Starting phenix.real_space_refine on Tue Dec 31 05:18:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmt_16125/12_2024/8bmt_16125.cif" } resolution = 2.5 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= 0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 294 5.16 5 C 39886 2.51 5 N 11130 2.21 5 O 14331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 65711 Number of models: 1 Model: "" Number of chains: 17 Chain: "AA" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "BA" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "BA" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "J" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "N" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "P" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "T" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "Z" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "BA" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Restraints were copied for chains: CA, B, D, F, H, K, M, O, Q, S, W, V, Y, A, C, E, G, I, J, L, N, P, R, T, X, Z Time building chain proxies: 13.68, per 1000 atoms: 0.21 Number of scatterers: 65711 At special positions: 0 Unit cell: (152.64, 151.68, 255.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 294 16.00 P 42 15.00 Mg 14 11.99 O 14331 8.00 N 11130 7.00 C 39886 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: 13.27 Conformation dependent library (CDL) restraints added in 6.8 seconds 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 322 helices and 112 sheets defined 52.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.55 Creating SS restraints... Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 297 Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 373 Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 373 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEU E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 297 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 373 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.686A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.891A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 Processing helix chain 'G' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEU G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 459 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'J' and resid 64 through 85 removed outlier: 4.165A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU J 259 " --> pdb=" O GLU J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 297 Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 373 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 426 Processing helix chain 'J' and resid 427 through 429 No H-bonds generated for 'chain 'J' and resid 427 through 429' Processing helix chain 'J' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 85 removed outlier: 4.165A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU L 259 " --> pdb=" O GLU L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 297 Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 373 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 427 through 429 No H-bonds generated for 'chain 'L' and resid 427 through 429' Processing helix chain 'L' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 459 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEU N 259 " --> pdb=" O GLU N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 297 Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 373 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 427 through 429 No H-bonds generated for 'chain 'N' and resid 427 through 429' Processing helix chain 'N' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 497 through 516 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.891A pdb=" N VAL P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 60 Processing helix chain 'P' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL P 77 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA P 78 " --> pdb=" O VAL P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 109 Processing helix chain 'P' and resid 112 through 135 Processing helix chain 'P' and resid 140 through 152 Processing helix chain 'P' and resid 155 through 170 Processing helix chain 'P' and resid 201 through 205 Processing helix chain 'P' and resid 233 through 244 Processing helix chain 'P' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU P 259 " --> pdb=" O GLU P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 297 Processing helix chain 'P' and resid 308 through 312 Processing helix chain 'P' and resid 338 through 356 Processing helix chain 'P' and resid 358 through 373 Processing helix chain 'P' and resid 385 through 410 Processing helix chain 'P' and resid 416 through 426 Processing helix chain 'P' and resid 427 through 429 No H-bonds generated for 'chain 'P' and resid 427 through 429' Processing helix chain 'P' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU P 448 " --> pdb=" O LEU P 444 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 459 Processing helix chain 'P' and resid 461 through 472 Processing helix chain 'P' and resid 488 through 492 Processing helix chain 'P' and resid 497 through 516 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'R' and resid 9 through 29 removed outlier: 3.893A pdb=" N VAL R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 Processing helix chain 'R' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 109 Processing helix chain 'R' and resid 112 through 135 Processing helix chain 'R' and resid 140 through 152 Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 233 through 244 Processing helix chain 'R' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEU R 259 " --> pdb=" O GLU R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 297 Processing helix chain 'R' and resid 308 through 312 Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'R' and resid 358 through 373 Processing helix chain 'R' and resid 385 through 410 Processing helix chain 'R' and resid 416 through 426 Processing helix chain 'R' and resid 427 through 429 No H-bonds generated for 'chain 'R' and resid 427 through 429' Processing helix chain 'R' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 459 Processing helix chain 'R' and resid 461 through 472 Processing helix chain 'R' and resid 488 through 492 Processing helix chain 'R' and resid 497 through 516 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'T' and resid 9 through 29 removed outlier: 3.893A pdb=" N VAL T 29 " --> pdb=" O ASP T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 60 Processing helix chain 'T' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 109 Processing helix chain 'T' and resid 112 through 135 Processing helix chain 'T' and resid 140 through 152 Processing helix chain 'T' and resid 155 through 170 Processing helix chain 'T' and resid 201 through 205 Processing helix chain 'T' and resid 233 through 244 Processing helix chain 'T' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEU T 259 " --> pdb=" O GLU T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 297 Processing helix chain 'T' and resid 308 through 312 Processing helix chain 'T' and resid 338 through 356 Processing helix chain 'T' and resid 358 through 373 Processing helix chain 'T' and resid 385 through 410 Processing helix chain 'T' and resid 416 through 426 Processing helix chain 'T' and resid 427 through 429 No H-bonds generated for 'chain 'T' and resid 427 through 429' Processing helix chain 'T' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLU T 448 " --> pdb=" O LEU T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'T' and resid 461 through 472 Processing helix chain 'T' and resid 488 through 492 Processing helix chain 'T' and resid 497 through 516 Processing helix chain 'V' and resid 28 through 32 Processing helix chain 'X' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL X 29 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 60 Processing helix chain 'X' and resid 64 through 85 removed outlier: 4.166A pdb=" N VAL X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA X 78 " --> pdb=" O VAL X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 109 Processing helix chain 'X' and resid 112 through 135 Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'X' and resid 155 through 170 Processing helix chain 'X' and resid 201 through 205 Processing helix chain 'X' and resid 233 through 244 Processing helix chain 'X' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU X 259 " --> pdb=" O GLU X 255 " (cutoff:3.500A) Processing helix chain 'X' and resid 284 through 297 Processing helix chain 'X' and resid 308 through 312 Processing helix chain 'X' and resid 338 through 356 Processing helix chain 'X' and resid 358 through 373 Processing helix chain 'X' and resid 385 through 410 Processing helix chain 'X' and resid 416 through 426 Processing helix chain 'X' and resid 427 through 429 No H-bonds generated for 'chain 'X' and resid 427 through 429' Processing helix chain 'X' and resid 433 through 448 removed outlier: 3.686A pdb=" N GLU X 448 " --> pdb=" O LEU X 444 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'X' and resid 461 through 472 Processing helix chain 'X' and resid 488 through 492 Processing helix chain 'X' and resid 497 through 516 Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Z' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL Z 29 " --> pdb=" O ASP Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 Processing helix chain 'Z' and resid 64 through 85 removed outlier: 4.165A pdb=" N VAL Z 77 " --> pdb=" O MET Z 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA Z 78 " --> pdb=" O VAL Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 109 Processing helix chain 'Z' and resid 112 through 135 Processing helix chain 'Z' and resid 140 through 152 Processing helix chain 'Z' and resid 155 through 170 Processing helix chain 'Z' and resid 201 through 205 Processing helix chain 'Z' and resid 233 through 244 Processing helix chain 'Z' and resid 255 through 269 removed outlier: 3.740A pdb=" N LEU Z 259 " --> pdb=" O GLU Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 284 through 297 Processing helix chain 'Z' and resid 308 through 312 Processing helix chain 'Z' and resid 338 through 356 Processing helix chain 'Z' and resid 358 through 373 Processing helix chain 'Z' and resid 385 through 410 Processing helix chain 'Z' and resid 416 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 433 through 448 removed outlier: 3.686A pdb=" N GLU Z 448 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 459 Processing helix chain 'Z' and resid 461 through 472 Processing helix chain 'Z' and resid 488 through 492 Processing helix chain 'Z' and resid 497 through 516 Processing helix chain 'AA' and resid 28 through 32 Processing