Starting phenix.real_space_refine on Sun Jun 29 19:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q05_18050/06_2025/8q05_18050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q05_18050/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q05_18050/06_2025/8q05_18050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q05_18050/06_2025/8q05_18050.map" model { file = "/net/cci-nas-00/data/ceres_data/8q05_18050/06_2025/8q05_18050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q05_18050/06_2025/8q05_18050.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.38, per 1000 atoms: 0.32 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: 7.90 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 4.14 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: 14.14 Time building geometry restraints manager: 9.47 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 67.120 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (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 TRP 0.024 0.002 TRP L 385 HIS 0.004 0.001 HIS O 298 PHE 0.019 0.002 PHE Z 173 TYR 0.015 0.002 TYR I 24 ARG 0.004 0.001 ARG F 187 Details of bonding type rmsd hydrogen bonds : bond 0.14247 ( 1537) hydrogen bonds : angle 7.04701 ( 4371) covalent geometry : bond 0.00834 (35681) covalent geometry : angle 1.02122 (48403) *********************** 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 : 3.747 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: 0.6965 (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: 0.7416 (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: 0.7166 (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: 0.8270 (m) REVERT: G 92 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7603 (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: 0.6609 (tttm) REVERT: I 249 GLU cc_start: 0.8440 (tp30) cc_final: 0.8213 (tp30) REVERT: I 449 CYS cc_start: 0.6145 (t) cc_final: 0.5045 (m) 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: 0.8791 (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: 0.6152 (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: 0.7208 (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: 0.7631 (mt) REVERT: S 41 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8462 (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: 1.7497 time to fit residues: 1595.9754 Evaluate side-chains 595 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 592 time to evaluate : 3.641 ------------------------------------------------------------------------------- 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 372 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 345 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 56 ASN G 94 GLN G 124 ASN I 153 HIS I 413 ASN J 2 GLN J 8 ASN 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098645 restraints weight = 41247.032| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.77 r_work: 0.2861 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 35681 Z= 0.162 Angle : 0.548 6.449 48403 Z= 0.298 Chirality : 0.044 0.174 5136 Planarity : 0.005 0.046 6378 Dihedral : 4.483 60.797 4942 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.22 % Allowed : 15.77 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4374 helix: 2.29 (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 TRP 0.015 0.001 TRP C 385 HIS 0.009 0.001 HIS I 153 PHE 0.030 0.002 PHE O 345 TYR 0.017 0.002 TYR A 269 ARG 0.009 0.001 ARG O 446 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1537) hydrogen bonds : angle 5.44418 ( 4371) covalent geometry : bond 0.00368 (35681) covalent geometry : angle 0.54763 (48403) *********************** 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 668 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 588 time to evaluate : 3.691 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: 0.7854 (mt0) cc_final: 0.7462 (mt0) REVERT: A 106 ASP cc_start: 0.8524 (m-30) cc_final: 0.8228 (m-30) REVERT: A 355 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: P 88 GLN cc_start: 0.7322 (tp40) cc_final: 0.6736 (tp40) REVERT: P 102 ASP cc_start: 0.8050 (m-30) cc_final: 0.7767 (m-30) REVERT: C 255 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: C 339 ARG cc_start: 0.7314 (ttm170) cc_final: 0.6977 (ttm-80) REVERT: C 358 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: D 13 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 27 SER cc_start: 0.8315 (t) cc_final: 0.8037 (p) REVERT: D 94 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: D 132 TYR cc_start: 0.8041 (p90) cc_final: 0.7831 (p90) REVERT: D 133 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7135 (mm-40) REVERT: F 41 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8578 (ttm-80) REVERT: F 81 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.6072 (pttt) REVERT: F 128 LYS cc_start: 0.8130 (mptt) cc_final: 0.7650 (mmmm) REVERT: F 175 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7631 (mmpt) REVERT: F 203 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7360 (t0) REVERT: F 249 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: F 435 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6805 (mtt-85) REVERT: F 446 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5813 (mmp-170) REVERT: G 49 SER cc_start: 0.8704 (p) cc_final: 0.8230 (m) REVERT: G 88 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7559 (tm130) REVERT: G 92 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7675 (mm-30) REVERT: G 98 ARG cc_start: 0.7056 (mtm110) cc_final: 0.6297 (mtt180) REVERT: I 52 GLU cc_start: 0.7986 (tt0) cc_final: 0.7536 (mt-10) REVERT: I 83 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7763 (ptm160) REVERT: I 249 GLU cc_start: 0.8472 (tp30) cc_final: 0.8261 (tp30) REVERT: I 302 ASP cc_start: 0.8280 (p0) cc_final: 0.8048 (p0) REVERT: I 449 CYS cc_start: 0.6041 (t) cc_final: 0.4705 (m) REVERT: J 9 ASN cc_start: 0.8217 (t0) cc_final: 0.7899 (t160) REVERT: J 21 MET cc_start: 0.8435 (mtp) cc_final: 0.7945 (ttp) REVERT: J 29 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8214 (mp-120) REVERT: J 88 GLN cc_start: 0.7866 (tp40) cc_final: 0.7371 (tp-100) REVERT: L 255 GLU cc_start: 0.8817 (tp30) cc_final: 0.8406 (tt0) REVERT: L 383 HIS cc_start: 0.6987 (m-70) cc_final: 0.6271 (m-70) REVERT: L 386 HIS cc_start: 0.6851 (m-70) cc_final: 0.6518 (m90) REVERT: L 413 ASN cc_start: 0.6800 (m-40) cc_final: 0.6296 (m-40) REVERT: L 454 GLU cc_start: 0.7111 (mp0) cc_final: 0.6739 (mp0) REVERT: M 32 TYR cc_start: 0.8865 (t80) cc_final: 0.8596 (t80) REVERT: M 90 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7572 (mt) REVERT: O 22 LEU cc_start: 0.7927 (mm) cc_final: 0.7606 (mt) REVERT: O 128 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7488 (mmtp) REVERT: O 203 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7903 (t70) REVERT: O 305 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: Q 51 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: Q 66 LEU cc_start: 0.8607 (mt) cc_final: 0.8398 (mp) REVERT: S 22 LEU cc_start: 0.7994 (mm) cc_final: 0.7682 (mt) REVERT: S 41 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8507 (ttm-80) REVERT: S 339 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7133 (ttt180) REVERT: S 454 GLU cc_start: 0.6653 (mp0) cc_final: 0.6249 (pm20) REVERT: T 21 MET cc_start: 0.8288 (mtm) cc_final: 0.7738 (OUTLIER) REVERT: T 66 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7780 (mp) REVERT: X 2 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.5249 (mt0) REVERT: X 66 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7979 (mp) outliers start: 80 outliers final: 29 residues processed: 626 average time/residue: 1.7726 time to fit residues: 1302.9891 Evaluate side-chains 583 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 539 time to evaluate : 3.690 ------------------------------------------------------------------------------- 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 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 51 GLU 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 344 optimal weight: 7.9990 chunk 424 optimal weight: 9.9990 chunk 287 optimal weight: 0.0970 chunk 229 optimal weight: 0.0070 chunk 54 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 332 optimal weight: 0.6980 chunk 301 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 overall best weight: 3.