Starting phenix.real_space_refine on Thu Sep 26 13:34:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/09_2024/8hrg_34972.cif" } resolution = 4.5 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= 0.179 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 38472 2.51 5 N 9996 2.21 5 O 12537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61173 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T Time building chain proxies: 10.81, per 1000 atoms: 0.18 Number of scatterers: 61173 At special positions: 0 Unit cell: (124.6, 123.2, 316.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 12537 8.00 N 9996 7.00 C 38472 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: 11.08 Conformation dependent library (CDL) restraints added in 6.2 seconds 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14616 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 105 sheets defined 13.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 192 through 200 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 192 through 200 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU G 287 " --> pdb=" O LEU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'H' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'I' and resid 91 through 100 Processing helix chain 'I' and resid 192 through 200 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU I 287 " --> pdb=" O LEU I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'J' and resid 91 through 100 Processing helix chain 'J' and resid 192 through 200 Processing helix chain 'J' and resid 205 through 209 Processing helix chain 'J' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU J 287 " --> pdb=" O LEU J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 369 Processing helix chain 'K' and resid 91 through 100 Processing helix chain 'K' and resid 192 through 200 Processing helix chain 'K' and resid 205 through 209 Processing helix chain 'K' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU K 287 " --> pdb=" O LEU K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 369 Processing helix chain 'L' and resid 91 through 100 Processing helix chain 'L' and resid 192 through 200 Processing helix chain 'L' and resid 205 through 209 Processing helix chain 'L' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU L 287 " --> pdb=" O LEU L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 369 Processing helix chain 'M' and resid 91 through 100 Processing helix chain 'M' and resid 192 through 200 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 369 Processing helix chain 'N' and resid 91 through 100 Processing helix chain 'N' and resid 192 through 200 Processing helix chain 'N' and resid 205 through 209 Processing helix chain 'N' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 369 Processing helix chain 'O' and resid 91 through 100 Processing helix chain 'O' and resid 192 through 200 Processing helix chain 'O' and resid 205 through 209 Processing helix chain 'O' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU O 287 " --> pdb=" O LEU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 369 Processing helix chain 'P' and resid 91 through 100 Processing helix chain 'P' and resid 192 through 200 Processing helix chain 'P' and resid 205 through 209 Processing helix chain 'P' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU P 287 " --> pdb=" O LEU P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 369 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 192 through 200 Processing helix chain 'Q' and resid 205 through 209 Processing helix chain 'Q' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU Q 287 " --> pdb=" O LEU Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 358 through 369 Processing helix chain 'R' and resid 91 through 100 Processing helix chain 'R' and resid 192 through 200 Processing helix chain 'R' and resid 205 through 209 Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU R 287 " --> pdb=" O LEU R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 369 Processing helix chain 'S' and resid 91 through 100 Processing helix chain 'S' and resid 192 through 200 Processing helix chain 'S' and resid 205 through 209 Processing helix chain 'S' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU S 287 " --> pdb=" O LEU S 283 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 369 Processing helix chain 'T' and resid 91 through 100 Processing helix chain 'T' and resid 192 through 200 Processing helix chain 'T' and resid 205 through 209 Processing helix chain 'T' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU T 287 " --> pdb=" O LEU T 283 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 369 Processing helix chain 'U' and resid 91 through 100 Processing helix chain 'U' and resid 192 through 200 Processing helix chain 'U' and resid 205 through 209 Processing helix chain 'U' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU U 287 " --> pdb=" O LEU U 283 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 369 Processing sheet with id=1, first strand: chain 'D' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER D 170 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 155 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR D 168 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL D 157 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG D 166 " --> pdb=" O VAL D 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 331 through 337 Processing sheet with id=2, first strand: chain 'D' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS D 86 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG D 307 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE D 213 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 222 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY D 253 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER A 170 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 155 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 168 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 157 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 166 " --> pdb=" O VAL A 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 331 through 337 Processing sheet with id=7, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER A 64 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A 43 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN A 62 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS A 86 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG A 307 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 213 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 222 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY A 253 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER B 170 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 155 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B 168 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL B 157 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG B 166 " --> pdb=" O VAL B 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 331 through 337 Processing sheet with id=12, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER B 64 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR B 43 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 62 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS B 86 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG B 307 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 213 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 222 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY B 253 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER C 170 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 