helix chain 'BA' and resid 9 through 29 removed outlier: 3.892A pdb=" N VALBA 29 " --> pdb=" O ASPBA 25 " (cutoff:3.500A) Processing helix chain 'BA' and resid 52 through 60 Processing helix chain 'BA' and resid 64 through 85 removed outlier: 4.165A pdb=" N VALBA 77 " --> pdb=" O METBA 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALABA 78 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing helix chain 'BA' and resid 88 through 109 Processing helix chain 'BA' and resid 112 through 135 Processing helix chain 'BA' and resid 140 through 152 Processing helix chain 'BA' and resid 155 through 170 Processing helix chain 'BA' and resid 201 through 205 Processing helix chain 'BA' and resid 233 through 244 Processing helix chain 'BA' and resid 255 through 269 removed outlier: 3.739A pdb=" N LEUBA 259 " --> pdb=" O GLUBA 255 " (cutoff:3.500A) Processing helix chain 'BA' and resid 284 through 297 Processing helix chain 'BA' and resid 308 through 312 Processing helix chain 'BA' and resid 338 through 356 Processing helix chain 'BA' and resid 358 through 373 Processing helix chain 'BA' and resid 385 through 410 Processing helix chain 'BA' and resid 416 through 426 Processing helix chain 'BA' and resid 427 through 429 No H-bonds generated for 'chain 'BA' and resid 427 through 429' Processing helix chain 'BA' and resid 433 through 448 removed outlier: 3.685A pdb=" N GLUBA 448 " --> pdb=" O LEUBA 444 " (cutoff:3.500A) Processing helix chain 'BA' and resid 448 through 459 Processing helix chain 'BA' and resid 461 through 472 Processing helix chain 'BA' and resid 488 through 492 Processing helix chain 'BA' and resid 497 through 516 Processing helix chain 'CA' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 8 removed outlier: 7.367A pdb=" N VAL L 39 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET I 520 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.273A pdb=" N ASN I 37 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET A 520 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL I 39 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR A 522 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.521A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'W' and resid 3 through 5 removed outlier: 4.658A pdb=" N ARG W 4 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE B 94 " --> pdb=" O ARG W 4 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 64 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 11 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 9 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG W 9 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL W 43 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE W 11 " --> pdb=" O LEU W 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE W 94 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG M 4 " --> pdb=" O ILE W 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.263A pdb=" N ASN A 37 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET C 520 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 39 " --> pdb=" O MET C 520 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR C 522 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 213 through 216 removed outlier: 8.378A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB7, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.253A pdb=" N ASN C 37 " --> pdb=" O GLU E 518 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET E 520 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL C 39 " --> pdb=" O MET E 520 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 522 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC5, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 5 removed outlier: 4.633A pdb=" N ARG D 4 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE F 94 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE F 64 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE F 11 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL F 43 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG F 9 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG F 14 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU F 82 " --> pdb=" O ARG F 14 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 74 through 78 removed outlier: 7.968A pdb=" N GLU D 82 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG D 14 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG D 9 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL D 43 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 11 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AC9, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.260A pdb=" N ASN E 37 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N MET G 520 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 39 " --> pdb=" O MET G 520 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR G 522 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.413A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD5, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD6, first strand: chain 'F' and resid 3 through 5 removed outlier: 4.579A pdb=" N ARG F 4 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE H 94 " --> pdb=" O ARG F 4 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE H 64 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 11 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL H 43 " --> pdb=" O ARG H 9 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG H 9 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG H 14 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU H 82 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AD8, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.253A pdb=" N ASN G 37 " --> pdb=" O GLU J 518 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET J 520 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL G 39 " --> pdb=" O MET J 520 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR J 522 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE4, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AE5, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain 'J' and resid 48 through 50 removed outlier: 7.276A pdb=" N ASN J 37 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET L 520 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL J 39 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR L 522 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 174 through 179 removed outlier: 6.521A pdb=" N VAL J 174 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE J 379 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AF2, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AF3, first strand: chain 'K' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU K 82 " --> pdb=" O ARG K 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG K 14 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG K 9 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL K 43 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE K 11 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE K 64 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 47 through 48 Processing sheet with id=AF5, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 213 through 216 removed outlier: 8.376A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.415A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AF9, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AG1, first strand: chain 'M' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG M 9 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE M 11 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE M 64 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AG3, first strand: chain 'N' and resid 4 through 8 removed outlier: 7.360A pdb=" N VALBA 39 " --> pdb=" O GLU N 518 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET N 520 " --> pdb=" O VALBA 39 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 48 through 50 removed outlier: 7.275A pdb=" N ASN N 37 " --> pdb=" O GLU P 518 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N MET P 520 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL N 39 " --> pdb=" O MET P 520 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR P 522 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.521A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 213 through 216 removed outlier: 8.378A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AG9, first strand: chain 'N' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU O 82 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG O 14 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG O 9 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL O 43 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE O 11 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 47 through 48 Processing sheet with id=AH3, first strand: chain 'P' and resid 48 through 50 removed outlier: 7.275A pdb=" N ASN P 37 " --> pdb=" O GLU R 518 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N MET R 520 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL P 39 " --> pdb=" O MET R 520 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR R 522 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL P 174 " --> pdb=" O ALA P 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE P 379 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR P 176 " --> pdb=" O ILE P 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL P 381 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU P 178 " --> pdb=" O VAL P 381 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE P 301 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU P 222 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE P 219 " --> pdb=" O LEU P 248 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE P 250 " --> pdb=" O PHE P 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU P 221 " --> pdb=" O ILE P 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA P 320 " --> pdb=" O GLY P 335 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY P 335 " --> pdb=" O ALA P 320 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'P' and resid 476 through 479 Processing sheet with id=AH9, first strand: chain 'Q' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG Q 9 " --> pdb=" O VAL Q 43 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE Q 64 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AI2, first strand: chain 'R' and resid 48 through 50 removed outlier: 7.274A pdb=" N ASN R 37 " --> pdb=" O GLU T 518 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET T 520 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL R 39 " --> pdb=" O MET T 520 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR T 522 " --> pdb=" O VAL R 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 174 through 