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 133 GLN D 29 GLN G 29 GLN G 94 GLN M 88 GLN M 94 GLN O 383 HIS Q 115 GLN ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 29 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 = 0.3458 r_free = 0.3458 target = 0.132014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097433 restraints weight = 41533.412| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.75 r_work: 0.2832 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35681 Z= 0.137 Angle : 0.507 6.088 48403 Z= 0.274 Chirality : 0.043 0.166 5136 Planarity : 0.004 0.039 6378 Dihedral : 4.315 18.357 4936 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.55 % Allowed : 16.02 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4374 helix: 2.43 (0.12), residues: 1676 sheet: -0.65 (0.18), residues: 760 loop : -0.11 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 385 HIS 0.004 0.001 HIS A 325 PHE 0.025 0.002 PHE S 345 TYR 0.014 0.002 TYR A 269 ARG 0.005 0.000 ARG W 358 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1537) hydrogen bonds : angle 5.12686 ( 4371) covalent geometry : bond 0.00311 (35681) covalent geometry : angle 0.50705 (48403) *********************** 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 658 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 566 time to evaluate : 3.665 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: 0.7907 (mt0) cc_final: 0.7591 (mt0) REVERT: A 106 ASP cc_start: 0.8543 (m-30) cc_final: 0.8254 (m-30) REVERT: A 302 ASP cc_start: 0.8313 (p0) cc_final: 0.8007 (p0) REVERT: A 355 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: P 88 GLN cc_start: 0.7369 (tp40) cc_final: 0.6894 (tp-100) REVERT: P 90 LEU cc_start: 0.8310 (tp) cc_final: 0.8091 (tm) REVERT: P 102 ASP cc_start: 0.7949 (m-30) cc_final: 0.7697 (m-30) REVERT: C 175 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7364 (mtmt) REVERT: C 255 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: D 2 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5729 (mt0) REVERT: D 27 SER cc_start: 0.8367 (t) cc_final: 0.8120 (p) REVERT: D 133 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7181 (mm-40) REVERT: F 41 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8636 (ttm-80) REVERT: F 128 LYS cc_start: 0.8199 (mptt) cc_final: 0.7678 (mmmm) REVERT: F 203 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7269 (t0) REVERT: F 249 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: F 255 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: F 331 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.7012 (p) REVERT: F 435 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6903 (mtt-85) REVERT: F 446 ARG cc_start: 0.6687 (mtt180) cc_final: 0.5941 (mmp-170) REVERT: G 49 SER cc_start: 0.8686 (p) cc_final: 0.8223 (m) REVERT: G 92 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7769 (mm-30) REVERT: G 98 ARG cc_start: 0.7050 (mtm110) cc_final: 0.6309 (mtt180) REVERT: I 83 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7859 (ptm160) REVERT: I 249 GLU cc_start: 0.8487 (tp30) cc_final: 0.8259 (tp30) REVERT: I 302 ASP cc_start: 0.8270 (p0) cc_final: 0.8058 (p0) REVERT: I 331 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7122 (t) REVERT: I 357 ASP cc_start: 0.8366 (t70) cc_final: 0.8143 (t70) REVERT: I 449 CYS cc_start: 0.6071 (t) cc_final: 0.4947 (m) REVERT: J 16 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8706 (p) REVERT: J 21 MET cc_start: 0.8614 (mtp) cc_final: 0.8070 (ttp) REVERT: J 88 GLN cc_start: 0.7760 (tp40) cc_final: 0.7287 (tp-100) REVERT: L 175 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7946 (mttp) REVERT: L 255 GLU cc_start: 0.8800 (tp30) cc_final: 0.8408 (tt0) REVERT: L 383 HIS cc_start: 0.7009 (m-70) cc_final: 0.6335 (m-70) REVERT: L 386 HIS cc_start: 0.6859 (m-70) cc_final: 0.6517 (m90) REVERT: L 413 ASN cc_start: 0.6815 (m-40) cc_final: 0.6310 (m-40) REVERT: L 454 GLU cc_start: 0.7162 (mp0) cc_final: 0.6798 (mp0) REVERT: M 90 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7532 (mt) REVERT: O 22 LEU cc_start: 0.7953 (mm) cc_final: 0.7568 (mt) REVERT: O 128 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7404 (mmtp) REVERT: O 203 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7867 (t70) REVERT: O 305 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7840 (ttm-80) REVERT: O 340 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7496 (mt-10) REVERT: Q 51 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: Q 66 LEU cc_start: 0.8640 (mt) cc_final: 0.8417 (mp) REVERT: Q 90 LEU cc_start: 0.8002 (tp) cc_final: 0.7689 (tm) REVERT: Q 111 ASP cc_start: 0.8495 (t0) cc_final: 0.8202 (t0) REVERT: Q 113 VAL cc_start: 0.8196 (m) cc_final: 0.7853 (p) REVERT: S 22 LEU cc_start: 0.8129 (mm) cc_final: 0.7794 (mt) REVERT: S 41 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8489 (ttm-80) REVERT: S 95 ASN cc_start: 0.5417 (t0) cc_final: 0.4751 (t0) REVERT: T 21 MET cc_start: 0.8301 (mtm) cc_final: 0.7793 (mtp) REVERT: T 66 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7781 (mp) REVERT: T 113 VAL cc_start: 0.8203 (m) cc_final: 0.7875 (p) REVERT: T 115 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8310 (mm110) REVERT: T 130 ARG cc_start: 0.5618 (mmp-170) cc_final: 0.5115 (mmm160) REVERT: T 133 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8305 (mm-40) REVERT: W 128 LYS cc_start: 0.8229 (mmtm) cc_final: 0.8022 (mptt) REVERT: W 440 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: X 66 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7942 (mp) REVERT: X 133 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6789 (mm110) outliers start: 92 outliers final: 28 residues processed: 615 average time/residue: 1.6499 time to fit residues: 1200.0130 Evaluate side-chains 576 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 530 time to evaluate : 3.961 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 392 GLU 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 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 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 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 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 33 optimal weight: 10.0000 chunk 116 optimal weight: 0.0000 chunk 381 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 276 optimal weight: 5.9990 chunk 437 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 overall best weight: 6.3994 ------------------------------------------------------------------------------- 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 C 327 HIS G 29 GLN G 94 GLN L 207 ASN M 94 GLN O 383 HIS Q 115 GLN Q 133 GLN S 207 ASN S 413 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3426 r_free = 0.3426 target = 0.129197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094364 restraints weight = 41420.715| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.72 r_work: 0.2814 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 35681 Z= 0.206 Angle : 0.568 6.265 48403 Z= 0.306 Chirality : 0.045 0.180 5136 Planarity : 0.005 0.043 6378 Dihedral : 4.573 20.384 4936 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.61 % Allowed : 15.