Starting phenix.real_space_refine on Fri Sep 27 12:09:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_2024/8bmt_16125.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_2024/8bmt_16125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_2024/8bmt_16125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_2024/8bmt_16125.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/09_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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.20, per 1000 atoms: 0.20 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: 12.36 Conformation dependent library (CDL) restraints added in 6.4 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: 7.57 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: 32.40 Time building geometry restraints manager: 14.71 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 107.710 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.110 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 75 poor density : 770 time to evaluate : 5.410 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: 1.4447 time to fit residues: 1533.7659 Evaluate side-chains 661 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 635 time to evaluate : 5.473 ------------------------------------------------------------------------------- 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 90.609 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 fitting. rotamer outliers: 175 poor density : 661 time to evaluate : 5.363 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: 0.6273 (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: 0.7718 (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: 0.8561 (mtp) REVERT: H 7 HIS cc_start: 0.7553 (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: 0.8555 (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: 0.8726 (OUTLIER) cc_final: 0.8259 (pmm) REVERT: V 11 ILE cc_start: 0.9473 (mm) cc_final: 0.9068 (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: 1.2431 time to fit residues: 1279.5903 Evaluate side-chains 669 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 617 time to evaluate : 5.331 ------------------------------------------------------------------------------- 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: 8.9990 chunk 240 optimal weight: 4.9990 chunk 645 optimal weight: 8.9990 chunk 528 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 776 optimal weight: 2.9990 chunk 839 optimal weight: 0.6980 chunk 691 optimal weight: 0.0370 chunk 770 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 623 optimal weight: 6.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 64820 Z= 0.255 Angle : 0.583 8.228 87612 Z= 0.307 Chirality : 0.045 0.201 10640 Planarity : 0.003 0.036 11396 Dihedral : 8.071 92.470 9645 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.34 % Allowed : 18.17 % Favored : 79.49 % 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: 1.67 (0.08), residues: 4284 sheet: 0.56 (0.13), residues: 1302 loop : 0.29 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 7 PHE 0.021 0.001 PHE Z 195 TYR 0.012 0.002 TYR E 199 ARG 0.012 0.001 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 807 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 650 time to evaluate : 5.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6255 (p90) cc_final: 0.5867 (p90) REVERT: I 193 MET cc_start: 0.8620 (mmm) cc_final: 0.8359 (tpt) REVERT: I 326 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7501 (p0) REVERT: I 362 ARG cc_start: 0.6672 (ptp-110) cc_final: 0.6427 (ptp-110) REVERT: I 514 MET cc_start: 0.9194 (mtp) cc_final: 0.8899 (mtp) REVERT: W 11 ILE cc_start: 0.8761 (mm) cc_final: 0.8375 (mp) REVERT: C 305 ILE cc_start: 0.8678 (tp) cc_final: 0.8427 (tp) REVERT: C 362 ARG cc_start: 0.6848 (ptp-110) cc_final: 0.6629 (ptp-110) REVERT: C 389 MET cc_start: 0.8942 (tpp) cc_final: 0.8554 (tpp) REVERT: E 111 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8195 (mpt) REVERT: E 193 MET cc_start: 0.8629 (mmm) cc_final: 0.8320 (mmm) REVERT: E 195 PHE cc_start: 0.8845 (p90) cc_final: 0.8576 (p90) REVERT: E 222 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (mp) REVERT: E 290 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8881 (tp-100) REVERT: E 305 ILE cc_start: 0.8714 (tp) cc_final: 0.8469 (tp) REVERT: E 348 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7674 (tp-100) REVERT: E 389 MET cc_start: 0.8976 (tpp) cc_final: 0.8622 (tpp) REVERT: F 7 HIS cc_start: 0.7753 (m90) cc_final: 0.7460 (m90) REVERT: G 193 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: G 195 PHE cc_start: 0.8799 (p90) cc_final: 0.8387 (p90) REVERT: G 514 MET cc_start: 0.9109 (mtp) cc_final: 0.8537 (mtp) REVERT: H 11 ILE cc_start: 0.8783 (mm) cc_final: 0.8414 (mp) REVERT: J 111 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (mpt) REVERT: J 193 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: J 348 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7513 (tp-100) REVERT: J 362 ARG cc_start: 0.6543 (ptp-110) cc_final: 0.6185 (ptp-170) REVERT: J 514 MET cc_start: 0.9243 (mtp) cc_final: 0.8864 (mtp) REVERT: K 11 ILE cc_start: 0.8666 (mm) cc_final: 0.8422 (mp) REVERT: L 193 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: L 267 MET cc_start: 0.8596 (mpt) cc_final: 0.8269 (mpt) REVERT: L 348 GLN cc_start: 0.7817 (tp-100) cc_final: 0.7544 (tp-100) REVERT: L 362 ARG cc_start: 0.6735 (ptp-110) cc_final: 0.6459 (ptp-110) REVERT: L 491 MET cc_start: 0.9361 (mtm) cc_final: 0.9126 (mtm) REVERT: N 362 ARG cc_start: 0.6710 (ptp-110) cc_final: 0.6466 (mtp180) REVERT: P 195 PHE cc_start: 0.8731 (p90) cc_final: 0.8371 (p90) REVERT: P 362 ARG cc_start: 0.6450 (ptp-110) cc_final: 0.6132 (ptp90) REVERT: R 285 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7937 (mtt-85) REVERT: T 267 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8256 (pmm) REVERT: T 284 ARG cc_start: 0.8344 (pmm-80) cc_final: 0.8143 (pmm-80) REVERT: V 11 ILE cc_start: 0.9457 (mm) cc_final: 0.9090 (pp) REVERT: X 488 MET cc_start: 0.9478 (mmm) cc_final: 0.9142 (mmm) REVERT: Z 59 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8317 (mm-30) REVERT: AA 11 ILE cc_start: 0.9467 (mm) cc_final: 0.9137 (pp) REVERT: BA 267 