179 removed outlier: 6.521A pdb=" N VAL R 174 " --> pdb=" O ALA R 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE R 379 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR R 176 " --> pdb=" O ILE R 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL R 381 " --> pdb=" O THR R 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU R 178 " --> pdb=" O VAL R 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE R 301 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU R 222 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE R 219 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE R 250 " --> pdb=" O PHE R 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU R 221 " --> pdb=" O ILE R 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA R 320 " --> pdb=" O GLY R 335 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY R 335 " --> pdb=" O ALA R 320 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'R' and resid 476 through 479 Processing sheet with id=AI8, first strand: chain 'S' and resid 3 through 5 removed outlier: 4.574A pdb=" N ARG S 4 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE V 94 " --> pdb=" O ARG S 4 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE V 64 " --> pdb=" O VAL V 95 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE V 11 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL V 43 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG V 9 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG V 14 " --> pdb=" O GLU V 82 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU V 82 " --> pdb=" O ARG V 14 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'S' and resid 74 through 78 removed outlier: 7.968A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG S 9 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE S 11 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE S 64 " --> pdb=" O VAL S 95 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'S' and resid 47 through 48 Processing sheet with id=AJ2, first strand: chain 'T' and resid 48 through 50 removed outlier: 7.303A pdb=" N ASN T 37 " --> pdb=" O GLU X 518 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET X 520 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL T 39 " --> pdb=" O MET X 520 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR X 522 " --> pdb=" O VAL T 39 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'T' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL T 174 " --> pdb=" O ALA T 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE T 379 " --> pdb=" O VAL T 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR T 176 " --> pdb=" O ILE T 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL T 381 " --> pdb=" O THR T 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU T 178 " --> pdb=" O VAL T 381 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'T' and resid 213 through 216 removed outlier: 8.378A pdb=" N ILE T 301 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU T 222 " --> pdb=" O ILE T 301 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'T' and resid 273 through 277 removed outlier: 6.415A pdb=" N PHE T 219 " --> pdb=" O LEU T 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE T 250 " --> pdb=" O PHE T 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU T 221 " --> pdb=" O ILE T 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA T 320 " --> pdb=" O GLY T 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY T 335 " --> pdb=" O ALA T 320 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'T' and resid 411 through 413 Processing sheet with id=AJ7, first strand: chain 'T' and resid 476 through 479 Processing sheet with id=AJ8, first strand: chain 'V' and resid 47 through 48 Processing sheet with id=AJ9, first strand: chain 'X' and resid 48 through 50 removed outlier: 7.293A pdb=" N ASN X 37 " --> pdb=" O GLU Z 518 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET Z 520 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL X 39 " --> pdb=" O MET Z 520 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR Z 522 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'X' and resid 174 through 179 removed outlier: 6.520A pdb=" N VAL X 174 " --> pdb=" O ALA X 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE X 379 " --> pdb=" O VAL X 174 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR X 176 " --> pdb=" O ILE X 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL X 381 " --> pdb=" O THR X 176 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU X 178 " --> pdb=" O VAL X 381 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'X' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE X 301 " --> pdb=" O ILE X 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU X 222 " --> pdb=" O ILE X 301 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'X' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHE X 219 " --> pdb=" O LEU X 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE X 250 " --> pdb=" O PHE X 219 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU X 221 " --> pdb=" O ILE X 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA X 320 " --> pdb=" O GLY X 335 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY X 335 " --> pdb=" O ALA X 320 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'X' and resid 411 through 413 Processing sheet with id=AK5, first strand: chain 'X' and resid 476 through 479 Processing sheet with id=AK6, first strand: chain 'Y' and resid 3 through 5 removed outlier: 4.564A pdb=" N ARG Y 4 " --> pdb=" O ILEAA 94 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILEAA 94 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILEAA 64 " --> pdb=" O VALAA 95 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILEAA 11 " --> pdb=" O LEUAA 41 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VALAA 43 " --> pdb=" O ARGAA 9 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARGAA 9 " --> pdb=" O VALAA 43 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARGAA 14 " --> pdb=" O GLUAA 82 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLUAA 82 " --> pdb=" O ARGAA 14 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'Y' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU Y 82 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG Y 14 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG Y 9 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL Y 43 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE Y 11 " --> pdb=" O LEU Y 41 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE Y 64 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Y' and resid 47 through 48 Processing sheet with id=AK9, first strand: chain 'Z' and resid 48 through 50 removed outlier: 7.307A pdb=" N ASN Z 37 " --> pdb=" O GLUBA 518 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N METBA 520 " --> pdb=" O ASN Z 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL Z 39 " --> pdb=" O METBA 520 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THRBA 522 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Z' and resid 174 through 179 removed outlier: 6.521A pdb=" N VAL Z 174 " --> pdb=" O ALA Z 377 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE Z 379 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR Z 176 " --> pdb=" O ILE Z 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL Z 381 " --> pdb=" O THR Z 176 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU Z 178 " --> pdb=" O VAL Z 381 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Z' and resid 213 through 216 removed outlier: 8.377A pdb=" N ILE Z 301 " --> pdb=" O ILE Z 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU Z 222 " --> pdb=" O ILE Z 301 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Z' and resid 273 through 277 removed outlier: 6.413A pdb=" N PHE Z 219 " --> pdb=" O LEU Z 248 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE Z 250 " --> pdb=" O PHE Z 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU Z 221 " --> pdb=" O ILE Z 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA Z 320 " --> pdb=" O GLY Z 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY Z 335 " --> pdb=" O ALA Z 320 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'Z' and resid 411 through 413 Processing sheet with id=AL5, first strand: chain 'Z' and resid 476 through 479 Processing sheet with id=AL6, first strand: chain 'AA' and resid 47 through 48 Processing sheet with id=AL7, first strand: chain 'BA' and resid 174 through 179 removed outlier: 6.520A pdb=" N VALBA 174 " --> pdb=" O ALABA 377 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILEBA 379 " --> pdb=" O VALBA 174 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THRBA 176 " --> pdb=" O ILEBA 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VALBA 381 " --> pdb=" O THRBA 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLUBA 178 " --> pdb=" O VALBA 381 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'BA' and resid 213 through 216 removed outlier: 8.378A pdb=" N ILEBA 301 " --> pdb=" O ILEBA 220 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEUBA 222 " --> pdb=" O ILEBA 301 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'BA' and resid 273 through 277 removed outlier: 6.414A pdb=" N PHEBA 219 " --> pdb=" O LEUBA 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILEBA 250 " --> pdb=" O PHEBA 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEUBA 221 " --> pdb=" O ILEBA 250 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALABA 320 " --> pdb=" O GLYBA 335 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLYBA 335 " --> pdb=" O ALABA 320 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'BA' and resid 411 through 413 Processing sheet with id=AM2, first strand: chain 'BA' and resid 476 through 479 Processing sheet with id=AM3, first strand: chain 'CA' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLUCA 82 " --> pdb=" O ARGCA 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARGCA 14 " --> pdb=" O GLUCA 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARGCA 9 " --> pdb=" O VALCA 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VALCA 43 " --> pdb=" O ARGCA 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILECA 11 " --> pdb=" O LEUCA 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILECA 64 " --> pdb=" O VALCA 95 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'CA' and resid 47 through 48 4006 hydrogen bonds defined for protein. 11388 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: 34.05 Time building geometry restraints manager: 15.