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 4374 helix: 2.22 (0.12), residues: 1660 sheet: -0.66 (0.18), residues: 760 loop : -0.31 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 385 HIS 0.006 0.001 HIS C 238 PHE 0.027 0.002 PHE S 345 TYR 0.018 0.002 TYR A 269 ARG 0.006 0.001 ARG W 131 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 1537) hydrogen bonds : angle 5.20681 ( 4371) covalent geometry : bond 0.00482 (35681) covalent geometry : angle 0.56823 (48403) *********************** 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 629 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 535 time to evaluate : 4.123 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8389 (m-30) cc_final: 0.8120 (m-30) REVERT: A 302 ASP cc_start: 0.8390 (p0) cc_final: 0.8027 (p0) REVERT: A 355 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: P 75 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8659 (ttm) REVERT: P 88 GLN cc_start: 0.7360 (tp40) cc_final: 0.6872 (tp40) REVERT: P 102 ASP cc_start: 0.8103 (m-30) cc_final: 0.7853 (m-30) REVERT: P 133 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7635 (mm-40) REVERT: C 175 LYS cc_start: 0.7495 (mtmt) cc_final: 0.7154 (mtmt) REVERT: C 339 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6909 (ttp80) REVERT: D 27 SER cc_start: 0.8452 (t) cc_final: 0.8196 (p) REVERT: D 91 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7169 (mpp80) REVERT: D 133 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7184 (mm-40) REVERT: F 41 ARG cc_start: 0.8963 (ttm110) cc_final: 0.8638 (ttm-80) REVERT: F 107 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8368 (mp) REVERT: F 128 LYS cc_start: 0.8179 (mptt) cc_final: 0.7701 (mmmm) REVERT: F 175 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7639 (mmpt) REVERT: F 203 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7594 (t0) REVERT: F 248 GLU cc_start: 0.8423 (mp0) cc_final: 0.8158 (mp0) REVERT: F 249 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: F 255 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: F 303 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7601 (ttt180) REVERT: F 336 GLU cc_start: 0.5758 (mm-30) cc_final: 0.5393 (mm-30) REVERT: F 435 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6984 (mtt-85) REVERT: F 446 ARG cc_start: 0.6711 (mtt180) cc_final: 0.5911 (mmp-170) REVERT: G 29 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8646 (mp-120) REVERT: G 49 SER cc_start: 0.8698 (p) cc_final: 0.8198 (m) REVERT: G 98 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6330 (mtt180) REVERT: I 83 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8150 (ptm160) REVERT: I 249 GLU cc_start: 0.8537 (tp30) cc_final: 0.8259 (tp30) REVERT: I 302 ASP cc_start: 0.8397 (p0) cc_final: 0.8155 (p0) REVERT: I 355 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7424 (tm-30) REVERT: I 449 CYS cc_start: 0.6005 (t) cc_final: 0.5322 (m) REVERT: J 16 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8756 (p) REVERT: J 88 GLN cc_start: 0.7819 (tp40) cc_final: 0.7236 (tp-100) REVERT: L 175 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7951 (mttp) REVERT: L 255 GLU cc_start: 0.8802 (tp30) cc_final: 0.8399 (tt0) REVERT: L 383 HIS cc_start: 0.7040 (m-70) cc_final: 0.6342 (m-70) REVERT: L 386 HIS cc_start: 0.6794 (m-70) cc_final: 0.6483 (m-70) REVERT: L 413 ASN cc_start: 0.6711 (m-40) cc_final: 0.6254 (m-40) REVERT: M 60 MET cc_start: 0.8935 (mtp) cc_final: 0.8644 (mtt) REVERT: M 90 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7732 (mt) REVERT: O 22 LEU cc_start: 0.8006 (mm) cc_final: 0.7598 (mt) REVERT: O 128 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7486 (mmtp) REVERT: O 203 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7935 (t70) REVERT: O 340 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7432 (mt-10) REVERT: Q 51 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: Q 66 LEU cc_start: 0.8766 (mt) cc_final: 0.8405 (mp) REVERT: Q 90 LEU cc_start: 0.7991 (tp) cc_final: 0.7603 (tm) REVERT: Q 111 ASP cc_start: 0.8477 (t0) cc_final: 0.8238 (t0) REVERT: Q 113 VAL cc_start: 0.8234 (m) cc_final: 0.7867 (p) REVERT: S 22 LEU cc_start: 0.8089 (mm) cc_final: 0.7775 (mt) REVERT: S 41 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8520 (ttm-80) REVERT: T 66 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7875 (mp) REVERT: T 113 VAL cc_start: 0.8249 (m) cc_final: 0.7948 (p) REVERT: T 130 ARG cc_start: 0.5576 (mmp-170) cc_final: 0.5067 (mmm160) REVERT: W 128 LYS cc_start: 0.8236 (mmtm) cc_final: 0.8004 (mptt) REVERT: W 358 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7624 (ttm-80) REVERT: W 440 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5516 (mp0) outliers start: 94 outliers final: 36 residues processed: 586 average time/residue: 1.8124 time to fit residues: 1250.5549 Evaluate side-chains 567 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 513 time to evaluate : 3.711 ------------------------------------------------------------------------------- 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 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 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 107 LEU 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 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 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 L residue 300 VAL 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 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 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 0 optimal weight: 40.0000 chunk 322 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 417 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 389 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 401 GLN G 94 GLN M 94 GLN O 383 HIS Q 133 GLN S 207 ASN S 383 HIS S 413 ASN T 29 GLN T 115 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 GLN X 133 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.095468 restraints weight = 41316.519| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.71 r_work: 0.2833 rms_B_bonded: 2.23 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: 0.8434 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35681 Z= 0.162 Angle : 0.522 5.693 48403 Z= 0.282 Chirality : 0.043 0.171 5136 Planarity : 0.004 0.041 6378 Dihedral : 4.484 21.216 4936 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.38 % Allowed : 16.