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8633 (pmm) outliers start: 157 outliers final: 42 residues processed: 742 average time/residue: 1.1955 time to fit residues: 1216.8818 Evaluate side-chains 665 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 614 time to evaluate : 5.300 ------------------------------------------------------------------------------- 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 114 MET Chi-restraints excluded: chain A residue 174 VAL 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 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 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 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain L residue 174 VAL 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 248 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain T residue 174 VAL 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 185 ASP Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 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: 9.9990 chunk 584 optimal weight: 30.0000 chunk 403 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 370 optimal weight: 0.5980 chunk 521 optimal weight: 6.9990 chunk 779 optimal weight: 0.7980 chunk 825 optimal weight: 20.0000 chunk 407 optimal weight: 2.9990 chunk 738 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 64820 Z= 0.232 Angle : 0.578 10.094 87612 Z= 0.301 Chirality : 0.045 0.242 10640 Planarity : 0.003 0.032 11396 Dihedral : 7.899 93.282 9637 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.76 % Allowed : 18.84 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.09), residues: 8624 helix: 1.78 (0.08), residues: 4228 sheet: 0.46 (0.13), residues: 1330 loop : 0.31 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 7 PHE 0.023 0.002 PHE J 219 TYR 0.011 0.001 TYR I 478 ARG 0.007 0.000 ARG G 284 *********************** 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 751 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 633 time to evaluate : 5.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6208 (p90) cc_final: 0.5857 (p90) REVERT: I 193 MET cc_start: 0.8602 (mmm) cc_final: 0.8352 (tpt) REVERT: I 220 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7951 (mp) REVERT: I 267 MET cc_start: 0.8692 (mpt) cc_final: 0.8423 (mpt) REVERT: I 326 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.6840 (p0) REVERT: I 514 MET cc_start: 0.9182 (mtp) cc_final: 0.8975 (mtp) REVERT: W 11 ILE cc_start: 0.8775 (mm) cc_final: 0.8480 (mp) REVERT: A 267 MET cc_start: 0.8564 (mpt) cc_final: 0.8247 (mpt) REVERT: A 343 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (mm-40) REVERT: B 7 HIS cc_start: 0.7810 (m90) cc_final: 0.7523 (m90) REVERT: C 193 MET cc_start: 0.8624 (mmm) cc_final: 0.8255 (tpt) REVERT: C 267 MET cc_start: 0.8560 (mpt) cc_final: 0.8274 (mpt) REVERT: C 326 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.6761 (p0) REVERT: C 389 MET cc_start: 0.8959 (tpp) cc_final: 0.8589 (tpp) REVERT: E 111 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8107 (mpt) REVERT: E 193 MET cc_start: 0.8530 (mmm) cc_final: 0.8115 (mmm) REVERT: E 267 MET cc_start: 0.8838 (mpt) cc_final: 0.8295 (mpt) REVERT: E 290 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8898 (tp-100) REVERT: E 348 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7672 (tp-100) REVERT: E 362 ARG cc_start: 0.6830 (ptp-110) cc_final: 0.6589 (ptp-110) REVERT: E 389 MET cc_start: 0.8988 (tpp) cc_final: 0.8647 (tpp) REVERT: G 76 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: G 111 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8044 (mtm) REVERT: G 193 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (mmm) REVERT: G 195 PHE cc_start: 0.8870 (p90) cc_final: 0.8442 (p90) REVERT: G 326 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6861 (p0) REVERT: G 362 ARG cc_start: 0.6612 (ptp-110) cc_final: 0.6315 (ttp-110) REVERT: G 514 MET cc_start: 0.9124 (mtp) cc_final: 0.8616 (mtp) REVERT: H 11 ILE cc_start: 0.8834 (mm) cc_final: 0.8559 (mp) REVERT: J 111 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8665 (mpt) REVERT: J 193 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: J 222 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7208 (mt) REVERT: J 348 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7458 (tp-100) REVERT: K 86 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8135 (pp-130) REVERT: L 193 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (mmm) REVERT: L 195 PHE cc_start: 0.8825 (p90) cc_final: 0.8525 (p90) REVERT: L 348 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7555 (tp-100) REVERT: N 362 ARG cc_start: 0.6601 (ptp-110) cc_final: 0.5832 (mtm180) REVERT: P 195 PHE cc_start: 0.8715 (p90) cc_final: 0.8255 (p90) REVERT: P 290 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8623 (tm-30) REVERT: P 362 ARG cc_start: 0.6505 (ptp-110) cc_final: 0.6104 (ptp90) REVERT: S 11 ILE cc_start: 0.9487 (mm) cc_final: 0.9118 (pp) REVERT: V 11 ILE cc_start: 0.9474 (mm) cc_final: 0.9148 (pp) REVERT: X 16 MET cc_start: 0.8977 (ttp) cc_final: 0.8719 (ttm) REVERT: X 467 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8546 (m-40) REVERT: X 488 MET cc_start: 0.9476 (mmm) cc_final: 0.9117 (mmm) REVERT: Z 59 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8291 (mm-30) REVERT: Z 193 MET cc_start: 0.8282 (mmm) cc_final: 0.8073 (mmm) REVERT: AA 11 ILE cc_start: 0.9466 (mm) cc_final: 0.9191 (pp) REVERT: BA 285 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.7824 (mtp85) REVERT: CA 11 ILE cc_start: 0.9474 (mm) cc_final: 0.9084 (pp) outliers start: 118 outliers final: 41 residues processed: 698 average time/residue: 1.2641 time to fit residues: 1192.4686 Evaluate side-chains 652 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 596 time to evaluate : 5.305 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 343 GLN 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 325 ILE 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 G residue 326 ASN 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 222 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 86 MET 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 144 ILE 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 