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22330 1.34 - 1.46: 10917 1.46 - 1.58: 30957 1.58 - 1.69: 70 1.69 - 1.81: 546 Bond restraints: 64820 Sorted by residual: bond pdb=" N ASN H 2 " pdb=" CA ASN H 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ASN M 2 " pdb=" CA ASN M 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASN D 2 " pdb=" CA ASN D 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASN V 2 " pdb=" CA ASN V 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASN O 2 " pdb=" CA ASN O 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 64815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 84883 1.42 - 2.85: 2032 2.85 - 4.27: 530 4.27 - 5.69: 84 5.69 - 7.11: 83 Bond angle restraints: 87612 Sorted by residual: angle pdb=" N MET J 267 " pdb=" CA MET J 267 " pdb=" CB MET J 267 " ideal model delta sigma weight residual 110.01 115.13 -5.12 1.45e+00 4.76e-01 1.25e+01 angle pdb=" N MET N 267 " pdb=" CA MET N 267 " pdb=" CB MET N 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N MET G 267 " pdb=" CA MET G 267 " pdb=" CB MET G 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N METBA 267 " pdb=" CA METBA 267 " pdb=" CB METBA 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N MET I 267 " pdb=" CA MET I 267 " pdb=" CB MET I 267 " ideal model delta sigma weight residual 110.01 115.11 -5.10 1.45e+00 4.76e-01 1.24e+01 ... (remaining 87607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 36076 17.84 - 35.69: 3222 35.69 - 53.53: 784 53.53 - 71.37: 280 71.37 - 89.21: 56 Dihedral angle restraints: 40418 sinusoidal: 15974 harmonic: 24444 Sorted by residual: dihedral pdb=" CB GLU N 172 " pdb=" CG GLU N 172 " pdb=" CD GLU N 172 " pdb=" OE1 GLU N 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 172 " pdb=" CG GLU E 172 " pdb=" CD GLU E 172 " pdb=" OE1 GLU E 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU L 172 " pdb=" CG GLU L 172 " pdb=" CD GLU L 172 " pdb=" OE1 GLU L 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 40415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 9097 0.060 - 0.120: 1325 0.120 - 0.179: 162 0.179 - 0.239: 14 0.239 - 0.299: 42 Chirality restraints: 10640 Sorted by residual: chirality pdb=" C3' ATP A 603 " pdb=" C2' ATP A 603 " pdb=" C4' ATP A 603 " pdb=" O3' ATP A 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP Z 603 " pdb=" C2' ATP Z 603 " pdb=" C4' ATP Z 603 " pdb=" O3' ATP Z 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' ATP C 603 " pdb=" C2' ATP C 603 " pdb=" C4' ATP C 603 " pdb=" O3' ATP C 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 10637 not shown) Planarity restraints: 11396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 44 " 0.018 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE A 44 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 44 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 44 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 44 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE A 44 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 44 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 44 " -0.018 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE X 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE X 44 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE X 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE X 44 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE X 44 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE X 44 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 44 " -0.018 2.00e-02 2.50e+03 1.54e-02 4.16e+00 pdb=" CG PHE L 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE L 44 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE L 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 44 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE L 44 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE L 44 " -0.001 2.00e-02 2.50e+03 ... (remaining 11393 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.57: 1017 2.57 - 3.21: 65618 3.21 - 3.85: 142565 3.85 - 4.50: 194435 4.50 - 5.14: 297808 Nonbonded interactions: 701443 Sorted by model distance: nonbonded pdb=" OD1 ASP G 121 " pdb=" O HOH G 701 " model vdw 1.922 3.040 nonbonded pdb=" O LYSBA 470 " pdb=" O HOHBA 701 " model vdw 1.990 3.040 nonbonded pdb=" O GLY Z 35 " pdb=" O HOH Z 701 " model vdw 1.995 3.040 nonbonded pdb=" OE2 GLU L 102 " pdb=" O HOH L 701 " model vdw 1.998 3.040 nonbonded pdb=" O GLY P 35 " pdb=" O HOH P 701 " model vdw 1.999 3.040 ... (remaining 701438 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 'BA' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'AA' selection = chain 'B' selection = chain 'CA' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'Y' } 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: 3.510 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: 0.050 Extract box with map and model: 2.060 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 110.100 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.490 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.003 0.085 64820 Z= 0.230 Angle : 0.624 7.115 87612 Z= 0.343 Chirality : 0.047 0.299 10640 Planarity : 0.004 0.053 11396 Dihedral : 15.402 89.214 24738 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.12 % Allowed : 17.43 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.09), residues: 8624 helix: 2.31 (0.08), residues: 4242 sheet: 0.11 (0.13), residues: 1218 loop : 0.31 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 7 PHE 0.022 0.003 PHE A 44 TYR 0.014 0.001 TYR L 203 ARG 0.004 0.001 ARG D 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 770 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 362 ARG cc_start: 0.6237 (ptp-110) cc_final: 0.5975 (ptp-110) REVERT: I 520 MET cc_start: 0.9160 (mtp) cc_final: 0.8958 (mtm) REVERT: W 90 ASP cc_start: 0.9523 (m-30) cc_final: 0.9265 (m-30) REVERT: A 193 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: B 90 ASP cc_start: 0.9492 (m-30) cc_final: 0.9199 (m-30) REVERT: C 193 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7985 (mmm) REVERT: C 195 PHE cc_start: 0.8726 (p90) cc_final: 0.8517 (p90) REVERT: C 362 ARG cc_start: 0.6342 (ptp-110) cc_final: 0.6101 (ptp-110) REVERT: D 11 ILE cc_start: 0.9172 (mm) cc_final: 0.8945 (mp) REVERT: D 90 ASP cc_start: 0.9504 (m-30) cc_final: 0.9229 (m-30) REVERT: E 362 ARG cc_start: 0.6198 (ptp-110) cc_final: 0.5941 (ptp-110) REVERT: E 514 MET cc_start: 0.9104 (mtp) cc_final: 0.8748 (mtp) REVERT: F 90 ASP cc_start: 0.9499 (m-30) cc_final: 0.9249 (m-30) REVERT: G 193 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: G 195 PHE cc_start: 0.8725 (p90) cc_final: 0.8510 (p90) REVERT: G 514 MET cc_start: 0.9087 (mtp) cc_final: 0.8516 (mtp) REVERT: H 90 ASP cc_start: 0.9499 (m-30) cc_final: 0.9245 (m-30) REVERT: J 195 PHE cc_start: 0.8709 (p90) cc_final: 0.8467 (p90) REVERT: J 362 ARG cc_start: 0.6168 (ptp-110) cc_final: 0.5956 (ptp-110) REVERT: J 514 MET cc_start: 0.9051 (mtp) cc_final: 0.8720 (mtp) REVERT: K 87 SER cc_start: 0.8982 (m) cc_final: 0.8771 (p) REVERT: K 90 ASP cc_start: 0.9525 (m-30) cc_final: 0.9237 (m-30) REVERT: L 195 PHE cc_start: 0.8743 (p90) cc_final: 0.8477 (p90) REVERT: L 322 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.7751 (tpt-90) REVERT: L 362 ARG cc_start: 0.6309 (ptp-110) cc_final: 0.6086 (ptp-110) REVERT: M 11 ILE cc_start: 0.9150 (mm) cc_final: 0.8912 (mp) REVERT: M 90 ASP cc_start: 0.9525 (m-30) cc_final: 0.9282 (m-30) REVERT: N 73 MET cc_start: 0.8804 (mtm) cc_final: 0.8347 (mtp) REVERT: N 195 PHE cc_start: 0.8631 (p90) cc_final: 0.8193 (p90) REVERT: P 195 PHE cc_start: 0.8662 (p90) cc_final: 0.8297 (p90) REVERT: R 69 MET cc_start: 0.9182 (mtp) cc_final: 0.8934 (mtm) REVERT: R 195 PHE cc_start: 0.8584 (p90) cc_final: 0.7920 (p90) REVERT: T 195 PHE cc_start: 0.8575 (p90) cc_final: 0.8191 (p90) REVERT: X 141 SER cc_start: 0.7982 (m) cc_final: 0.7508 (p) REVERT: X 195 PHE cc_start: 0.8685 (p90) cc_final: 0.8129 (p90) REVERT: Z 16 MET cc_start: 0.8884 (ttp) cc_final: 0.8682 (ttp) REVERT: Z 59 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8360 (mm-30) REVERT: Z 195 PHE cc_start: 0.8558 (p90) cc_final: 0.8226 (p90) REVERT: Z 219 PHE cc_start: 0.7374 (m-80) cc_final: 0.7138 (m-80) REVERT: BA 195 PHE cc_start: 0.8547 (p90) cc_final: 0.8213 (p90) outliers start: 75 outliers final: 23 residues processed: 813 average time/residue: 1.4351 time to fit residues: 1521.9731 Evaluate side-chains 661 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 635 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 4 ARG Chi-restraints excluded: chain J residue 473 ASP Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain L residue 473 ASP Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain O residue 4 ARG Chi-restraints excluded: chain Q residue 4 ARG Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 4 ARG Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain V residue 4 ARG Chi-restraints excluded: chain Y residue 4 ARG Chi-restraints excluded: chain AA residue 4 ARG Chi-restraints excluded: chain CA residue 4 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 3.9990 chunk 647 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 436 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 669 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 407 optimal weight: 1.9990 chunk 498 optimal weight: 0.9990 chunk 775 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 64820 Z= 0.348 Angle : 0.632 7.961 87612 Z= 0.338 Chirality : 0.047 0.226 10640 Planarity : 0.004 0.051 11396 Dihedral : 8.265 90.613 9715 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.60 % Allowed : 17.98 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.09), residues: 8624 helix: 1.68 (0.08), residues: 4284 sheet: 0.30 (0.13), residues: 1190 loop : 0.37 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.022 0.002 PHE J 219 TYR 0.014 0.002 TYR C 478 ARG 0.007 0.001 ARG P 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 661 time to evaluate : 5.