155 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 168 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL C 157 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG C 166 " --> pdb=" O VAL C 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 331 through 337 Processing sheet with id=17, first strand: chain 'C' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER C 64 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR C 43 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN C 62 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS C 86 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG C 307 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 213 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 222 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY C 253 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER E 170 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA E 155 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR E 168 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL E 157 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG E 166 " --> pdb=" O VAL E 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 331 through 337 Processing sheet with id=22, first strand: chain 'E' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS E 86 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG E 307 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 213 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR E 222 " --> pdb=" O ILE E 213 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 237 through 240 removed outlier: 4.037A pdb=" N GLY E 253 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER F 170 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F 155 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR F 168 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL F 157 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG F 166 " --> pdb=" O VAL F 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 331 through 337 Processing sheet with id=27, first strand: chain 'F' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS F 86 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'F' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG F 307 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE F 213 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 222 " --> pdb=" O ILE F 213 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY F 253 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER G 170 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA G 155 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR G 168 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL G 157 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG G 166 " --> pdb=" O VAL G 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 268 current: chain 'G' and resid 331 through 337 Processing sheet with id=32, first strand: chain 'G' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER G 64 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR G 43 " --> pdb=" O ASN G 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN G 62 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS G 86 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG G 307 " --> pdb=" O LYS G 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE G 213 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 222 " --> pdb=" O ILE G 213 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'G' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'H' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 75 current: chain 'H' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER H 170 " --> pdb=" O ASN H 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA H 155 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR H 168 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL H 157 " --> pdb=" O ARG H 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 260 through 268 current: chain 'H' and resid 331 through 337 Processing sheet with id=37, first strand: chain 'H' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER H 64 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR H 43 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN H 62 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS H 86 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG H 307 " --> pdb=" O LYS H 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE H 213 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 222 " --> pdb=" O ILE H 213 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'H' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY H 253 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 27 current: chain 'I' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 75 current: chain 'I' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER I 170 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA I 155 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR I 168 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL I 157 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG I 166 " --> pdb=" O VAL I 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 268 current: chain 'I' and resid 331 through 337 Processing sheet with id=42, first strand: chain 'I' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER I 64 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR I 43 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN I 62 " --> pdb=" O THR I 43 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS I 86 " --> pdb=" O ASP I 81 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG I 307 " --> pdb=" O LYS I 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE I 213 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR I 222 " --> pdb=" O ILE I 213 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'I' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'J' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 27 current: chain 'J' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 68 through 75 current: chain 'J' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER J 170 " --> pdb=" O ASN J 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA J 155 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR J 168 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL J 157 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG J 166 " --> pdb=" O VAL J 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 166 through 173 current: chain 'J' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 260 through 268 current: chain 'J' and resid 331 through 337 Processing sheet with id=47, first strand: chain 'J' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER J 64 " --> pdb=" O ASN J 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 43 " --> pdb=" O ASN J 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN J 62 " --> pdb=" O THR J 43 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS J 86 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'J' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG J 307 " --> pdb=" O LYS J 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE J 213 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR J 222 " --> pdb=" O ILE J 213 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'J' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY J 253 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'K' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 27 current: chain 'K' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 68 through 75 current: chain 'K' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER K 170 " --> pdb=" O ASN K 