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 215 LEU Chi-restraints excluded: chain Z residue 273 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: 1.9990 chunk 468 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 614 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 704 optimal weight: 10.0000 chunk 570 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 740 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 X 194 GLN CA 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 64820 Z= 0.296 Angle : 0.614 12.116 87612 Z= 0.319 Chirality : 0.046 0.222 10640 Planarity : 0.003 0.048 11396 Dihedral : 8.166 91.841 9637 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.07 % Allowed : 18.75 % Favored : 79.18 % 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: 1.37 (0.09), residues: 8624 helix: 1.58 (0.08), residues: 4284 sheet: 0.53 (0.13), residues: 1302 loop : 0.27 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 7 PHE 0.022 0.001 PHE C 219 TYR 0.013 0.002 TYR I 478 ARG 0.014 0.001 ARG P 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 747 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 608 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6300 (p90) cc_final: 0.5953 (p90) REVERT: I 193 MET cc_start: 0.8548 (mmm) cc_final: 0.8242 (mmm) REVERT: I 220 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8069 (mp) REVERT: I 362 ARG cc_start: 0.6560 (ptp-110) cc_final: 0.6326 (ptp-110) REVERT: I 514 MET cc_start: 0.9206 (mtp) cc_final: 0.8942 (mtp) REVERT: W 11 ILE cc_start: 0.8801 (mm) cc_final: 0.8598 (mp) REVERT: C 76 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: C 193 MET cc_start: 0.8605 (mmm) cc_final: 0.8219 (tpt) REVERT: C 326 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.7082 (p0) REVERT: C 348 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7664 (tp-100) REVERT: C 389 MET cc_start: 0.8978 (tpp) cc_final: 0.8600 (tpp) REVERT: E 111 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8099 (mpt) REVERT: E 193 MET cc_start: 0.8534 (mmm) cc_final: 0.8111 (mmm) REVERT: E 220 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8064 (mp) REVERT: E 290 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8904 (tp-100) REVERT: E 348 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7691 (tp-100) REVERT: E 362 ARG cc_start: 0.6795 (ptp-110) cc_final: 0.6489 (ptp-110) REVERT: E 389 MET cc_start: 0.8978 (tpp) cc_final: 0.8724 (tpp) REVERT: G 193 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: G 267 MET cc_start: 0.8788 (mpt) cc_final: 0.8456 (mpt) REVERT: G 326 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6876 (p0) REVERT: G 514 MET cc_start: 0.9178 (mtp) cc_final: 0.8651 (mtp) REVERT: H 11 ILE cc_start: 0.8802 (mm) cc_final: 0.8600 (mp) REVERT: J 76 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: J 111 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8703 (mpt) REVERT: J 193 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: J 204 PHE cc_start: 0.9093 (m-80) cc_final: 0.8725 (m-10) REVERT: J 220 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8289 (mp) REVERT: J 348 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7472 (tp-100) REVERT: L 76 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: L 111 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8259 (mtm) REVERT: L 193 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8007 (mmm) REVERT: L 267 MET cc_start: 0.8574 (mpt) cc_final: 0.8302 (mpt) REVERT: L 348 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7577 (tp-100) REVERT: N 199 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.6484 (p90) REVERT: N 290 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8725 (tm-30) REVERT: N 362 ARG cc_start: 0.6639 (ptp-110) cc_final: 0.5921 (mtm180) REVERT: P 290 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8705 (tm-30) REVERT: P 362 ARG cc_start: 0.6704 (ptp-110) cc_final: 0.6122 (mtm180) REVERT: P 491 MET cc_start: 0.9258 (mtm) cc_final: 0.8977 (mtm) REVERT: R 362 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7095 (mtp180) REVERT: S 11 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9128 (pp) REVERT: T 52 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8174 (t0) REVERT: T 199 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6468 (p90) REVERT: T 288 MET cc_start: 0.9000 (mtt) cc_final: 0.8760 (mtp) REVERT: V 11 ILE cc_start: 0.9466 (mm) cc_final: 0.9189 (pp) REVERT: X 16 MET cc_start: 0.8966 (ttp) cc_final: 0.8677 (ttm) REVERT: X 285 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7853 (mtp85) REVERT: Z 194 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7723 (tp40) REVERT: Z 362 ARG cc_start: 0.6476 (ptp-110) cc_final: 0.6167 (mtm110) REVERT: AA 11 ILE cc_start: 0.9441 (mm) cc_final: 0.9173 (pp) REVERT: BA 285 ARG cc_start: 0.8307 (mtt-85) cc_final: 0.7574 (mtt-85) REVERT: CA 11 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9115 (pp) outliers start: 139 outliers final: 50 residues processed: 692 average time/residue: 1.2618 time to fit residues: 1181.0264 Evaluate side-chains 638 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 568 time to evaluate : 5.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 271 VAL 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 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 326 ASN 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 174 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 220 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 G residue 111 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 326 ASN 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 220 ILE 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 111 MET Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 220 ILE 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 199 TYR 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 52 ASP 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 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 213 VAL 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 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: 2.9990 chunk 163 optimal weight: 1.9990 chunk 484 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 826 optimal weight: 7.9990 chunk 685 optimal weight: 0.0770 chunk 382 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 433 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2982 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= 0.238 Angle : 0.599 11.221 87612 Z= 0.309 Chirality : 0.045 0.213 10640 Planarity : 0.003 0.032 11396 Dihedral : 8.055 91.975 9637 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.83 % Allowed : 19.12 % Favored : 79.05 % 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: 1.40 (0.09), residues: 8624 helix: 1.73 (0.08), residues: 4228 sheet: 0.31 (0.14), residues: 1358 loop : 0.22 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 7 PHE 0.030 0.002 PHE I 204 TYR 0.011 0.001 TYR I 478 ARG 0.007 0.000 ARG G 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 733 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 610 time to evaluate : 5.