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6165 (p90) cc_final: 0.5800 (p90) REVERT: I 193 MET cc_start: 0.8742 (mmm) cc_final: 0.8507 (mmm) REVERT: I 267 MET cc_start: 0.8653 (mpt) cc_final: 0.8446 (mpt) REVERT: I 326 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7555 (p0) REVERT: I 362 ARG cc_start: 0.6578 (ptp-110) cc_final: 0.6274 (ptp-110) REVERT: W 7 HIS cc_start: 0.7548 (m90) cc_final: 0.7170 (m90) REVERT: W 90 ASP cc_start: 0.9621 (m-30) cc_final: 0.9406 (m-30) REVERT: A 193 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7908 (mmm) REVERT: A 267 MET cc_start: 0.8572 (mpt) cc_final: 0.8256 (mpt) REVERT: A 271 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7406 (m) REVERT: A 360 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: B 7 HIS cc_start: 0.7822 (m90) cc_final: 0.7390 (m90) REVERT: B 90 ASP cc_start: 0.9681 (m-30) cc_final: 0.9477 (m-30) REVERT: C 193 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: C 219 PHE cc_start: 0.8308 (m-80) cc_final: 0.8087 (m-80) REVERT: C 267 MET cc_start: 0.8484 (mpt) cc_final: 0.8215 (mpt) REVERT: C 362 ARG cc_start: 0.6719 (ptp-110) cc_final: 0.6467 (ptp-110) REVERT: C 389 MET cc_start: 0.8976 (tpp) cc_final: 0.8636 (tpp) REVERT: E 193 MET cc_start: 0.8689 (mmm) cc_final: 0.8473 (mmm) REVERT: E 267 MET cc_start: 0.8759 (mpt) cc_final: 0.8525 (mpt) REVERT: E 348 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7712 (tp-100) REVERT: E 362 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6257 (ptp-110) REVERT: E 389 MET cc_start: 0.8973 (tpp) cc_final: 0.8711 (tpp) REVERT: F 7 HIS cc_start: 0.7719 (m90) cc_final: 0.7285 (m90) REVERT: G 193 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8037 (mmm) REVERT: G 267 MET cc_start: 0.8684 (mpt) cc_final: 0.8476 (mpt) REVERT: G 271 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7501 (m) REVERT: G 362 ARG cc_start: 0.6528 (ptp-110) cc_final: 0.6206 (ptp-110) REVERT: G 514 MET cc_start: 0.9254 (mtp) cc_final: 0.8562 (mtp) REVERT: H 7 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7182 (m90) REVERT: H 90 ASP cc_start: 0.9620 (m-30) cc_final: 0.9315 (m-30) REVERT: J 193 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: J 271 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7451 (m) REVERT: J 348 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7603 (tp-100) REVERT: J 362 ARG cc_start: 0.6419 (ptp-110) cc_final: 0.6136 (ptp-110) REVERT: J 447 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8896 (mtt) REVERT: K 11 ILE cc_start: 0.8678 (mm) cc_final: 0.8384 (mm) REVERT: K 90 ASP cc_start: 0.9681 (m-30) cc_final: 0.9413 (m-30) REVERT: L 193 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: L 195 PHE cc_start: 0.8789 (p90) cc_final: 0.8554 (p90) REVERT: L 267 MET cc_start: 0.8634 (mpt) cc_final: 0.8183 (mpt) REVERT: L 348 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7593 (tp-100) REVERT: L 362 ARG cc_start: 0.6669 (ptp-110) cc_final: 0.6383 (ptp-110) REVERT: L 447 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8903 (mtt) REVERT: M 90 ASP cc_start: 0.9685 (m-30) cc_final: 0.9463 (m-30) REVERT: N 195 PHE cc_start: 0.8712 (p90) cc_final: 0.8489 (p90) REVERT: P 195 PHE cc_start: 0.8696 (p90) cc_final: 0.8275 (p90) REVERT: S 71 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.4715 (m-80) REVERT: T 267 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8259 (pmm) REVERT: V 11 ILE cc_start: 0.9473 (mm) cc_final: 0.9067 (pp) REVERT: X 467 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (m-40) REVERT: Z 59 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8335 (mm-30) REVERT: AA 11 ILE cc_start: 0.9470 (mm) cc_final: 0.9112 (pp) REVERT: BA 267 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (pmm) REVERT: BA 288 MET cc_start: 0.8972 (mtp) cc_final: 0.8763 (mtt) outliers start: 175 outliers final: 35 residues processed: 760 average time/residue: 1.2390 time to fit residues: 1273.7773 Evaluate side-chains 669 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 617 time to evaluate : 5.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 447 MET Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 467 ASN Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 645 optimal weight: 6.9990 chunk 528 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 776 optimal weight: 2.9990 chunk 839 optimal weight: 0.9980 chunk 691 optimal weight: 0.0970 chunk 770 optimal weight: 5.9990 chunk 264 optimal weight: 0.0670 chunk 623 optimal weight: 6.9990 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 GLN R 194 GLN X 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 64820 Z= 0.217 Angle : 0.573 8.255 87612 Z= 0.302 Chirality : 0.044 0.201 10640 Planarity : 0.003 0.037 11396 Dihedral : 7.925 94.927 9645 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.25 % Allowed : 18.07 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.09), residues: 8624 helix: 1.82 (0.08), residues: 4228 sheet: 0.44 (0.13), residues: 1330 loop : 0.34 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 7 PHE 0.025 0.002 PHE Z 195 TYR 0.011 0.002 TYR I 478 ARG 0.013 0.000 ARG T 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 652 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6231 (p90) cc_final: 0.5845 (p90) REVERT: I 193 MET cc_start: 0.8633 (mmm) cc_final: 0.8323 (tpt) REVERT: I 326 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7503 (p0) REVERT: I 514 MET cc_start: 0.9188 (mtp) cc_final: 0.8899 (mtp) REVERT: W 11 ILE cc_start: 0.8761 (mm) cc_final: 0.8381 (mp) REVERT: A 193 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7891 (mmm) REVERT: A 447 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (mtt) REVERT: C 305 ILE cc_start: 0.8675 (tp) cc_final: 0.8410 (tp) REVERT: C 362 ARG cc_start: 0.6846 (ptp-110) cc_final: 0.6634 (ptp-110) REVERT: C 389 MET cc_start: 0.8951 (tpp) cc_final: 0.8565 (tpp) REVERT: E 111 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8116 (mpt) REVERT: E 193 MET cc_start: 0.8618 (mmm) cc_final: 0.8244 (mmm) REVERT: E 222 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7879 (mp) REVERT: E 290 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8868 (tp-100) REVERT: E 348 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7644 (tp-100) REVERT: E 389 MET cc_start: 0.8981 (tpp) cc_final: 0.8629 (tpp) REVERT: F 7 HIS cc_start: 0.7741 (m90) cc_final: 0.7445 (m90) REVERT: G 111 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8155 (mtm) REVERT: G 193 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: G 195 PHE cc_start: 0.8787 (p90) cc_final: 0.8378 (p90) REVERT: G 305 ILE cc_start: 0.8663 (tp) cc_final: 0.8348 (tp) REVERT: G 514 MET cc_start: 0.9116 (mtp) cc_final: 0.8538 (mtp) REVERT: H 11 ILE cc_start: 0.8775 (mm) cc_final: 0.8410 (mp) REVERT: J 111 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8668 (mpt) REVERT: J 193 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8039 (mmm) REVERT: J 222 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7975 (mp) REVERT: J 348 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7501 (tp-100) REVERT: J 362 ARG cc_start: 0.6527 (ptp-110) cc_final: 0.6290 (ttp-110) REVERT: J 447 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8864 (mtt) REVERT: J 514 MET cc_start: 0.9218 (mtp) cc_final: 0.8829 (mtp) REVERT: K 11 ILE cc_start: 0.8656 (mm) cc_final: 0.8416 (mp) REVERT: L 193 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7974 (mmm) REVERT: L 267 MET cc_start: 0.8619 (mpt) cc_final: 0.8263 (mpt) REVERT: L 305 ILE cc_start: 0.8596 (tp) cc_final: 0.8341 (tp) REVERT: L 348 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7536 (tp-100) REVERT: L 362 ARG cc_start: 0.6747 (ptp-110) cc_final: 0.6495 (ptp-110) REVERT: L 447 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8845 (mtt) REVERT: L 491 MET cc_start: 0.9306 (mtm) cc_final: 0.9060 (mtm) REVERT: N 362 ARG cc_start: 0.6764 (ptp-110) cc_final: 0.6300 (mtp180) REVERT: P 195 PHE cc_start: 0.8729 (p90) cc_final: 0.8345 (p90) REVERT: P 362 ARG cc_start: 0.6430 (ptp-110) cc_final: 0.6096 (ptp90) REVERT: R 285 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7949 (mtt-85) REVERT: T 267 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8256 (pmm) REVERT: T 284 ARG cc_start: 0.8322 (pmm-80) cc_final: 0.8121 (pmm-80) REVERT: V 11 ILE cc_start: 0.9454 (mm) cc_final: 0.9084 (pp) REVERT: X 16 MET cc_start: 0.8989 (ttp) cc_final: 0.8710 (ttm) REVERT: X 488 MET cc_start: 0.9470 (mmm) cc_final: 0.9129 (mmm) REVERT: Z 59 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8293 (mm-30) REVERT: AA 11 ILE cc_start: 0.9463 (mm) cc_final: 0.9131 (pp) REVERT: BA 267 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8697 (pmm) REVERT: BA 288 MET cc_start: 0.8970 (mtp) cc_final: 0.8755 (mtt) outliers start: 151 outliers final: 36 residues processed: 740 average time/residue: 1.1989 time to fit residues: 1217.7552 Evaluate side-chains 657 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 606 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 325 ILE Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 447 MET Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 248 LEU Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 10.0000 chunk 584 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 370 optimal weight: 0.1980 chunk 521 optimal weight: 8.9990 chunk 779 optimal weight: 0.7980 chunk 825 optimal weight: 8.9990 chunk 407 optimal weight: 4.9990 chunk 738 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 GLN AA 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 64820 Z= 0.257 Angle : 0.586 9.947 87612 Z= 0.306 Chirality : 0.045 0.213 10640 Planarity : 0.003 0.032 11396 Dihedral : 7.954 96.858 9640 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.70 % Allowed : 18.85 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.09), residues: 8624 helix: 1.76 (0.08), residues: 4228 sheet: 0.45 (0.13), residues: 1330 loop : 0.32 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 7 PHE 0.022 0.002 PHE A 219 TYR 0.012 0.002 TYR I 478 ARG 0.005 0.000 ARGAA 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 627 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6165 (p90) cc_final: 0.5813 (p90) REVERT: I 193 MET cc_start: 0.8603 (mmm) cc_final: 0.8240 (mmm) REVERT: I 220 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7872 (mp) REVERT: I 267 MET cc_start: 0.8653 (mpt) cc_final: 0.8414 (mpt) REVERT: I 326 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.6824 (p0) REVERT: I 514 MET cc_start: 0.9195 (mtp) cc_final: 0.8909 (mtp) REVERT: W 11 ILE cc_start: 0.8775 (mm) cc_final: 0.8461 (mp) REVERT: A 267 MET cc_start: 0.8602 (mpt) cc_final: 0.8188 (mpt) REVERT: C 193 MET cc_start: 0.8654 (mmm) cc_final: 0.8273 (tpt) REVERT: C 267 MET cc_start: 0.8702 (mpt) cc_final: 0.8310 (mpt) REVERT: C 326 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.6760 (p0) REVERT: C 362 ARG cc_start: 0.6915 (ptp-110) cc_final: 0.6618 (ptp-110) REVERT: C 389 MET cc_start: 0.8944 (tpp) cc_final: 0.8555 (tpp) REVERT: E 111 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8140 (mpt) REVERT: E 193 MET cc_start: 0.8560 (mmm) cc_final: 0.8161 (mmm) REVERT: E 267 MET cc_start: 0.8718 (mpt) cc_final: 0.8388 (mpt) REVERT: E 290 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8880 (tp-100) REVERT: E 348 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7670 (tp-100) REVERT: E 389 MET cc_start: 0.8991 (tpp) cc_final: 0.8636 (tpp) REVERT: F 86 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8238 (pp-130) REVERT: G 76 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: G 111 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: G 193 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7990 (mmm) REVERT: G 195 PHE cc_start: 0.8855 (p90) cc_final: 0.8411 (p90) REVERT: G 514 MET cc_start: 0.9136 (mtp) cc_final: 0.8625 (mtp) REVERT: H 11 ILE cc_start: 0.8867 (mm) cc_final: 0.8588 (mp) REVERT: J 111 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8644 (mpt) REVERT: J 193 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: J 348 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7459 (tp-100) REVERT: J 362 ARG cc_start: 0.6553 (ptp-110) cc_final: 0.6208 (ptp-170) REVERT: L 76 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: L 193 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7999 (mmm) REVERT: L 195 PHE cc_start: 0.8825 (p90) cc_final: 0.8523 (p90) REVERT: L 348 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7550 (tp-100) REVERT: L 491 MET cc_start: 0.9366 (mtm) cc_final: 0.9119 (mtm) REVERT: N 111 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8242 (mpt) REVERT: N 362 ARG cc_start: 0.6602 (ptp-110) cc_final: 0.5854 (mtm180) REVERT: P 195 PHE cc_start: 0.8718 (p90) cc_final: 0.8232 (p90) REVERT: P 281 PHE cc_start: 0.7925 (m-10) cc_final: 0.7694 (m-10) REVERT: P 290 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8646 (tm-30) REVERT: P 362 ARG cc_start: 0.6524 (ptp-110) cc_final: 0.6113 (ptp90) REVERT: S 11 ILE cc_start: 0.9479 (mm) cc_final: 0.9103 (pp) REVERT: T 284 ARG cc_start: 0.8269 (pmm-80) cc_final: 0.8069 (pmm-80) REVERT: V 11 ILE cc_start: 0.9482 (mm) cc_final: 0.9140 (pp) REVERT: X 16 MET cc_start: 0.8918 (ttp) cc_final: 0.8661 (ttm) REVERT: Z 59 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8352 (mm-30) REVERT: AA 11 ILE cc_start: 0.9474 (mm) cc_final: 0.9182 (pp) REVERT: BA 288 MET cc_start: 0.8989 (mtp) cc_final: 0.8788 (mtt) REVERT: CA 11 ILE cc_start: 0.9479 (mm) cc_final: 0.9083 (pp) outliers start: 114 outliers final: 41 residues processed: 688 average time/residue: 1.2598 time to fit residues: 1168.3922 Evaluate side-chains 646 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 592 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 325 ILE Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 215 LEU Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 199 TYR Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 0.9990 chunk 468 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 614 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 704 optimal weight: 4.9990 chunk 570 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 421 optimal weight: 0.9980 chunk 740 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 GLN O 68 ASN Q 68 ASN V 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 64820 Z= 0.243 Angle : 0.589 9.494 87612 Z= 0.306 Chirality : 0.045 0.212 10640 Planarity : 0.003 0.035 11396 Dihedral : 7.944 95.503 9637 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.93 % Allowed : 18.93 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.09), residues: 8624 helix: 1.75 (0.08), residues: 4228 sheet: 0.22 (0.13), residues: 1386 loop : 0.29 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 7 PHE 0.031 0.002 PHE J 204 TYR 0.011 0.001 TYR C 478 ARG 0.009 0.000 ARG Z 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 603 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6250 (p90) cc_final: 0.5910 (p90) REVERT: I 193 MET cc_start: 0.8548 (mmm) cc_final: 0.8295 (mmm) REVERT: I 220 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7944 (mp) REVERT: I 514 MET cc_start: 0.9180 (mtp) cc_final: 0.8933 (mtp) REVERT: W 11 ILE cc_start: 0.8766 (mm) cc_final: 0.8537 (mp) REVERT: A 193 MET cc_start: 0.8565 (mmm) cc_final: 0.8200 (tpt) REVERT: A 267 MET cc_start: 0.8577 (mpt) cc_final: 0.8346 (mpt) REVERT: C 76 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: C 193 MET cc_start: 0.8584 (mmm) cc_final: 0.8174 (mmm) REVERT: C 348 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7642 (tp-100) REVERT: C 362 ARG cc_start: 0.6968 (ptp-110) cc_final: 0.6696 (ptp-110) REVERT: C 389 MET cc_start: 0.8961 (tpp) cc_final: 0.8586 (tpp) REVERT: E 111 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8077 (mpt) REVERT: E 193 MET cc_start: 0.8501 (mmm) cc_final: 0.8079 (mmm) REVERT: E 290 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8886 (tp-100) REVERT: E 348 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7632 (tp-100) REVERT: E 362 ARG cc_start: 0.6804 (ptp-110) cc_final: 0.6579 (ptp-110) REVERT: E 389 MET cc_start: 0.8986 (tpp) cc_final: 0.8637 (tpp) REVERT: F 86 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8310 (pp-130) REVERT: G 76 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: G 111 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8038 (mtm) REVERT: G 193 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: G 195 PHE cc_start: 0.8877 (p90) cc_final: 0.8431 (p90) REVERT: G 514 MET cc_start: 0.9161 (mtp) cc_final: 0.8627 (mtp) REVERT: H 11 ILE cc_start: 0.8821 (mm) cc_final: 0.8603 (mp) REVERT: J 76 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: J 111 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8659 (mpt) REVERT: J 193 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: J 348 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7433 (tp-100) REVERT: L 76 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: L 193 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: L 195 PHE cc_start: 0.8867 (p90) cc_final: 0.8544 (p90) REVERT: L 222 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.6800 (mt) REVERT: L 267 MET cc_start: 0.8494 (mpt) cc_final: 0.8160 (mpt) REVERT: L 348 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7557 (tp-100) REVERT: N 205 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8117 (tt) REVERT: N 285 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7914 (mtt-85) REVERT: N 290 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8747 (tm-30) REVERT: N 362 ARG cc_start: 0.6672 (ptp-110) cc_final: 0.5945 (mtm180) REVERT: P 290 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8724 (tm-30) REVERT: P 362 ARG cc_start: 0.6629 (ptp-110) cc_final: 0.6083 (mtm180) REVERT: R 362 ARG cc_start: 0.7481 (mtm110) cc_final: 0.6974 (mtp180) REVERT: S 11 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9111 (pp) REVERT: T 199 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6538 (p90) REVERT: V 11 ILE cc_start: 0.9467 (mm) cc_final: 0.9181 (pp) REVERT: X 16 MET cc_start: 0.8893 (ttp) cc_final: 0.8669 (ttm) REVERT: X 285 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7859 (mtp85) REVERT: X 467 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (m-40) REVERT: Z 59 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8297 (mm-30) REVERT: Z 362 ARG cc_start: 0.7299 (mtm110) cc_final: 0.7019 (mtm-85) REVERT: AA 11 ILE cc_start: 0.9489 (mm) cc_final: 0.9235 (pp) REVERT: BA 267 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8672 (pmm) REVERT: CA 11 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9137 (pp) outliers start: 130 outliers final: 47 residues processed: 676 average time/residue: 1.2483 time to fit residues: 1142.0976 Evaluate side-chains 649 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 583 time to evaluate : 5.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 199 TYR Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 467 ASN Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 199 TYR Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain CA residue 11 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 20.0000 chunk 743 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 484 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 826 optimal weight: 0.9980 chunk 685 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 433 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN N 194 GLN CA 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 64820 Z= 0.195 Angle : 0.585 9.805 87612 Z= 0.303 Chirality : 0.045 0.219 10640 Planarity : 0.003 0.032 11396 Dihedral : 7.715 90.301 9637 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.80 % Allowed : 18.97 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.09), residues: 8624 helix: 1.86 (0.08), residues: 4228 sheet: 0.27 (0.14), residues: 1386 loop : 0.26 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.039 0.002 PHE J 204 TYR 0.009 0.001 TYR P 199 ARG 0.010 0.000 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 615 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6153 (p90) cc_final: 0.5828 (p90) REVERT: I 193 MET cc_start: 0.8532 (mmm) cc_final: 0.8270 (mmm) REVERT: I 220 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 193 MET cc_start: 0.8489 (mmm) cc_final: 0.8146 (tpt) REVERT: A 447 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8769 (mtt) REVERT: B 6 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7544 (tt) REVERT: C 76 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: C 193 MET cc_start: 0.8602 (mmm) cc_final: 0.8242 (tpt) REVERT: C 343 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8599 (mp10) REVERT: C 362 ARG cc_start: 0.6974 (ptp-110) cc_final: 0.6694 (ptp-110) REVERT: C 389 MET cc_start: 0.8961 (tpp) cc_final: 0.8609 (tpp) REVERT: E 111 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: E 193 MET cc_start: 0.8487 (mmm) cc_final: 0.8063 (mmm) REVERT: E 290 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8877 (tp-100) REVERT: E 348 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7706 (tp-100) REVERT: E 362 ARG cc_start: 0.6803 (ptp-110) cc_final: 0.6473 (ptp-110) REVERT: E 389 MET cc_start: 0.8983 (tpp) cc_final: 0.8679 (tpp) REVERT: G 111 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8132 (mtm) REVERT: G 193 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: G 514 MET cc_start: 0.9138 (mtp) cc_final: 0.8651 (mtp) REVERT: H 6 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7619 (tt) REVERT: H 66 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8946 (tp) REVERT: J 193 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7952 (mmm) REVERT: J 348 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7409 (tp-100) REVERT: J 447 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8862 (mtt) REVERT: J 514 MET cc_start: 0.9181 (mtp) cc_final: 0.8895 (mtp) REVERT: K 6 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7464 (tt) REVERT: L 193 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7965 (mmm) REVERT: L 195 PHE cc_start: 0.8876 (p90) cc_final: 0.8559 (p90) REVERT: L 348 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7522 (tp-100) REVERT: L 360 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6566 (t80) REVERT: L 447 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8827 (mtt) REVERT: M 66 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (tp) REVERT: N 285 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7893 (mtt-85) REVERT: N 290 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8714 (tm-30) REVERT: N 362 ARG cc_start: 0.6684 (ptp-110) cc_final: 0.5884 (mtm180) REVERT: O 11 ILE