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 4374 helix: 2.27 (0.12), residues: 1668 sheet: -0.64 (0.18), residues: 760 loop : -0.31 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 385 HIS 0.004 0.001 HIS S 238 PHE 0.025 0.002 PHE S 345 TYR 0.015 0.002 TYR A 269 ARG 0.007 0.000 ARG G 114 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1537) hydrogen bonds : angle 5.10035 ( 4371) covalent geometry : bond 0.00375 (35681) covalent geometry : angle 0.52228 (48403) *********************** 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 607 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 521 time to evaluate : 3.826 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8375 (m-30) cc_final: 0.8099 (m-30) REVERT: A 302 ASP cc_start: 0.8373 (p0) cc_final: 0.8015 (p0) REVERT: A 355 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: P 75 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8593 (ttm) REVERT: P 88 GLN cc_start: 0.7398 (tp40) cc_final: 0.6904 (tp40) REVERT: P 90 LEU cc_start: 0.8345 (tp) cc_final: 0.8143 (tm) REVERT: P 102 ASP cc_start: 0.8077 (m-30) cc_final: 0.7830 (m-30) REVERT: P 133 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7644 (mm-40) REVERT: C 175 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7222 (mtmt) REVERT: C 387 MET cc_start: 0.8125 (tpp) cc_final: 0.7901 (ttm) REVERT: D 27 SER cc_start: 0.8457 (t) cc_final: 0.8167 (p) REVERT: D 91 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7330 (mpp80) REVERT: D 133 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7190 (mm-40) REVERT: F 41 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8633 (ttm-80) REVERT: F 128 LYS cc_start: 0.8210 (mptt) cc_final: 0.7729 (mmmm) REVERT: F 175 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7528 (mmpt) REVERT: F 203 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7710 (t0) REVERT: F 248 GLU cc_start: 0.8371 (mp0) cc_final: 0.8145 (mp0) REVERT: F 249 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: F 255 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: F 303 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7596 (ttt180) REVERT: F 336 GLU cc_start: 0.5580 (mm-30) cc_final: 0.5159 (mm-30) REVERT: F 435 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6980 (mtt-85) REVERT: F 446 ARG cc_start: 0.6772 (mtt180) cc_final: 0.5928 (mmm160) REVERT: G 49 SER cc_start: 0.8708 (p) cc_final: 0.8192 (m) REVERT: G 98 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6496 (mtt180) REVERT: G 114 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7783 (mtm180) REVERT: I 83 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8165 (ptm160) REVERT: I 249 GLU cc_start: 0.8500 (tp30) cc_final: 0.8281 (tp30) REVERT: I 302 ASP cc_start: 0.8371 (p0) cc_final: 0.8147 (p0) REVERT: I 305 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7712 (ptm160) REVERT: I 331 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7140 (t) REVERT: I 360 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7767 (mtm180) REVERT: I 449 CYS cc_start: 0.5781 (t) cc_final: 0.5406 (m) REVERT: J 16 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8784 (p) REVERT: J 21 MET cc_start: 0.8565 (mtp) cc_final: 0.8041 (ttp) REVERT: J 88 GLN cc_start: 0.7798 (tp40) cc_final: 0.7236 (tp-100) REVERT: L 175 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7855 (mmtp) REVERT: L 255 GLU cc_start: 0.8781 (tp30) cc_final: 0.8402 (tt0) REVERT: L 383 HIS cc_start: 0.7045 (m-70) cc_final: 0.6361 (m-70) REVERT: L 386 HIS cc_start: 0.6776 (m-70) cc_final: 0.6553 (m-70) REVERT: M 60 MET cc_start: 0.8922 (mtp) cc_final: 0.8615 (mtt) REVERT: O 22 LEU cc_start: 0.7909 (mm) cc_final: 0.7493 (mt) REVERT: O 128 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7495 (mmtp) REVERT: O 203 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (t70) REVERT: O 340 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7411 (mt-10) REVERT: Q 51 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: Q 66 LEU cc_start: 0.8740 (mt) cc_final: 0.8381 (mp) REVERT: Q 90 LEU cc_start: 0.8065 (tp) cc_final: 0.7694 (tm) REVERT: Q 111 ASP cc_start: 0.8461 (t0) cc_final: 0.8225 (t0) REVERT: Q 113 VAL cc_start: 0.8367 (m) cc_final: 0.7973 (p) REVERT: S 22 LEU cc_start: 0.8121 (mm) cc_final: 0.7793 (mt) REVERT: S 41 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8524 (ttm-80) REVERT: T 66 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7856 (mp) REVERT: T 113 VAL cc_start: 0.8301 (m) cc_final: 0.8060 (p) REVERT: T 130 ARG cc_start: 0.5670 (mmp-170) cc_final: 0.5124 (mmm160) REVERT: W 128 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7594 (mppt) REVERT: W 130 LEU cc_start: 0.8322 (mt) cc_final: 0.8117 (mt) REVERT: W 303 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7352 (ttt180) REVERT: W 440 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5555 (mp0) REVERT: X 66 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8076 (mp) outliers start: 86 outliers final: 36 residues processed: 569 average time/residue: 1.7661 time to fit residues: 1179.5304 Evaluate side-chains 564 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 510 time to evaluate : 3.879 ------------------------------------------------------------------------------- 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 75 MET 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 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 175 LYS Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain M residue 35 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 293 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 233 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 271 optimal weight: 20.0000 chunk 399 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 301 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 94 GLN G 29 GLN G 88 GLN G 94 GLN M 94 GLN O 383 HIS Q 133 GLN S 207 ASN S 294 HIS S 413 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 GLN X 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.094289 restraints weight = 41365.944| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.73 r_work: 0.2806 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35681 Z= 0.253 Angle : 0.606 6.973 48403 Z= 0.325 Chirality : 0.047 0.193 5136 Planarity : 0.005 0.053 6378 Dihedral : 4.755 20.955 4936 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 15.75 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.12), residues: 4374 helix: 1.96 (0.12), residues: 1660 sheet: -0.63 (0.18), residues: 768 loop : -0.41 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 385 HIS 0.006 0.001 HIS L 386 PHE 0.027 0.003 PHE S 345 TYR 0.018 0.002 TYR A 269 ARG 0.008 0.001 ARG C 435 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 1537) hydrogen bonds : angle 5.28773 ( 4371) covalent geometry : bond 0.00595 (35681) covalent geometry : angle 0.60645 (48403) *********************** 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 621 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 518 time to evaluate : 3.693 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8368 (m-30) cc_final: 0.8120 (m-30) REVERT: A 355 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: A 443 ASP cc_start: 0.5939 (m-30) cc_final: 0.5579 (t0) REVERT: P 88 GLN cc_start: 0.7324 (tp40) cc_final: 0.6899 (tp40) REVERT: P 94 GLN cc_start: 0.8095 (mt0) cc_final: 0.7867 (mt0) REVERT: C 175 LYS cc_start: 0.7584 (mtmt) cc_final: 0.7288 (mtmt) REVERT: C 339 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6880 (ttp80) REVERT: D 27 SER cc_start: 0.8497 (t) cc_final: 0.8182 (p) REVERT: D 91 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7347 (mpp80) REVERT: D 133 GLN cc_start: 0.7527 (mm-40) cc_final: 0.6956 (mm110) REVERT: F 128 LYS cc_start: 0.8191 (mptt) cc_final: 0.7717 (mmmm) REVERT: F 175 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7554 (mmtp) REVERT: F 203 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7677 (t0) REVERT: F 248 GLU cc_start: 0.8395 (mp0) cc_final: 0.8156 (mp0) REVERT: F 249 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: F 255 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: F 303 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7637 (ttt180) REVERT: F 336 GLU cc_start: 0.5429 (mm-30) cc_final: 0.5105 (mm-30) REVERT: F 435 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7102 (mtt-85) REVERT: F 446 ARG cc_start: 0.6849 (mtt180) cc_final: 0.5976 (mmm160) REVERT: G 29 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8632 (mp-120) REVERT: G 49 SER cc_start: 0.8713 (p) cc_final: 0.8145 (m) REVERT: G 98 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6427 (mtt180) REVERT: I 83 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8247 (ptm160) REVERT: I 249 GLU cc_start: 0.8578 (tp30) cc_final: 0.8295 (tp30) REVERT: I 302 ASP cc_start: 0.8448 (p0) cc_final: 0.8168 (p0) REVERT: I 305 ARG cc_start: 0.7995 (ptm-80) cc_final: 0.7726 (ptm160) REVERT: I 331 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.7153 (t) REVERT: J 16 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8775 (p) REVERT: J 21 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8144 (ttp) REVERT: J 88 GLN cc_start: 0.7693 (tp40) cc_final: 0.7211 (tp-100) REVERT: L 175 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7847 (mttp) REVERT: L 255 GLU cc_start: 0.8780 (tp30) cc_final: 0.8384 (tt0) REVERT: L 383 HIS cc_start: 0.7091 (m-70) cc_final: 0.6385 (m-70) REVERT: L 386 HIS cc_start: 0.6799 (m-70) cc_final: 0.6556 (m-70) REVERT: L 390 LEU cc_start: 0.8802 (mt) cc_final: 0.8598 (tp) REVERT: L 413 ASN cc_start: 0.6673 (m-40) cc_final: 0.6259 (m-40) REVERT: M 60 MET cc_start: 0.8978 (mtp) cc_final: 0.8600 (mtt) REVERT: O 128 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7532 (mmtp) REVERT: O 203 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7888 (t70) REVERT: O 340 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7434 (mt-10) REVERT: O 384 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8184 (p) REVERT: Q 51 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: Q 90 LEU cc_start: 0.8068 (tp) cc_final: 0.7701 (tm) REVERT: Q 113 VAL cc_start: 0.8426 (m) cc_final: 0.8008 (t) REVERT: S 22 LEU cc_start: 0.8109 (mm) cc_final: 0.7749 (mt) REVERT: S 95 ASN cc_start: 0.5468 (t0) cc_final: 0.4795 (t0) REVERT: T 55 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: T 66 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7965 (mp) REVERT: T 113 VAL cc_start: 0.8237 (m) cc_final: 0.7993 (p) REVERT: T 130 ARG cc_start: 0.5687 (mmp-170) cc_final: 0.5104 (mmm160) REVERT: W 128 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7567 (mppt) REVERT: W 303 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7435 (ttt180) REVERT: W 358 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7703 (ttm-80) REVERT: W 440 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: X 26 ILE cc_start: 0.9002 (mt) cc_final: 0.8726 (mt) outliers start: 103 outliers final: 46 residues processed: 578 average time/residue: 1.7695 time to fit residues: 1200.9008 Evaluate side-chains 575 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 509 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 D residue 129 VAL 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 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 384 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 52 THR 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 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 O residue 28 ASP 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 O residue 384 VAL 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 42 MET Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 55 GLU 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 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 Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 227 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 312 optimal weight: 0.3980 chunk 390 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 133 GLN G 88 GLN G 94 GLN M 94 GLN O 383 HIS Q 133 GLN S 207 ASN S 413 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.094751 restraints weight = 41503.848| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.71 r_work: 0.2819 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2341 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= 0.172 Angle : 0.540 6.855 48403 Z= 0.291 Chirality : 0.044 0.169 5136 Planarity : 0.005 0.042 6378 Dihedral : 4.604 20.083 4936 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.38 % Allowed : 16.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.12), residues: 4374 helix: 2.17 (0.12), residues: 1660 sheet: -0.59 (0.18), residues: 768 loop : -0.37 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 385 HIS 0.005 0.001 HIS L 386 PHE 0.026 0.002 PHE W 345 TYR 0.015 0.002 TYR O 29 ARG 0.008 0.001 ARG G 114 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 1537) hydrogen bonds : angle 5.14359 ( 4371) covalent geometry : bond 0.00400 (35681) covalent geometry : angle 0.53955 (48403) *********************** 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 609 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 523 time to evaluate : 3.674 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8352 (m-30) cc_final: 0.8093 (m-30) REVERT: A 355 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: A 443 ASP cc_start: 0.5908 (m-30) cc_final: 0.5544 (t0) REVERT: P 88 GLN cc_start: 0.7343 (tp40) cc_final: 0.6918 (tp40) REVERT: P 94 GLN cc_start: 0.8221 (mt0) cc_final: 0.7991 (mt0) REVERT: P 133 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7682 (mm-40) REVERT: C 175 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7243 (mtmt) REVERT: C 339 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6968 (ttp80) REVERT: D 27 SER cc_start: 0.8474 (t) cc_final: 0.8204 (p) REVERT: D 91 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7323 (mpp80) REVERT: D 133 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7148 (mm-40) REVERT: F 128 LYS cc_start: 0.8183 (mptt) cc_final: 0.7717 (mmmm) REVERT: F 175 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7481 (mmtp) REVERT: F 203 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7717 (t0) REVERT: F 248 GLU cc_start: 0.8378 (mp0) cc_final: 0.8154 (mp0) REVERT: F 249 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: F 255 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: F 303 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7565 (ttt180) REVERT: F 435 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7141 (mtt-85) REVERT: F 446 ARG cc_start: 0.6839 (mtt180) cc_final: 0.5965 (mmm160) REVERT: G 29 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8638 (mp-120) REVERT: G 49 SER cc_start: 0.8717 (p) cc_final: 0.8125 (m) REVERT: G 92 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 98 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6428 (mtt180) REVERT: I 83 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8201 (ptm160) REVERT: I 249 GLU cc_start: 0.8510 (tp30) cc_final: 0.8273 (tp30) REVERT: I 302 ASP cc_start: 0.8429 (p0) cc_final: 0.8170 (p0) REVERT: I 305 ARG cc_start: 0.8012 (ptm-80) cc_final: 0.7761 (ptm160) REVERT: I 331 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7149 (t) REVERT: I 355 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7562 (tm-30) REVERT: I 360 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7766 (mtm180) REVERT: J 21 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: J 88 GLN cc_start: 0.7837 (tp40) cc_final: 0.7329 (tp-100) REVERT: L 175 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7842 (mttp) REVERT: L 255 GLU cc_start: 0.8796 (tp30) cc_final: 0.8408 (tt0) REVERT: L 383 HIS cc_start: 0.7096 (m-70) cc_final: 0.6401 (m-70) REVERT: L 386 HIS cc_start: 0.6787 (m-70) cc_final: 0.6535 (m-70) REVERT: M 60 MET cc_start: 0.8953 (mtp) cc_final: 0.8592 (mtt) REVERT: O 128 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7559 (mmtp) REVERT: O 203 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7835 (t70) REVERT: O 340 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7436 (mt-10) REVERT: Q 51 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: Q 66 LEU cc_start: 0.8839 (mt) cc_final: 0.8584 (mp) REVERT: Q 90 LEU cc_start: 0.8061 (tp) cc_final: 0.7729 (tm) REVERT: Q 111 ASP cc_start: 0.8386 (t0) cc_final: 0.8128 (t0) REVERT: Q 113 VAL cc_start: 0.8381 (m) cc_final: 0.8046 (p) REVERT: Q 133 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7310 (mm-40) REVERT: S 22 LEU cc_start: 0.8111 (mm) cc_final: 0.7683 (mt) REVERT: S 95 ASN cc_start: 0.5517 (t0) cc_final: 0.4899 (t0) REVERT: T 66 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7900 (mp) REVERT: T 113 VAL cc_start: 0.8249 (m) cc_final: 0.8003 (p) REVERT: T 130 ARG cc_start: 0.5732 (mmp-170) cc_final: 0.5128 (mmm160) REVERT: W 128 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7533 (mppt) REVERT: W 303 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7330 (ttt180) REVERT: W 358 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7657 (ttm-80) REVERT: W 440 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: X 26 ILE cc_start: 0.8998 (mt) cc_final: 0.8717 (mt) REVERT: X 66 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8198 (mp) outliers start: 86 outliers final: 42 residues processed: 571 average time/residue: 1.7836 time to fit residues: 1197.3871 Evaluate side-chains 568 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 508 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 21 MET 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 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 M residue 35 SER Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 122 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 42 MET Chi-restraints excluded: chain S residue 271 THR 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 28 ASP Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 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 Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 239 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 408 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 278 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN F 96 GLN G 94 GLN M 94 GLN O 383 HIS S 207 ASN S 413 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 GLN X 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095336 restraints weight = 41297.955| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.79 r_work: 0.2808 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35681 Z= 0.180 Angle : 0.549 6.912 48403 Z= 0.295 Chirality : 0.044 0.174 5136 Planarity : 0.005 0.044 6378 Dihedral : 4.601 20.098 4936 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.19 % Allowed : 16.41 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.12), residues: 4374 helix: 2.15 (0.12), residues: 1660 sheet: -0.60 (0.17), residues: 768 loop : -0.38 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 385 HIS 0.005 0.001 HIS L 386 PHE 0.026 0.002 PHE W 345 TYR 0.016 0.002 TYR A 269 ARG 0.009 0.001 ARG Q 28 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1537) hydrogen bonds : angle 5.14132 ( 4371) covalent geometry : bond 0.00421 (35681) covalent geometry : angle 0.54909 (48403) *********************** 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 595 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 516 time to evaluate : 4.011 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8348 (m-30) cc_final: 0.8091 (m-30) REVERT: A 355 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: A 443 ASP cc_start: 0.5896 (m-30) cc_final: 0.5547 (t0) REVERT: P 88 GLN cc_start: 0.7337 (tp40) cc_final: 0.6898 (tp40) REVERT: P 94 GLN cc_start: 0.8165 (mt0) cc_final: 0.7939 (mt0) REVERT: P 133 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7574 (mm-40) REVERT: C 127 PHE cc_start: 0.8225 (m-10) cc_final: 0.7848 (m-10) REVERT: C 339 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7077 (ttt90) REVERT: D 27 SER cc_start: 0.8488 (t) cc_final: 0.8206 (p) REVERT: D 91 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7379 (mpp80) REVERT: D 133 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7073 (mm-40) REVERT: F 26 THR cc_start: 0.8310 (m) cc_final: 0.7734 (p) REVERT: F 128 LYS cc_start: 0.8162 (mptt) cc_final: 0.7701 (mmmm) REVERT: F 175 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7544 (mmtp) REVERT: F 203 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7705 (t0) REVERT: F 248 GLU cc_start: 0.8383 (mp0) cc_final: 0.8161 (mp0) REVERT: F 249 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: F 255 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: F 303 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7581 (ttt180) REVERT: F 336 GLU cc_start: 0.5419 (mm-30) cc_final: 0.4998 (mm-30) REVERT: F 387 MET cc_start: 0.8503 (tpp) cc_final: 0.7874 (mtt) REVERT: F 435 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (mtt-85) REVERT: F 446 ARG cc_start: 0.6838 (mtt180) cc_final: 0.5946 (mmm160) REVERT: G 29 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8622 (mp-120) REVERT: G 49 SER cc_start: 0.8726 (p) cc_final: 0.8090 (m) REVERT: G 98 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6454 (mtt180) REVERT: G 114 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7814 (mtp180) REVERT: I 83 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8192 (ptm160) REVERT: I 249 GLU cc_start: 0.8526 (tp30) cc_final: 0.8287 (tp30) REVERT: I 302 ASP cc_start: 0.8433 (p0) cc_final: 0.8176 (p0) REVERT: I 305 ARG cc_start: 0.8046 (ptm-80) cc_final: 0.7822 (ptm160) REVERT: I 331 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7109 (t) REVERT: I 360 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7775 (mtm180) REVERT: I 392 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7683 (tm-30) REVERT: J 21 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: J 88 GLN cc_start: 0.7835 (tp40) cc_final: 0.7264 (tp-100) REVERT: L 175 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: L 255 GLU cc_start: 0.8804 (tp30) cc_final: 0.8410 (tt0) REVERT: L 383 HIS cc_start: 0.7106 (m-70) cc_final: 0.6385 (m-70) REVERT: L 386 HIS cc_start: 0.6747 (m-70) cc_final: 0.6508 (m-70) REVERT: L 390 LEU cc_start: 0.8795 (mt) cc_final: 0.8588 (tp) REVERT: M 60 MET cc_start: 0.8960 (mtp) cc_final: 0.8595 (mtt) REVERT: O 30 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8315 (mm-40) REVERT: O 128 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7668 (mmtp) REVERT: O 203 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7810 (t70) REVERT: O 340 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7521 (mt-10) REVERT: Q 49 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8643 (m) REVERT: Q 51 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: Q 90 LEU cc_start: 0.8040 (tp) cc_final: 0.7605 (tm) REVERT: Q 94 GLN cc_start: 0.7483 (mp10) cc_final: 0.6877 (mp10) REVERT: Q 111 ASP cc_start: 0.8414 (t0) cc_final: 0.8190 (t0) REVERT: Q 113 VAL cc_start: 0.8484 (m) cc_final: 0.8169 (t) REVERT: S 22 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7663 (mt) REVERT: S 95 ASN cc_start: 0.5524 (t0) cc_final: 0.4928 (t0) REVERT: S 358 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7852 (mmm-85) REVERT: S 413 ASN cc_start: 0.7072 (m-40) cc_final: 0.6305 (m-40) REVERT: T 66 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7898 (mp) REVERT: T 113 VAL cc_start: 0.8243 (m) cc_final: 0.8003 (p) REVERT: T 130 ARG cc_start: 0.5596 (mmp-170) cc_final: 0.4984 (mmm160) REVERT: W 128 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7587 (mppt) REVERT: W 303 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7342 (ttt180) REVERT: W 358 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7669 (ttm-80) REVERT: X 26 ILE cc_start: 0.8982 (mt) cc_final: 0.8720 (mt) outliers start: 79 outliers final: 43 residues processed: 559 average time/residue: 1.8248 time to fit residues: 1198.1197 Evaluate side-chains 571 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 