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6250 (p90) cc_final: 0.5912 (p90) REVERT: I 193 MET cc_start: 0.8598 (mmm) cc_final: 0.8348 (mmm) REVERT: B 6 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7759 (tt) REVERT: C 76 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 193 MET cc_start: 0.8631 (mmm) cc_final: 0.8171 (tpt) REVERT: C 326 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6989 (p0) REVERT: C 362 ARG cc_start: 0.6843 (ptp-110) cc_final: 0.6450 (ptp-110) REVERT: C 389 MET cc_start: 0.8952 (tpp) cc_final: 0.8589 (tpp) REVERT: E 111 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8063 (mpt) REVERT: E 193 MET cc_start: 0.8472 (mmm) cc_final: 0.8090 (mmm) REVERT: E 195 PHE cc_start: 0.8830 (p90) cc_final: 0.8565 (p90) REVERT: E 267 MET cc_start: 0.8664 (mpt) cc_final: 0.8385 (mpt) REVERT: E 348 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7713 (tp-100) REVERT: E 389 MET cc_start: 0.8983 (tpp) cc_final: 0.8676 (tpp) REVERT: F 66 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8925 (tp) REVERT: G 111 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7935 (mtm) REVERT: G 193 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7907 (mmm) REVERT: G 514 MET cc_start: 0.9122 (mtp) cc_final: 0.8617 (mtp) REVERT: H 66 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8969 (tp) REVERT: J 76 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: J 111 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8684 (mtm) REVERT: J 193 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8129 (mmm) REVERT: J 204 PHE cc_start: 0.9103 (m-80) cc_final: 0.8816 (m-10) REVERT: J 348 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7478 (tp-100) REVERT: L 111 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: L 348 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7543 (tp-100) REVERT: L 360 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6645 (t80) REVERT: M 6 LEU cc_start: 0.8367 (mp) cc_final: 0.7723 (tt) REVERT: M 66 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9013 (tp) REVERT: N 199 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.6332 (p90) REVERT: N 290 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8731 (tm-30) REVERT: N 362 ARG cc_start: 0.6729 (ptp-110) cc_final: 0.5962 (mtm180) REVERT: O 11 ILE cc_start: 0.9459 (mm) cc_final: 0.9181 (pp) REVERT: P 290 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8687 (tm-30) REVERT: P 362 ARG cc_start: 0.6716 (ptp-110) cc_final: 0.6028 (mtm180) REVERT: Q 11 ILE cc_start: 0.9416 (mm) cc_final: 0.9030 (pp) REVERT: R 285 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7838 (mtt-85) REVERT: R 362 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7241 (mtm-85) REVERT: S 11 ILE cc_start: 0.9434 (mm) cc_final: 0.9129 (pp) REVERT: T 288 MET cc_start: 0.9026 (mtt) cc_final: 0.8778 (mtp) REVERT: T 390 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8155 (mmmt) REVERT: V 11 ILE cc_start: 0.9455 (mm) cc_final: 0.9185 (pp) REVERT: X 16 MET cc_start: 0.8908 (ttp) cc_final: 0.8684 (ttm) REVERT: X 467 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8586 (m-40) REVERT: AA 11 ILE cc_start: 0.9446 (mm) cc_final: 0.9208 (pp) REVERT: BA 267 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8236 (mpp) REVERT: CA 11 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9099 (pp) outliers start: 123 outliers final: 53 residues processed: 688 average time/residue: 1.2243 time to fit residues: 1148.1170 Evaluate side-chains 664 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 592 time to evaluate : 5.342 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain A residue 271 VAL 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 144 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 66 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 F residue 90 ASP 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 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 213 VAL 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 111 MET Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 360 TYR 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 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 199 TYR Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 139 SER 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 139 SER Chi-restraints excluded: chain T residue 144 ILE 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 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 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain BA residue 144 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 470 optimal weight: 0.8980 chunk 603 optimal weight: 0.5980 chunk 467 optimal weight: 6.9990 chunk 695 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 823 optimal weight: 3.9990 chunk 515 optimal weight: 7.9990 chunk 501 optimal weight: 2.9990 chunk 380 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 X 194 GLN Y 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 64820 Z= 0.218 Angle : 0.618 13.712 87612 Z= 0.316 Chirality : 0.045 0.212 10640 Planarity : 0.003 0.036 11396 Dihedral : 7.938 93.202 9637 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.65 % Allowed : 19.60 % Favored : 78.75 % 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: 1.78 (0.08), residues: 4228 sheet: 0.30 (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 