cc_start: 0.9519 (mm) cc_final: 0.9238 (pp) REVERT: P 290 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8676 (tm-30) REVERT: P 362 ARG cc_start: 0.6694 (ptp-110) cc_final: 0.5968 (mtm180) REVERT: Q 11 ILE cc_start: 0.9412 (mm) cc_final: 0.9014 (pp) REVERT: R 362 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7161 (mtm-85) REVERT: S 11 ILE cc_start: 0.9437 (mm) cc_final: 0.9127 (pp) REVERT: T 288 MET cc_start: 0.9027 (mtt) cc_final: 0.8779 (mtp) REVERT: V 11 ILE cc_start: 0.9466 (mm) cc_final: 0.9181 (pp) REVERT: Z 59 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8231 (mm-30) REVERT: Z 194 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: Z 362 ARG cc_start: 0.7324 (mtm110) cc_final: 0.7008 (mtm-85) REVERT: AA 11 ILE cc_start: 0.9443 (mm) cc_final: 0.9199 (pp) REVERT: BA 290 GLN cc_start: 0.9054 (tp40) cc_final: 0.8812 (tp40) REVERT: CA 11 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9083 (pt) outliers start: 121 outliers final: 42 residues processed: 678 average time/residue: 1.2315 time to fit residues: 1135.4778 Evaluate side-chains 653 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 592 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 447 MET Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain BA residue 199 TYR Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain CA residue 11 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 470 optimal weight: 2.9990 chunk 603 optimal weight: 0.2980 chunk 467 optimal weight: 3.9990 chunk 695 optimal weight: 9.9990 chunk 461 optimal weight: 20.0000 chunk 823 optimal weight: 20.0000 chunk 515 optimal weight: 6.9990 chunk 501 optimal weight: 0.4980 chunk 380 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN S 68 ASN Y 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 64820 Z= 0.267 Angle : 0.624 12.048 87612 Z= 0.321 Chirality : 0.046 0.392 10640 Planarity : 0.003 0.038 11396 Dihedral : 7.988 93.520 9637 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.62 % Allowed : 19.21 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.09), residues: 8624 helix: 1.76 (0.08), residues: 4228 sheet: 0.32 (0.14), residues: 1358 loop : 0.19 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 7 PHE 0.030 0.001 PHE I 204 TYR 0.012 0.002 TYR I 478 ARG 0.007 0.001 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 604 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6237 (p90) cc_final: 0.5902 (p90) REVERT: I 193 MET cc_start: 0.8588 (mmm) cc_final: 0.8371 (mmm) REVERT: A 193 MET cc_start: 0.8482 (mmm) cc_final: 0.8141 (mmm) REVERT: C 76 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 193 MET cc_start: 0.8556 (mmm) cc_final: 0.8119 (tpt) REVERT: C 343 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: C 362 ARG cc_start: 0.7004 (ptp-110) cc_final: 0.6749 (ptp-110) REVERT: C 389 MET cc_start: 0.8962 (tpp) cc_final: 0.8596 (tpp) REVERT: E 111 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8074 (mpt) REVERT: E 193 MET cc_start: 0.8465 (mmm) cc_final: 0.8089 (mmm) REVERT: E 348 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7706 (tp-100) REVERT: E 389 MET cc_start: 0.8986 (tpp) cc_final: 0.8682 (tpp) REVERT: F 6 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7737 (tt) REVERT: F 66 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8865 (tp) REVERT: G 76 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: G 111 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: G 193 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7896 (mmm) REVERT: G 514 MET cc_start: 0.9147 (mtp) cc_final: 0.8698 (mtp) REVERT: H 66 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8975 (tp) REVERT: J 193 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: J 194 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: J 348 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7411 (tp-100) REVERT: L 76 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: L 193 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: L 348 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7532 (tp-100) REVERT: M 6 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7844 (tt) REVERT: M 66 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8902 (tp) REVERT: N 290 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8723 (tm-30) REVERT: N 362 ARG cc_start: 0.6838 (ptp-110) cc_final: 0.6191 (mtm180) REVERT: O 11 ILE cc_start: 0.9504 (mm) cc_final: 0.9195 (pp) REVERT: P 290 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8707 (tm-30) REVERT: P 362 ARG cc_start: 0.6732 (ptp-110) cc_final: 0.6039 (mtm180) REVERT: P 491 MET cc_start: 0.9312 (mtm) cc_final: 0.9052 (mtp) REVERT: R 199 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6481 (p90) REVERT: R 362 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7285 (mtm-85) REVERT: S 11 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9125 (pp) REVERT: T 288 MET cc_start: 0.9051 (mtt) cc_final: 0.8793 (mtp) REVERT: V 11 ILE cc_start: 0.9462 (mm) cc_final: 0.9204 (pp) REVERT: Y 11 ILE cc_start: 0.9093 (mm) cc_final: 0.8842 (mm) REVERT: Z 194 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7638 (tp40) REVERT: Z 290 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8677 (tm-30) REVERT: Z 362 ARG cc_start: 0.7344 (mtm110) cc_final: 0.7067 (mtm-85) REVERT: BA 267 MET cc_start: 0.8492 (pmm) cc_final: 0.8089 (pmm) REVERT: BA 285 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7814 (mtp85) REVERT: BA 290 GLN cc_start: 0.9083 (tp40) cc_final: 0.8871 (tp40) REVERT: BA 327 LYS cc_start: 0.8962 (tptp) cc_final: 0.8753 (tptp) REVERT: CA 11 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9084 (pt) outliers start: 109 outliers final: 51 residues processed: 664 average time/residue: 1.2618 time to fit residues: 1130.7797 Evaluate side-chains 647 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 577 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 TYR Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 215 LEU Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 144 ILE Chi-restraints excluded: chain BA residue 199 TYR Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Chi-restraints excluded: chain CA residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 0.2980 chunk 328 optimal weight: 5.9990 chunk 491 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 523 optimal weight: 0.8980 chunk 560 optimal weight: 0.7980 chunk 406 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 646 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64820 Z= 0.200 Angle : 0.626 11.290 87612 Z= 0.318 Chirality : 0.045 0.205 10640 Planarity : 0.003 0.036 11396 Dihedral : 7.801 96.479 9637 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.21 % Allowed : 19.91 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.09), residues: 8624 helix: 1.83 (0.08), residues: 4228 sheet: 0.34 (0.14), residues: 1358 loop : 0.15 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 7 PHE 0.050 0.002 PHE J 204 TYR 0.010 0.001 TYR N 199 ARG 0.006 0.000 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 605 time to evaluate : 5.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 193 MET cc_start: 0.8556 (mmm) cc_final: 0.8308 (mmm) REVERT: A 193 MET cc_start: 0.8453 (mmm) cc_final: 0.8140 (mmm) REVERT: A 267 MET cc_start: 0.8757 (mpt) cc_final: 0.8441 (mpt) REVERT: B 6 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 66 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (tp) REVERT: C 76 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: C 193 MET cc_start: 0.8535 (mmm) cc_final: 0.8090 (mmm) REVERT: C 343 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: C 362 ARG cc_start: 0.7041 (ptp-110) cc_final: 0.6780 (ptp-110) REVERT: C 389 MET cc_start: 0.8944 (tpp) cc_final: 0.8533 (tpp) REVERT: E 111 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8023 (mtm) REVERT: E 193 MET cc_start: 0.8427 (mmm) cc_final: 0.7969 (mmm) REVERT: E 348 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7693 (tp-100) REVERT: E 389 MET cc_start: 0.8978 (tpp) cc_final: 0.8595 (tpp) REVERT: F 6 LEU cc_start: 0.8265 (mp) cc_final: 0.7795 (tt) REVERT: F 66 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8902 (tp) REVERT: G 76 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: G 111 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: G 193 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: G 514 MET cc_start: 0.9134 (mtp) cc_final: 0.8677 (mtp) REVERT: H 6 LEU cc_start: 0.8339 (mp) cc_final: 0.7643 (tp) REVERT: H 66 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8989 (tp) REVERT: J 193 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: J 331 THR cc_start: 0.8939 (m) cc_final: 0.8701 (p) REVERT: J 348 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7362 (tp-100) REVERT: K 6 LEU cc_start: 0.8360 (mp) cc_final: 0.7521 (tp) REVERT: L 111 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8201 (mtm) REVERT: L 348 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7561 (tp-100) REVERT: M 6 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7945 (tt) REVERT: M 66 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8870 (tp) REVERT: N 215 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (mp) REVERT: N 285 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7881 (mtt-85) REVERT: N 290 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8709 (tm-30) REVERT: N 362 ARG cc_start: 0.6863 (ptp-110) cc_final: 0.6170 (mtm180) REVERT: O 11 ILE cc_start: 0.9489 (mm) cc_final: 0.9189 (pp) REVERT: P 290 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8706 (tm-30) REVERT: P 362 ARG cc_start: 0.6735 (ptp-110) cc_final: 0.6090 (mtm180) REVERT: P 491 MET cc_start: 0.9294 (mtm) cc_final: 0.9033 (mtp) REVERT: R 199 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6416 (p90) REVERT: S 11 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9078 (pt) REVERT: T 288 MET cc_start: 0.9038 (mtt) cc_final: 0.8776 (mtp) REVERT: V 11 ILE cc_start: 0.9459 (mm) cc_final: 0.9184 (pp) REVERT: Z 194 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: Z 290 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8681 (tm-30) REVERT: AA 11 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9101 (pt) REVERT: BA 267 MET cc_start: 0.8515 (pmm) cc_final: 0.8152 (pmm) REVERT: BA 285 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7769 (mtp85) REVERT: BA 290 GLN cc_start: 0.9096 (tp40) cc_final: 0.8871 (tp40) REVERT: BA 467 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8523 (m-40) outliers start: 81 outliers final: 44 residues processed: 644 average time/residue: 1.2764 time to fit residues: 1118.5769 Evaluate side-chains 655 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 591 time to evaluate : 5.