp30) cc_final: 0.8434 (tt0) REVERT: L 303 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8516 (tmt170) REVERT: L 383 HIS cc_start: 0.7043 (m-70) cc_final: 0.6286 (m-70) REVERT: L 386 HIS cc_start: 0.6772 (m-70) cc_final: 0.6475 (m90) REVERT: O 22 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7487 (mt) REVERT: O 128 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7496 (mmtp) REVERT: O 203 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7768 (t70) REVERT: O 339 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7319 (tpp80) REVERT: O 340 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7380 (mt-10) REVERT: Q 49 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8651 (m) REVERT: Q 66 LEU cc_start: 0.8713 (mt) cc_final: 0.8354 (mp) REVERT: Q 90 LEU cc_start: 0.7996 (tp) cc_final: 0.7693 (tm) REVERT: Q 111 ASP cc_start: 0.8403 (t0) cc_final: 0.8162 (t0) REVERT: Q 113 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7898 (t) REVERT: S 22 LEU cc_start: 0.8124 (mm) cc_final: 0.7785 (mt) REVERT: S 358 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: S 413 ASN cc_start: 0.6903 (m-40) cc_final: 0.6241 (m-40) REVERT: S 440 GLU cc_start: 0.5704 (mt-10) cc_final: 0.4708 (mm-30) REVERT: T 94 GLN cc_start: 0.6906 (mp10) cc_final: 0.6342 (mp10) REVERT: T 113 VAL cc_start: 0.8282 (m) cc_final: 0.8029 (p) REVERT: T 130 ARG cc_start: 0.5622 (mmp-170) cc_final: 0.5134 (mmm160) REVERT: W 128 LYS cc_start: 0.8313 (mptt) cc_final: 0.7749 (mppt) REVERT: W 130 LEU cc_start: 0.8300 (mt) cc_final: 0.8052 (mt) REVERT: W 303 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7311 (ttt180) REVERT: W 358 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7684 (ttm-80) REVERT: W 440 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5728 (mp0) outliers start: 57 outliers final: 28 residues processed: 573 average time/residue: 0.7550 time to fit residues: 509.3742 Evaluate side-chains 569 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 524 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 159 optimal weight: 9.9990 chunk 386 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 394 optimal weight: 9.9990 chunk 284 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 424 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 94 GLN D 29 GLN G 29 GLN G 94 GLN ** L 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN O 383 HIS Q 133 GLN ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN X 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097503 restraints weight = 41178.553| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.70 r_work: 0.2858 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35681 Z= 0.118 Angle : 0.497 9.735 48403 Z= 0.266 Chirality : 0.042 0.165 5136 Planarity : 0.004 0.041 6378 Dihedral : 4.170 18.696 4936 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.41 % Allowed : 17.80 % Favored : 80.79 % 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 aren not related in a simple way. whole: 1.18 (0.13), residues: 4374 helix: 2.58 (0.12), residues: 1676 sheet: -0.59 (0.18), residues: 760 loop : -0.20 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 435 TYR 0.015 0.001 TYR F 269 PHE 0.027 0.002 PHE W 345 TRP 0.032 0.001 TRP I 385 HIS 0.003 0.001 HIS L 386 Details of bonding type rmsd covalent geometry : bond 0.00270 (35681) covalent geometry : angle 0.49695 (48403) hydrogen bonds : bond 0.03414 ( 1537) hydrogen bonds : angle 4.85211 ( 4371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 529 time to evaluate : 1.483 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8508 (m-30) cc_final: 0.8222 (m-30) REVERT: A 175 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7817 (mmtm) REVERT: A 302 ASP cc_start: 0.8270 (p0) cc_final: 0.7940 (p0) REVERT: A 340 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7433 (mt-10) REVERT: A 355 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: A 443 ASP cc_start: 0.5803 (m-30) cc_final: 0.5438 (t0) REVERT: P 16 SER cc_start: 0.8785 (t) cc_final: 0.8419 (p) REVERT: P 84 THR cc_start: 0.7692 (p) cc_final: 0.7468 (t) REVERT: P 88 GLN cc_start: 0.7450 (tp40) cc_final: 0.6963 (tp40) REVERT: P 102 ASP cc_start: 0.8006 (m-30) cc_final: 0.7751 (m-30) REVERT: P 133 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7713 (mm-40) REVERT: C 107 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8160 (mp) REVERT: C 339 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (ttt90) REVERT: D 27 SER cc_start: 0.8374 (t) cc_final: 0.7998 (p) REVERT: D 91 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7286 (mpp80) REVERT: D 133 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7077 (mm-40) REVERT: F 26 THR cc_start: 0.8277 (m) cc_final: 0.7770 (p) REVERT: F 41 ARG cc_start: 0.8953 (ttm110) cc_final: 0.8707 (ttm-80) REVERT: F 203 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7571 (t0) REVERT: F 248 GLU cc_start: 0.8423 (mp0) cc_final: 0.8120 (mp0) REVERT: F 249 