0.038 0.001 PHE I 204 TYR 0.012 0.001 TYR E 199 ARG 0.009 0.000 ARG L 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 719 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 608 time to evaluate : 5.413 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: 0.6239 (p90) cc_final: 0.5912 (p90) REVERT: I 171 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7878 (mmpt) REVERT: I 193 MET cc_start: 0.8611 (mmm) cc_final: 0.8343 (mmm) REVERT: I 267 MET cc_start: 0.8792 (mpt) cc_final: 0.8559 (mpt) REVERT: B 6 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7789 (tt) REVERT: C 76 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: C 193 MET cc_start: 0.8559 (mmm) cc_final: 0.8141 (tpt) REVERT: C 326 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6992 (p0) REVERT: C 389 MET cc_start: 0.8952 (tpp) cc_final: 0.8601 (tpp) REVERT: E 111 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: E 193 MET cc_start: 0.8448 (mmm) cc_final: 0.8103 (mmm) REVERT: E 195 PHE cc_start: 0.8767 (p90) cc_final: 0.8507 (p90) REVERT: E 267 MET cc_start: 0.8828 (mpt) cc_final: 0.8512 (mpt) REVERT: E 348 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7714 (tp-100) REVERT: E 389 MET cc_start: 0.8979 (tpp) cc_final: 0.8677 (tpp) REVERT: F 6 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7772 (tt) REVERT: F 66 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (tp) REVERT: G 111 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: G 193 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: G 514 MET cc_start: 0.9105 (mtp) cc_final: 0.8637 (mtp) REVERT: H 6 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7471 (tp) REVERT: H 66 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8978 (tp) REVERT: J 111 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8659 (mtm) REVERT: J 193 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7981 (mmm) REVERT: J 348 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7409 (tp-100) REVERT: L 111 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8230 (mtm) REVERT: L 348 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7538 (tp-100) REVERT: M 6 LEU cc_start: 0.8430 (mp) cc_final: 0.7909 (tt) REVERT: M 66 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (tp) REVERT: N 199 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6448 (p90) REVERT: N 285 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7910 (mtt-85) REVERT: N 290 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8722 (tm-30) REVERT: N 362 ARG cc_start: 0.6901 (ptp-110) cc_final: 0.6243 (mtm180) REVERT: O 11 ILE cc_start: 0.9497 (mm) cc_final: 0.9201 (pp) REVERT: P 290 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8700 (tm-30) REVERT: P 362 ARG cc_start: 0.6697 (ptp-110) cc_final: 0.6065 (mtm180) REVERT: R 285 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7807 (mtt-85) REVERT: R 362 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7318 (mtm-85) REVERT: S 11 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9130 (pp) REVERT: T 288 MET cc_start: 0.9039 (mtt) cc_final: 0.8783 (mtp) REVERT: T 362 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7241 (mtp180) REVERT: T 390 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8273 (mtpt) REVERT: V 11 ILE cc_start: 0.9455 (mm) cc_final: 0.9201 (pp) REVERT: X 323 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7579 (t) REVERT: X 362 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7165 (mtp180) REVERT: X 467 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: Z 194 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: Z 290 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8684 (tm-30) REVERT: Z 362 ARG cc_start: 0.7086 (ptp90) cc_final: 0.6811 (mtm-85) REVERT: AA 11 ILE cc_start: 0.9449 (mm) cc_final: 0.9129 (pp) REVERT: BA 267 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8294 (mpp) REVERT: CA 11 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9051 (pt) outliers start: 111 outliers final: 54 residues processed: 667 average time/residue: 1.2523 time to fit residues: 1129.3450 Evaluate side-chains 665 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 589 time to evaluate : 5.368 ------------------------------------------------------------------------------- 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 271 VAL 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 144 ILE Chi-restraints excluded: chain C residue 326 ASN 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 6 LEU 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 144 ILE 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 111 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 66 ILE 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 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 199 TYR 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 139 SER 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 S residue 11 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 390 LYS Chi-restraints excluded: chain X residue 52 ASP 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 323 VAL Chi-restraints excluded: chain X residue 467 ASN Chi-restraints excluded: chain Z residue 139 SER 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 215 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 0.0770 chunk 328 optimal weight: 4.9990 chunk 491 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 523 optimal weight: 8.9990 chunk 560 optimal weight: 0.6980 chunk 406 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 646 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.8382 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 64820 Z= 0.183 Angle : 0.621 14.366 87612 Z= 0.314 Chirality : 0.045 0.318 10640 Planarity : 0.003 0.044 11396 Dihedral : 7.660 90.939 9637 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.43 % Allowed : 20.13 % Favored : 78.44 % 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: 1.49 (0.09), residues: 8624 helix: 1.89 (0.08), residues: 4228 sheet: 0.22 (0.14), residues: 1386 loop : 0.18 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 7 PHE 0.041 0.002 PHE A 204 TYR 0.009 0.001 TYR E 199 ARG 0.009 0.000 ARG X 322 *********************** 