510 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 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 21 MET Chi-restraints excluded: chain J residue 35 SER 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 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 M residue 35 SER Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ASP Chi-restraints excluded: chain O residue 384 VAL 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 22 LEU 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 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 Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 47 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 324 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 264 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN G 94 GLN M 94 GLN O 383 HIS Q 133 GLN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.095656 restraints weight = 41370.537| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.72 r_work: 0.2831 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2419 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= 0.138 Angle : 0.520 9.155 48403 Z= 0.280 Chirality : 0.043 0.166 5136 Planarity : 0.004 0.052 6378 Dihedral : 4.484 19.583 4936 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.94 % Allowed : 16.88 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4374 helix: 2.28 (0.12), residues: 1668 sheet: -0.61 (0.18), residues: 760 loop : -0.31 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 385 HIS 0.004 0.001 HIS L 386 PHE 0.026 0.002 PHE W 345 TYR 0.015 0.001 TYR O 29 ARG 0.011 0.000 ARG Q 28 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1537) hydrogen bonds : angle 5.04283 ( 4371) covalent geometry : bond 0.00317 (35681) covalent geometry : angle 0.51993 (48403) *********************** 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 587 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 517 time to evaluate : 3.936 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8334 (m-30) cc_final: 0.8077 (m-30) REVERT: A 355 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 443 ASP cc_start: 0.5866 (m-30) cc_final: 0.5512 (t0) REVERT: P 88 GLN cc_start: 0.7310 (tp40) cc_final: 0.6788 (tp40) REVERT: P 94 GLN cc_start: 0.8224 (mt0) cc_final: 0.8003 (mt0) REVERT: P 133 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7601 (mm-40) REVERT: C 127 PHE cc_start: 0.8226 (m-10) cc_final: 0.7838 (m-10) REVERT: C 175 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7401 (mtmt) REVERT: C 339 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7103 (ttt90) REVERT: D 27 SER cc_start: 0.8484 (t) cc_final: 0.8205 (p) REVERT: D 91 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7384 (mpp80) REVERT: D 133 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6972 (mm-40) REVERT: F 26 THR cc_start: 0.8373 (m) cc_final: 0.7825 (p) REVERT: F 128 LYS cc_start: 0.8157 (mptt) cc_final: 0.7686 (mmmm) REVERT: F 203 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7698 (t0) REVERT: F 248 GLU cc_start: 0.8355 (mp0) cc_final: 0.8136 (mp0) REVERT: F 249 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: F 255 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: F 303 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7606 (ttt180) REVERT: F 387 MET cc_start: 0.8502 (tpp) cc_final: 0.7859 (mtt) REVERT: F 446 ARG cc_start: 0.6835 (mtt180) cc_final: 0.5947 (mmm160) REVERT: G 29 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8625 (mp-120) REVERT: G 98 ARG cc_start: 0.7105 (mtm110) cc_final: 0.6453 (mtt180) REVERT: G 114 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7819 (mtp180) REVERT: G 132 TYR cc_start: 0.7646 (p90) cc_final: 0.7306 (p90) REVERT: I 83 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8174 (ptm160) REVERT: I 249 GLU cc_start: 0.8517 (tp30) cc_final: 0.8295 (tp30) REVERT: I 302 ASP cc_start: 0.8394 (p0) cc_final: 0.8157 (p0) REVERT: I 305 ARG cc_start: 0.8040 (ptm-80) cc_final: 0.7811 (ptm160) REVERT: I 331 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7012 (t) REVERT: I 355 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7562 (tm-30) REVERT: I 360 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7767 (mtm180) REVERT: I 392 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7679 (tm-30) REVERT: J 21 MET cc_start: 0.8687 (mtp) cc_final: 0.8158 (ttp) REVERT: J 88 GLN cc_start: 0.7827 (tp40) cc_final: 0.7264 (tp-100) REVERT: L 22 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6752 (mp) REVERT: L 175 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7903 (mttp) REVERT: L 255 GLU cc_start: 0.8779 (tp30) cc_final: 0.8415 (tt0) REVERT: L 383 HIS cc_start: 0.7121 (m-70) cc_final: 0.6386 (m-70) REVERT: L 386 HIS cc_start: 0.6771 (m-70) cc_final: 0.6509 (m-70) REVERT: L 390 LEU cc_start: 0.8769 (mt) cc_final: 0.8553 (tp) REVERT: M 90 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7731 (mt) REVERT: O 30 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8311 (mm-40) REVERT: O 128 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7685 (mmtp) REVERT: O 203 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7854 (t70) REVERT: O 340 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7509 (mt-10) REVERT: Q 49 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8647 (m) REVERT: Q 51 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: Q 66 LEU cc_start: 0.8830 (mt) cc_final: 0.8583 (mp) REVERT: Q 90 LEU cc_start: 0.8091 (tp) cc_final: 0.7693 (tm) REVERT: Q 113 VAL cc_start: 0.8440 (m) cc_final: 0.8133 (t) REVERT: Q 133 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7265 (mm-40) REVERT: S 22 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7665 (mt) REVERT: S 303 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8226 (tmt170) REVERT: S 358 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7673 (mmm-85) REVERT: S 413 ASN cc_start: 0.7058 (m-40) cc_final: 0.6348 (m-40) REVERT: T 66 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7857 (mp) REVERT: T 113 VAL cc_start: 0.8248 (m) cc_final: 0.8017 (p) REVERT: T 130 ARG cc_start: 0.5582 (mmp-170) cc_final: 0.4972 (mmm160) REVERT: W 128 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7602 (mppt) REVERT: W 303 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7291 (ttt180) REVERT: W 358 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7676 (ttm-80) REVERT: X 66 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8018 (mp) outliers start: 70 outliers final: 39 residues processed: 556 average time/residue: 1.7589 time to fit residues: 1146.4699 Evaluate side-chains 567 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 508 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 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 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 51 TYR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain O residue 28 ASP 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 22 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 ARG 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 28 ASP Chi-restraints excluded: chain W residue 271 THR Chi-restraints excluded: chain W residue 303 ARG 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 Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 400 optimal weight: 2.9990 chunk 372 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 263 optimal weight: 0.0060 chunk 155 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- 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 94 GLN M 94 GLN O 383 HIS S 207 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3435 r_free = 0.3435 target = 