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 TYR Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 281 PHE Chi-restraints excluded: chain X residue 301 ILE Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain BA residue 144 ILE Chi-restraints excluded: chain BA residue 199 TYR Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Chi-restraints excluded: chain BA residue 467 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.9990 chunk 788 optimal weight: 2.9990 chunk 719 optimal weight: 1.9990 chunk 767 optimal weight: 1.9990 chunk 461 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 602 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 693 optimal weight: 30.0000 chunk 725 optimal weight: 20.0000 chunk 764 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 64820 Z= 0.322 Angle : 0.678 13.757 87612 Z= 0.343 Chirality : 0.047 0.266 10640 Planarity : 0.004 0.048 11396 Dihedral : 8.248 91.054 9637 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.24 % Allowed : 20.06 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.09), residues: 8624 helix: 1.57 (0.08), residues: 4284 sheet: 0.27 (0.14), residues: 1358 loop : 0.13 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 7 PHE 0.044 0.002 PHE A 204 TYR 0.014 0.002 TYR C 478 ARG 0.010 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 601 time to evaluate : 5.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6382 (p90) cc_final: 0.6012 (p90) REVERT: I 171 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7927 (mmpt) REVERT: I 193 MET cc_start: 0.8562 (mmm) cc_final: 0.8234 (mmm) REVERT: I 322 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7803 (mmm160) REVERT: W 6 LEU cc_start: 0.8166 (mp) cc_final: 0.7329 (tp) REVERT: A 193 MET cc_start: 0.8455 (mmm) cc_final: 0.8127 (mmm) REVERT: B 6 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 66 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9035 (tp) REVERT: C 76 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: C 193 MET cc_start: 0.8586 (mmm) cc_final: 0.8115 (tpt) REVERT: C 343 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: C 362 ARG cc_start: 0.7059 (ptp-110) cc_final: 0.6626 (ptp-170) REVERT: C 389 MET cc_start: 0.8954 (tpp) cc_final: 0.8574 (tpp) REVERT: E 111 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8093 (mpt) REVERT: E 193 MET cc_start: 0.8372 (mmm) cc_final: 0.7916 (mmm) REVERT: E 348 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7703 (tp-100) REVERT: E 389 MET cc_start: 0.8970 (tpp) cc_final: 0.8650 (tpp) REVERT: F 6 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7555 (tp) REVERT: F 66 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8916 (tp) REVERT: G 76 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: G 514 MET cc_start: 0.9183 (mtp) cc_final: 0.8746 (mtp) REVERT: H 6 LEU cc_start: 0.8340 (mp) cc_final: 0.7710 (tp) REVERT: H 66 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8927 (tp) REVERT: J 193 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: J 348 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7404 (tp-100) REVERT: K 6 LEU cc_start: 0.8428 (mp) cc_final: 0.7525 (tp) REVERT: L 348 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7541 (tp-100) REVERT: M 6 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7657 (tp) REVERT: M 66 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8873 (tp) REVERT: N 285 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7908 (mtt-85) REVERT: N 290 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8745 (tm-30) REVERT: N 362 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6185 (mtm180) REVERT: P 290 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8737 (tm-30) REVERT: P 362 ARG cc_start: 0.6754 (ptp-110) cc_final: 0.6277 (mtm180) REVERT: P 491 MET cc_start: 0.9356 (mtm) cc_final: 0.9075 (mtp) REVERT: R 199 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6382 (p90) REVERT: T 288 MET cc_start: 0.9054 (mtt) cc_final: 0.8777 (mtp) REVERT: T 362 ARG cc_start: 0.7336 (ttm110) cc_final: 0.6925 (mtp-110) REVERT: T 390 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8183 (mmmt) REVERT: V 11 ILE cc_start: 0.9434 (mm) cc_final: 0.9096 (pp) REVERT: Z 194 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7656 (tp40) REVERT: Z 290 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8703 (tm-30) REVERT: BA 267 MET cc_start: 0.8538 (pmm) cc_final: 0.8146 (pmm) REVERT: BA 285 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7516 (mtt-85) REVERT: BA 290 GLN cc_start: 0.9178 (tp40) cc_final: 0.8931 (tp40) REVERT: BA 327 LYS cc_start: 0.9013 (tptp) cc_final: 0.8765 (tptp) outliers start: 83 outliers final: 43 residues processed: 648 average time/residue: 1.2749 time to fit residues: 1111.3624 Evaluate side-chains 640 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 582 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 TYR Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 390 LYS Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 301 ILE Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain BA residue 144 ILE Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 1.9990 chunk 811 optimal weight: 3.9990 chunk 495 optimal weight: 0.9990 chunk 384 optimal weight: 2.9990 chunk 563 optimal weight: 5.9990 chunk 850 optimal weight: 6.9990 chunk 783 optimal weight: 9.9990 chunk 677 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 523 optimal weight: 20.0000 chunk 415 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 64820 Z= 0.245 Angle : 0.673 14.279 87612 Z= 0.340 Chirality : 0.047 0.378 10640 Planarity : 0.003 0.041 11396 Dihedral : 8.099 93.097 9634 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.00 % Allowed : 20.65 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.09), residues: 8624 helix: 1.68 (0.08), residues: 4228 sheet: 0.15 (0.14), residues: 1386 loop : 0.12 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS D 7 PHE 0.047 0.002 PHE J 204 TYR 0.019 0.002 TYR E 199 ARG 0.013 0.000 ARG G 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 608 time to evaluate : 5.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6349 (p90) cc_final: 0.5982 (p90) REVERT: I 171 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7883 (mmpt) REVERT: I 193 MET cc_start: 0.8509 (mmm) cc_final: 0.8263 (mmm) REVERT: I 322 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7820 (mmm160) REVERT: W 6 LEU cc_start: 0.8185 (mp) cc_final: 0.7407 (tp) REVERT: A 193 MET cc_start: 0.8397 (mmm) cc_final: 0.8080 (mmm) REVERT: B 6 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7746 (tp) REVERT: B 66 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9041 (tp) REVERT: C 76 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 193 MET cc_start: 0.8581 (mmm) cc_final: 0.8222 (mmm) REVERT: C 343 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: C 362 ARG cc_start: 0.7060 (ptp-110) cc_final: 0.6666 (ptp-110) REVERT: C 389 MET cc_start: 0.8949 (tpp) cc_final: 0.8573 (tpp) REVERT: E 111 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8054 (mpt) REVERT: E 193 MET cc_start: 0.8317 (mmm) cc_final: 0.7883 (mmm) REVERT: E 348 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7705 (tp-100) REVERT: E 389 MET cc_start: 0.8983 (tpp) cc_final: 0.8669 (tpp) REVERT: F 6 LEU cc_start: 0.8266 (mp) cc_final: 0.7594 (tp) REVERT: F 66 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8917 (tp) REVERT: G 76 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: G 111 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7918 (mtm) REVERT: G 514 MET cc_start: 0.9160 (mtp) cc_final: 0.8718 (mtp) REVERT: H 6 LEU cc_start: 0.8320 (mp) cc_final: 0.7802 (tp) REVERT: H 66 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8942 (tp) REVERT: J 76 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: J 193 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: J 322 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7526 (mmm160) REVERT: J 348 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7386 (tp-100) REVERT: K 6 LEU cc_start: 0.8417 (mp) cc_final: 0.7593 (tp) REVERT: L 348 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7537 (tp-100) REVERT: M 6 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7722 (tp) REVERT: M 66 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8874 (tp) REVERT: N 285 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7893 (mtt-85) REVERT: N 290 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8751 (tm-30) REVERT: P 290 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8732 (tm-30) REVERT: P 362 ARG cc_start: 0.6832 (ptp-110) cc_final: 0.6173 (mtm180) REVERT: P 491 MET cc_start: 0.9359 (mtm) cc_final: 0.9119 (mtm) REVERT: R 199 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6489 (p90) REVERT: S 11 ILE cc_start: 0.9355 (tp) cc_final: 0.9061 (pp) REVERT: T 288 MET cc_start: 0.9054 (mtt) cc_final: 0.8771 (mtp) REVERT: T 362 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6912 (mtp-110) REVERT: T 390 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: X 322 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7952 (tpp80) REVERT: Z 194 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: BA 267 MET cc_start: 0.8620 (pmm) cc_final: 0.8156 (pmm) REVERT: BA 288 MET cc_start: 0.8912 (mtt) cc_final: 0.8661 (mtp) REVERT: BA 290 GLN cc_start: 0.9141 (tp40) cc_final: 0.8902 (tp40) outliers start: 67 outliers final: 42 residues processed: 648 average time/residue: 1.2657 time to fit residues: 1107.0082 Evaluate side-chains 651 residues out of total 6762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 593 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 TYR Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 390 LYS Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain BA residue 144 ILE Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 1.9990 chunk 721 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 624 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 678 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 696 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105884 restraints weight = 95962.648| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.08 r_work: 0.3109 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 64820 Z= 0.226 Angle : 0.675 13.660 87612 Z= 0.340 Chirality : 0.046 0.296 10640 Planarity : 0.003 0.034 11396 Dihedral : 7.975 95.055 9634 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.97 % Allowed : 20.89 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.09), residues: 8624 helix: 1.72 (0.08), residues: 4228 sheet: 0.13 (0.14), residues: 1400 loop : 0.14 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 7 PHE 0.048 0.002 PHE G 204 TYR 0.013 0.001 TYR E 199 ARG 0.008 0.000 ARG N 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19032.93 seconds wall clock time: 331 minutes 56.85 seconds (19916.85 seconds total)