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 717 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 621 time to evaluate : 5.442 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: I 44 PHE cc_start: 0.6180 (p90) cc_final: 0.5872 (p90) REVERT: I 171 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7864 (mmpt) REVERT: I 193 MET cc_start: 0.8595 (mmm) cc_final: 0.8312 (mmm) REVERT: I 322 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7746 (mmm160) REVERT: W 6 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7351 (tp) REVERT: A 267 MET cc_start: 0.8627 (mpt) cc_final: 0.8304 (mpt) REVERT: B 6 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 66 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 193 MET cc_start: 0.8561 (mmm) cc_final: 0.8161 (mmm) REVERT: C 267 MET cc_start: 0.8628 (mpt) cc_final: 0.8328 (mpt) REVERT: C 326 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6948 (p0) REVERT: C 389 MET cc_start: 0.8937 (tpp) cc_final: 0.8544 (tpp) REVERT: E 111 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: E 193 MET cc_start: 0.8349 (mmm) cc_final: 0.8013 (mmm) REVERT: E 195 PHE cc_start: 0.8777 (p90) cc_final: 0.8551 (p90) REVERT: E 267 MET cc_start: 0.8908 (mpt) cc_final: 0.8705 (mpt) REVERT: E 348 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7700 (tp-100) REVERT: E 389 MET cc_start: 0.8941 (tpp) cc_final: 0.8560 (tpp) REVERT: F 6 LEU cc_start: 0.8299 (mp) cc_final: 0.7846 (tt) REVERT: F 66 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8921 (tp) REVERT: G 111 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8083 (mtm) REVERT: G 193 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: G 514 MET cc_start: 0.9080 (mtp) cc_final: 0.8641 (mtp) REVERT: H 6 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7510 (tp) REVERT: H 66 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8913 (tp) REVERT: J 193 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: J 348 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7358 (tp-100) REVERT: J 447 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8832 (mtt) REVERT: J 467 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8736 (m-40) REVERT: K 6 LEU cc_start: 0.8324 (mp) cc_final: 0.7522 (tp) REVERT: L 111 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8277 (mtm) REVERT: L 194 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: L 348 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7576 (tp-100) REVERT: M 6 LEU cc_start: 0.8406 (mp) cc_final: 0.7921 (tt) REVERT: M 66 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8890 (tp) REVERT: N 199 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6398 (p90) REVERT: N 285 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7939 (mtt-85) REVERT: N 290 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8710 (tm-30) REVERT: N 362 ARG cc_start: 0.7021 (ptp-110) cc_final: 0.6297 (mtm180) REVERT: P 290 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8700 (tm-30) REVERT: Q 11 ILE cc_start: 0.9418 (mm) cc_final: 0.9100 (pp) REVERT: R 199 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6391 (p90) REVERT: R 285 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7773 (mtt-85) REVERT: R 322 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.8042 (tpt-90) REVERT: R 362 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7310 (mtm-85) REVERT: S 11 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9077 (pt) REVERT: T 111 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: T 288 MET cc_start: 0.9042 (mtt) cc_final: 0.8781 (mtp) REVERT: T 362 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7214 (mtp180) REVERT: V 11 ILE cc_start: 0.9449 (mm) cc_final: 0.9162 (pp) REVERT: X 362 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7173 (mtp180) REVERT: X 467 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (m110) REVERT: Y 11 ILE cc_start: 0.9183 (mm) cc_final: 0.8734 (pt) REVERT: Z 111 MET cc_start: 0.9148 (mpp) cc_final: 0.8917 (mpp) REVERT: Z 194 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: Z 362 ARG cc_start: 0.7077 (ptp90) cc_final: 0.6823 (mtm-85) REVERT: AA 11 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9104 (pp) REVERT: BA 281 PHE cc_start: 0.7911 (m-10) cc_final: 0.7682 (m-10) outliers start: 96 outliers final: 43 residues processed: 669 average time/residue: 1.2369 time to fit residues: 1130.8616 Evaluate side-chains 671 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 605 time to evaluate : 5.413 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL 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 144 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 360 TYR 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 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 221 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 221 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 447 MET Chi-restraints excluded: chain J residue 467 ASN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 194 GLN 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 199 TYR Chi-restraints excluded: chain P residue 139 SER 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 S residue 11 ILE Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 139 SER 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 X residue 281 PHE Chi-restraints excluded: chain X residue 467 ASN Chi-restraints excluded: chain Z residue 139 SER 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 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.8980 chunk 788 optimal weight: 20.0000 chunk 719 optimal weight: 3.9990 chunk 767 optimal weight: 8.9990 chunk 461 optimal weight: 7.9990 chunk 334 optimal weight: 20.0000 chunk 602 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 693 optimal weight: 30.0000 chunk 725 optimal weight: 0.6980 chunk 764 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 64820 Z= 0.249 Angle : 0.658 14.018 87612 Z= 0.331 Chirality : 0.046 0.269 10640 Planarity : 0.003 0.035 11396 Dihedral : 7.831 85.880 9635 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.40 % Allowed : 20.28 % Favored : 78.32 % 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: 1.41 (0.09), residues: 8624 helix: 1.82 (0.08), residues: 4228 sheet: 0.19 (0.14), residues: 1386 loop : 0.15 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS D 7 PHE 0.045 0.002 PHE I 204 TYR 0.013 0.001 TYR E 199 ARG 0.009 0.001 ARGBA 284 *********************** 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 699 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 605 time to evaluate : 5.602 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: 0.6215 (p90) cc_final: 0.5900 (p90) REVERT: I 52 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8163 (t0) REVERT: I 171 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7903 (mmpt) REVERT: I 193 MET cc_start: 0.8627 (mmm) cc_final: 0.8385 (mmm) REVERT: I 488 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9092 (mmm) REVERT: W 6 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7464 (tp) REVERT: B 6 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7560 (tp) REVERT: B 66 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9043 (tp) REVERT: C 76 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: C 193 MET cc_start: 0.8576 (mmm) cc_final: 0.8124 (tpt) REVERT: C 326 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6718 (p0) REVERT: C 389 MET cc_start: 0.8948 (tpp) cc_final: 0.8597 (tpp) REVERT: E 111 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8018 (mtm) REVERT: E 193 MET cc_start: 0.8318 (mmm) cc_final: 0.8066 (mmm) REVERT: E 195 PHE cc_start: 0.8813 (p90) cc_final: 0.8603 (p90) REVERT: E 348 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7699 (tp-100) REVERT: E 389 MET cc_start: 0.8948 (tpp) cc_final: 0.8643 (tpp) REVERT: F 6 LEU cc_start: 0.8349 (mp) cc_final: 0.7611 (tp) REVERT: F 66 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8982 (tp) REVERT: G 76 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: G 111 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: G 514 MET cc_start: 0.9140 (mtp) cc_final: 0.8719 (mtp) REVERT: H 6 LEU cc_start: 0.8306 (mp) cc_final: 0.7618 (tp) REVERT: H 66 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8917 (tp) REVERT: J 193 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8015 (mmm) REVERT: J 348 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7381 (tp-100) REVERT: K 6 LEU cc_start: 0.8429 (mp) cc_final: 0.7531 (tp) REVERT: L 111 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8164 (mtm) REVERT: L 348 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7521 (tp-100) REVERT: M 6 LEU cc_start: 0.8384 (mp) cc_final: 0.7667 (tp) REVERT: M 66 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8843 (tp) REVERT: N 199 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6575 (p90) REVERT: N 285 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7918 (mtt-85) REVERT: N 290 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8718 (tm-30) REVERT: N 362 ARG cc_start: 0.6974 (ptp-110) cc_final: 0.6315 (mtm180) REVERT: P 290 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8714 (tm-30) REVERT: Q 11 ILE cc_start: 0.9408 (mm) cc_final: 0.9103 (pp) REVERT: R 199 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6476 (p90) REVERT: R 322 ARG cc_start: 0.8274 (tpt-90) cc_final: 0.8071 (tpt-90) REVERT: T 111 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: T 288 MET cc_start: 0.9038 (mtt) cc_final: 0.8753 (mtp) REVERT: T 390 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8313 (mtpt) REVERT: V 11 ILE cc_start: 0.9421 (mm) cc_final: 0.9112 (pp) REVERT: X 362 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7292 (mtp180) REVERT: X 467 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: Z 194 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7622 (tp40) REVERT: Z 290 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8684 (tm-30) REVERT: Z 362 ARG cc_start: 0.7103 (ptp90) cc_final: 0.6843 (mtm-85) REVERT: AA 11 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9080 (pt) REVERT: BA 267 MET cc_start: 0.8400 (mpp) cc_final: 0.7847 (pmm) outliers start: 94 outliers final: 56 residues processed: 662 average time/residue: 1.2726 time to fit residues: 1141.4018 Evaluate side-chains 671 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 593 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 488 MET 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 271 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL 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 221 LEU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 360 TYR 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 G residue 213 VAL Chi-restraints excluded: chain G residue 221 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 221 LEU Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain K residue 66 ILE 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 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 199 TYR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain R residue 139 SER 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 T residue 111 MET Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 144 ILE 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 X residue 467 ASN Chi-restraints excluded: chain Z residue 139 SER 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 227 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: 2.9990 chunk 495 optimal weight: 0.6980 chunk 384 optimal weight: 5.9990 chunk 563 optimal weight: 5.9990 chunk 850 optimal weight: 0.3980 chunk 783 optimal weight: 5.9990 chunk 677 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 523 optimal weight: 10.0000 chunk 415 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 64820 Z= 0.202 Angle : 0.669 15.043 87612 Z= 0.334 Chirality : 0.046 0.260 10640 Planarity : 0.003 0.034 11396 Dihedral : 7.646 80.334 9632 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.21 % Allowed : 20.70 % Favored : 78.10 % 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: 1.44 (0.09), residues: 8624 helix: 1.87 (0.08), residues: 4228 sheet: 0.18 (0.14), residues: 1400 loop : 0.14 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS D 7 PHE 0.040 0.002 PHE L 204 TYR 0.015 0.001 TYR E 199 ARG 0.009 0.000 ARG N 322 ********************** 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 703 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 622 time to evaluate : 