0.129907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095330 restraints weight = 41302.126| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.70 r_work: 0.2823 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2440 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= 0.157 Angle : 0.533 5.312 48403 Z= 0.287 Chirality : 0.043 0.169 5136 Planarity : 0.005 0.052 6378 Dihedral : 4.496 19.553 4936 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.83 % Allowed : 17.16 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 4374 helix: 2.25 (0.12), residues: 1668 sheet: -0.62 (0.18), residues: 760 loop : -0.31 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP I 385 HIS 0.004 0.001 HIS L 386 PHE 0.027 0.002 PHE W 345 TYR 0.015 0.001 TYR O 29 ARG 0.011 0.001 ARG Q 28 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1537) hydrogen bonds : angle 5.05773 ( 4371) covalent geometry : bond 0.00364 (35681) covalent geometry : angle 0.53309 (48403) ********************** 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 579 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 513 time to evaluate : 3.877 Fit side-chains TARDY: cannot create tardy model for: "VAL I 57 " (corrupted residue). Skipping it. REVERT: A 106 ASP cc_start: 0.8322 (m-30) cc_final: 0.8065 (m-30) REVERT: A 340 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7553 (mp0) REVERT: A 355 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: A 443 ASP cc_start: 0.5868 (m-30) cc_final: 0.5517 (t0) REVERT: P 88 GLN cc_start: 0.7268 (tp40) cc_final: 0.6798 (tp40) REVERT: P 94 GLN cc_start: 0.8220 (mt0) cc_final: 0.7998 (mt0) REVERT: P 133 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7609 (mm-40) REVERT: C 339 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7103 (ttt90) REVERT: D 27 SER cc_start: 0.8471 (t) cc_final: 0.8205 (p) REVERT: D 91 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7369 (mpp80) REVERT: D 133 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7095 (mm-40) REVERT: F 26 THR cc_start: 0.8368 (m) cc_final: 0.7808 (p) REVERT: F 128 LYS cc_start: 0.8142 (mptt) cc_final: 0.7678 (mmmm) REVERT: F 203 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7699 (t0) REVERT: F 248 GLU cc_start: 0.8376 (mp0) cc_final: 0.8157 (mp0) REVERT: F 249 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: F 255 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: F 303 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7567 (ttt180) REVERT: F 446 ARG cc_start: 0.6845 (mtt180) cc_final: 0.5953 (mmm160) REVERT: G 29 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8623 (mp-120) REVERT: G 98 ARG cc_start: 0.7111 (mtm110) cc_final: 0.6461 (mtt180) REVERT: G 132 TYR cc_start: 0.7647 (p90) cc_final: 0.7307 (p90) REVERT: I 83 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8194 (ptm160) REVERT: I 249 GLU cc_start: 0.8500 (tp30) cc_final: 0.8275 (tp30) REVERT: I 302 ASP cc_start: 0.8397 (p0) cc_final: 0.8161 (p0) REVERT: I 305 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7806 (ptm160) REVERT: I 331 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.6989 (t) REVERT: I 355 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7557 (tm-30) REVERT: I 360 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7700 (mtm180) REVERT: I 392 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7684 (tm-30) REVERT: J 21 MET cc_start: 0.8629 (mtp) cc_final: 0.8070 (ttp) REVERT: J 88 GLN cc_start: 0.7831 (tp40) cc_final: 0.7275 (tp-100) REVERT: L 22 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6757 (mp) REVERT: L 175 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7837 (mmtp) REVERT: L 255 GLU cc_start: 0.8784 (tp30) cc_final: 0.8418 (tt0) REVERT: L 383 HIS cc_start: 0.7082 (m-70) cc_final: 0.6286 (m-70) REVERT: L 386 HIS cc_start: 0.6702 (m-70) cc_final: 0.6432 (m-70) REVERT: L 390 LEU cc_start: 0.8759 (mt) cc_final: 0.8554 (tp) REVERT: O 30 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8298 (mm-40) REVERT: O 128 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7694 (mmtp) REVERT: O 203 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7851 (t70) REVERT: O 340 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7511 (mt-10) REVERT: Q 49 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8656 (m) REVERT: Q 51 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: Q 66 LEU cc_start: 0.8823 (mt) cc_final: 0.8575 (mp) REVERT: Q 90 LEU cc_start: 0.8053 (tp) cc_final: 0.7748 (tm) REVERT: Q 113 VAL cc_start: 0.8400 (m) cc_final: 0.8140 (p) REVERT: S 22 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7658 (mt) REVERT: S 303 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8222 (tmt170) REVERT: S 358 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7586 (mmm-85) REVERT: S 413 ASN cc_start: 0.6945 (m-40) cc_final: 0.6277 (m-40) REVERT: T 66 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7847 (mp) REVERT: T 113 VAL cc_start: 0.8226 (m) cc_final: 0.7985 (p) REVERT: T 130 ARG cc_start: 0.5594 (mmp-170) cc_final: 0.5011 (mmm160) REVERT: W 128 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7589 (mppt) REVERT: W 303 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7367 (ttt180) REVERT: W 358 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7670 (ttm-80) REVERT: X 26 ILE cc_start: 0.8977 (mt) cc_final: 0.8700 (mt) REVERT: X 66 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8032 (mp) outliers start: 66 outliers final: 41 residues processed: 547 average time/residue: 1.8047 time to fit residues: 1160.0734 Evaluate side-chains 568 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 508 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 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 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 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 384 VAL Chi-restraints excluded: chain I residue 387 MET 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 J residue 122 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 449 CYS Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain O residue 28 ASP 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 22 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 ARG 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 28 ASP 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 Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 194 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 425 optimal weight: 30.0000 chunk 263 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 382 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 94 GLN M 94 GLN O 383 HIS Q 133 GLN S 207 ASN T 29 GLN ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096358 restraints weight = 41406.300| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.72 r_work: 0.2845 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35681 Z= 0.124 Angle : 0.506 8.333 48403 Z= 0.272 Chirality : 0.042 0.166 5136 Planarity : 0.004 0.050 6378 Dihedral : 4.367 19.047 4936 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.66 % Allowed : 17.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 4374 helix: 2.38 (0.12), residues: 1676 sheet: -0.60 (0.18), residues: 760 loop : -0.26 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP I 385 HIS 0.003 0.001 HIS L 386 PHE 0.027 0.002 PHE W 345 TYR 0.012 0.001 TYR G 67 ARG 0.011 0.000 ARG Q 28 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1537) hydrogen bonds : angle 4.94423 ( 4371) covalent geometry : bond 0.00285 (35681) covalent geometry : angle 0.50647 (48403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29262.67 seconds wall clock time: 502 minutes 30.87 seconds (30150.87 seconds total)