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: F 255 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: F 303 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7478 (ttt180) REVERT: F 336 GLU cc_start: 0.5659 (mm-30) cc_final: 0.5267 (mm-30) REVERT: F 446 ARG cc_start: 0.6788 (mtt180) cc_final: 0.5902 (mmm160) REVERT: G 88 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7374 (tm-30) REVERT: G 98 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6489 (mtt180) REVERT: G 132 TYR cc_start: 0.7369 (p90) cc_final: 0.7035 (p90) REVERT: I 106 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: I 302 ASP cc_start: 0.8333 (p0) cc_final: 0.8102 (p0) REVERT: I 305 ARG cc_start: 0.7984 (ptm-80) cc_final: 0.7720 (ptm160) REVERT: I 331 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7034 (t) REVERT: I 355 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7574 (tm-30) REVERT: J 21 MET cc_start: 0.8562 (mtp) cc_final: 0.8077 (ttp) REVERT: J 29 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8577 (mp-120) REVERT: J 88 GLN cc_start: 0.7861 (tp40) cc_final: 0.7312 (tp-100) REVERT: L 33 ASP cc_start: 0.7991 (m-30) cc_final: 0.7736 (p0) REVERT: L 158 GLU cc_start: 0.8599 (tt0) cc_final: 0.8030 (pt0) REVERT: L 255 GLU cc_start: 0.8749 (tp30) cc_final: 0.8430 (tt0) REVERT: L 303 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8536 (tmt170) REVERT: L 383 HIS cc_start: 0.6999 (m-70) cc_final: 0.6217 (m-70) REVERT: L 386 HIS cc_start: 0.6790 (m-70) cc_final: 0.6519 (m-70) REVERT: O 22 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7542 (mt) REVERT: O 128 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7475 (mmtp) REVERT: O 203 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (t70) REVERT: O 339 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7324 (tpp80) REVERT: O 340 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7464 (mt-10) REVERT: Q 49 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8647 (m) REVERT: Q 51 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: Q 66 LEU cc_start: 0.8693 (mt) cc_final: 0.8328 (mp) REVERT: Q 90 LEU cc_start: 0.8032 (tp) cc_final: 0.7712 (tm) REVERT: Q 113 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7963 (t) REVERT: S 22 LEU cc_start: 0.8128 (mm) cc_final: 0.7738 (mt) REVERT: S 358 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7618 (mmm-85) REVERT: S 413 ASN cc_start: 0.6833 (m-40) cc_final: 0.6136 (m-40) REVERT: S 440 GLU cc_start: 0.5684 (mt-10) cc_final: 0.4698 (mm-30) REVERT: T 113 VAL cc_start: 0.8280 (m) cc_final: 0.8025 (p) REVERT: T 130 ARG cc_start: 0.5478 (mmp-170) cc_final: 0.4988 (mmm160) REVERT: W 128 LYS cc_start: 0.8315 (mptt) cc_final: 0.7747 (mppt) REVERT: W 130 LEU cc_start: 0.8298 (mt) cc_final: 0.8069 (mt) REVERT: W 303 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7334 (ttt180) REVERT: W 358 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7740 (ttm-80) REVERT: W 390 LEU cc_start: 0.8506 (mt) cc_final: 0.8161 (mt) REVERT: W 440 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5773 (mp0) outliers start: 51 outliers final: 28 residues processed: 557 average time/residue: 0.8635 time to fit residues: 564.5975 Evaluate side-chains 567 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 520 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 303 ARG Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain Q residue 51 TYR Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG Chi-restraints excluded: chain W residue 435 ARG Chi-restraints excluded: chain W residue 440 GLU Chi-restraints excluded: chain W residue 449 CYS Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 chunk 425 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 409 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN D 36 ASN G 29 GLN G 94 GLN M 94 GLN O 383 HIS Q 133 GLN S 207 ASN T 29 GLN X 88 GLN X 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095513 restraints weight = 41296.781| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.74 r_work: 0.2812 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 35681 Z= 0.217 Angle : 0.573 6.164 48403 Z= 0.307 Chirality : 0.046 0.180 5136 Planarity : 0.005 0.050 6378 Dihedral : 4.500 19.838 4936 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 17.63 % Favored : 80.70 % 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 aren not related in a simple way. whole: 0.90 (0.12), residues: 4374 helix: 2.21 (0.12), residues: 1676 sheet: -0.57 (0.18), residues: 728 loop : -0.30 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 114 TYR 0.020 0.002 TYR F 269 PHE 0.028 0.002 PHE F 345 TRP 0.036 0.002 TRP I 385 HIS 0.005 0.001 HIS L 386 Details of bonding type rmsd covalent geometry : bond 0.00510 (35681) covalent geometry : angle 0.57308 (48403) hydrogen bonds : bond 0.04298 ( 1537) hydrogen bonds : angle 5.10818 ( 4371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13663.23 seconds wall clock time: 233 minutes 58.77 seconds (14038.77 seconds total)