5.420 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: 0.6202 (p90) cc_final: 0.5895 (p90) REVERT: I 52 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8088 (t0) REVERT: I 171 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7875 (mmpt) REVERT: I 193 MET cc_start: 0.8596 (mmm) cc_final: 0.8360 (mmm) REVERT: I 322 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7857 (mmm160) REVERT: W 6 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7479 (tp) REVERT: B 6 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7605 (tp) REVERT: B 66 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9052 (tp) REVERT: C 193 MET cc_start: 0.8608 (mmm) cc_final: 0.8119 (tpt) REVERT: C 326 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6867 (p0) REVERT: C 362 ARG cc_start: 0.6981 (ptp-110) cc_final: 0.6762 (ptp-110) REVERT: C 389 MET cc_start: 0.8929 (tpp) cc_final: 0.8534 (tpp) REVERT: E 111 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8018 (mtm) REVERT: E 193 MET cc_start: 0.8421 (mmm) cc_final: 0.8126 (mmm) REVERT: E 195 PHE cc_start: 0.8806 (p90) cc_final: 0.8595 (p90) REVERT: E 348 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7688 (tp-100) REVERT: E 362 ARG cc_start: 0.6824 (ptp-110) cc_final: 0.6589 (ptp-110) REVERT: E 389 MET cc_start: 0.8935 (tpp) cc_final: 0.8551 (tpp) REVERT: F 6 LEU cc_start: 0.8270 (mp) cc_final: 0.7607 (tp) REVERT: F 66 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9033 (tp) REVERT: G 111 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8067 (mtm) REVERT: G 193 MET cc_start: 0.8238 (mmt) cc_final: 0.7977 (mmm) REVERT: G 514 MET cc_start: 0.9108 (mtp) cc_final: 0.8700 (mtp) REVERT: H 6 LEU cc_start: 0.8246 (mp) cc_final: 0.7682 (tp) REVERT: H 66 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8946 (tp) REVERT: J 193 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: J 322 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7502 (mmm160) REVERT: J 327 LYS cc_start: 0.9082 (tptp) cc_final: 0.8868 (tppt) REVERT: J 348 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7338 (tp-100) REVERT: K 6 LEU cc_start: 0.8411 (mp) cc_final: 0.7604 (tp) REVERT: L 194 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: L 348 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7519 (tp-100) REVERT: M 6 LEU cc_start: 0.8380 (mp) cc_final: 0.7724 (tp) REVERT: M 66 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8849 (tp) REVERT: N 285 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7899 (mtt-85) REVERT: N 290 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8710 (tm-30) REVERT: P 290 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8717 (tm-30) REVERT: Q 11 ILE cc_start: 0.9393 (mm) cc_final: 0.9160 (pp) REVERT: R 199 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6485 (p90) REVERT: R 322 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.8086 (tpt-90) REVERT: R 362 ARG cc_start: 0.6389 (mtm-85) cc_final: 0.6055 (mtp180) REVERT: R 390 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8082 (mtpt) REVERT: T 111 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8246 (mtt) REVERT: T 288 MET cc_start: 0.9050 (mtt) cc_final: 0.8765 (mtp) REVERT: X 322 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7713 (tpp80) REVERT: X 362 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7296 (mtp180) REVERT: X 467 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: Z 194 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7547 (tp40) REVERT: Z 290 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8677 (tm-30) REVERT: AA 11 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9087 (pt) REVERT: BA 267 MET cc_start: 0.8397 (mpp) cc_final: 0.7855 (pmm) REVERT: BA 467 ASN cc_start: 0.8803 (m-40) cc_final: 0.8491 (m110) outliers start: 81 outliers final: 50 residues processed: 668 average time/residue: 1.2668 time to fit residues: 1145.5613 Evaluate side-chains 675 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 607 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP 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 271 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL 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 144 ILE Chi-restraints excluded: chain C residue 326 ASN 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 E residue 491 MET 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 144 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 221 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 221 LEU Chi-restraints excluded: chain J residue 248 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 194 GLN 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 273 VAL Chi-restraints excluded: chain P residue 139 SER 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 390 LYS Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 139 SER 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 X residue 301 ILE Chi-restraints excluded: chain X residue 467 ASN 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 215 LEU 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 139 SER 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: 0.7980 chunk 721 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 624 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 678 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 696 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.171047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108396 restraints weight = 96356.118| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.62 r_work: 0.3165 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 64820 Z= 0.208 Angle : 0.672 14.145 87612 Z= 0.336 Chirality : 0.046 0.294 10640 Planarity : 0.003 0.045 11396 Dihedral : 7.562 77.341 9632 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.28 % Allowed : 20.98 % Favored : 77.74 % 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: 1.87 (0.08), residues: 4228 sheet: 0.20 (0.14), residues: 1400 loop : 0.14 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS D 7 PHE 0.046 0.002 PHE G 204 TYR 0.011 0.001 TYR E 199 ARG 0.011 0.000 ARG G 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20393.10 seconds wall clock time: 350 minutes 38.17 seconds (21038.17 seconds total)