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA K 155 " --> pdb=" O THR K 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR K 168 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL K 157 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG K 166 " --> pdb=" O VAL K 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 166 through 173 current: chain 'K' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 260 through 268 current: chain 'K' and resid 331 through 337 Processing sheet with id=52, first strand: chain 'K' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER K 64 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR K 43 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN K 62 " --> pdb=" O THR K 43 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'K' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS K 86 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG K 307 " --> pdb=" O LYS K 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE K 213 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR K 222 " --> pdb=" O ILE K 213 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'K' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY K 253 " --> pdb=" O LEU K 240 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'L' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 27 current: chain 'L' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 68 through 75 current: chain 'L' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER L 170 " --> pdb=" O ASN L 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA L 155 " --> pdb=" O THR L 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR L 168 " --> pdb=" O ALA L 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL L 157 " --> pdb=" O ARG L 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG L 166 " --> pdb=" O VAL L 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 166 through 173 current: chain 'L' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 260 through 268 current: chain 'L' and resid 331 through 337 Processing sheet with id=57, first strand: chain 'L' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER L 64 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR L 43 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN L 62 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'L' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS L 86 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'L' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG L 307 " --> pdb=" O LYS L 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE L 213 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 222 " --> pdb=" O ILE L 213 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'L' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY L 253 " --> pdb=" O LEU L 240 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'M' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 25 through 27 current: chain 'M' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 75 current: chain 'M' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER M 170 " --> pdb=" O ASN M 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 155 " --> pdb=" O THR M 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR M 168 " --> pdb=" O ALA M 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL M 157 " --> pdb=" O ARG M 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG M 166 " --> pdb=" O VAL M 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 166 through 173 current: chain 'M' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 260 through 268 current: chain 'M' and resid 331 through 337 Processing sheet with id=62, first strand: chain 'M' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER M 64 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR M 43 " --> pdb=" O ASN M 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN M 62 " --> pdb=" O THR M 43 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'M' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS M 86 " --> pdb=" O ASP M 81 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'M' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG M 307 " --> pdb=" O LYS M 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE M 213 " --> pdb=" O TYR M 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR M 222 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'M' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY M 253 " --> pdb=" O LEU M 240 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'N' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 25 through 27 current: chain 'N' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 68 through 75 current: chain 'N' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER N 170 " --> pdb=" O ASN N 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA N 155 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR N 168 " --> pdb=" O ALA N 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL N 157 " --> pdb=" O ARG N 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG N 166 " --> pdb=" O VAL N 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 166 through 173 current: chain 'N' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 260 through 268 current: chain 'N' and resid 331 through 337 Processing sheet with id=67, first strand: chain 'N' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER N 64 " --> pdb=" O ASN N 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR N 43 " --> pdb=" O ASN N 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN N 62 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.684A pdb=" N LYS N 86 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'N' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG N 307 " --> pdb=" O LYS N 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE N 213 " --> pdb=" O TYR N 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR N 222 " --> pdb=" O ILE N 213 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'N' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY N 253 " --> pdb=" O LEU N 240 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'O' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 27 current: chain 'O' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 68 through 75 current: chain 'O' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER O 170 " --> pdb=" O ASN O 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA O 155 " --> pdb=" O THR O 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR O 168 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL O 157 " --> pdb=" O ARG O 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG O 166 " --> pdb=" O VAL O 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 166 through 173 current: chain 'O' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 260 through 268 current: chain 'O' and resid 331 through 337 Processing sheet with id=72, first strand: chain 'O' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER O 64 " --> pdb=" O ASN O 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR O 43 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN O 62 " --> pdb=" O THR O 43 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'O' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS O 86 " --> pdb=" O ASP O 81 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'O' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG O 307 " --> pdb=" O LYS O 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE O 213 " --> pdb=" O TYR O 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR O 222 " --> pdb=" O ILE O 213 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'O' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY O 253 " --> pdb=" O LEU O 240 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'P' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 25 through 27 current: chain 'P' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 68 through 75 current: chain 'P' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER P 170 " --> pdb=" O ASN P 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA P 155 " --> pdb=" O THR P 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR P 168 " --> pdb=" O ALA P 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL P 157 " --> pdb=" O ARG P 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG P 166 " --> pdb=" O VAL P 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 166 through 173 current: chain 'P' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 260 through 268 current: chain 'P' and resid 331 through 337 Processing sheet with id=77, first strand: chain 'P' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER P 64 " --> pdb=" O ASN P 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR P 43 " --> pdb=" O ASN P 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN P 62 " --> pdb=" O THR P 43 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'P' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS P 86 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'P' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG P 307 " --> pdb=" O LYS P 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE P 213 " --> pdb=" O TYR P 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR P 222 " --> pdb=" O ILE P 213 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'P' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY P 253 " --> pdb=" O LEU P 240 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'Q' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 25 through 27 current: chain 'Q' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 68 through 75 current: chain 'Q' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER Q 170 " --> pdb=" O ASN Q 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA Q 155 " --> pdb=" O THR Q 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR Q 168 " --> pdb=" O ALA Q 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL Q 157 " --> pdb=" O ARG Q 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG Q 166 " --> pdb=" O VAL Q 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 166 through 173 current: chain 'Q' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 260 through 268 current: chain 'Q' and resid 331 through 337 Processing sheet with id=82, first strand: chain 'Q' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER Q 64 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR Q 43 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN Q 62 " --> pdb=" O THR Q 43 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'Q' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS Q 86 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'Q' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG Q 307 " --> pdb=" O LYS Q 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE Q 213 " --> pdb=" O TYR Q 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR Q 222 " --> pdb=" O ILE Q 213 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'Q' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY Q 253 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'R' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 25 through 27 current: chain 'R' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 68 through 75 current: chain 'R' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER R 170 " --> pdb=" O ASN R 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA R 155 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR R 168 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL R 157 " --> pdb=" O ARG R 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG R 166 " --> pdb=" O VAL R 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 166 through 173 current: chain 'R' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 260 through 268 current: chain 'R' and resid 331 through 337 Processing sheet with id=87, first strand: chain 'R' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER R 64 " --> pdb=" O ASN R 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR R 43 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN R 62 " --> pdb=" O THR R 43 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS R 86 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'R' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG R 307 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE R 213 " --> pdb=" O TYR R 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR R 222 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'R' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY R 253 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'S' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 25 through 27 current: chain 'S' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 68 through 75 current: chain 'S' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER S 170 " --> pdb=" O ASN S 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA S 155 " --> pdb=" O THR S 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR S 168 " --> pdb=" O ALA S 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL S 157 " --> pdb=" O ARG S 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG S 166 " --> pdb=" O VAL S 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 166 through 173 current: chain 'S' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 260 through 268 current: chain 'S' and resid 331 through 337 Processing sheet with id=92, first strand: chain 'S' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER S 64 " --> pdb=" O ASN S 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR S 43 " --> pdb=" O ASN S 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN S 62 " --> pdb=" O THR S 43 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'S' and resid 79 through 81 removed outlier: 3.684A pdb=" N LYS S 86 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain 'S' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG S 307 " --> pdb=" O LYS S 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE S 213 " --> pdb=" O TYR S 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR S 222 " --> pdb=" O ILE S 213 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'S' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY S 253 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'T' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 25 through 27 current: chain 'T' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 68 through 75 current: chain 'T' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER T 170 " --> pdb=" O ASN T 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA T 155 " --> pdb=" O THR T 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR T 168 " --> pdb=" O ALA T 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL T 157 " --> pdb=" O ARG T 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG T 166 " --> pdb=" O VAL T 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 166 through 173 current: chain 'T' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 260 through 268 current: chain 'T' and resid 331 through 337 Processing sheet with id=97, first strand: chain 'T' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER T 64 " --> pdb=" O ASN T 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR T 43 " --> pdb=" O ASN T 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN T 62 " --> pdb=" O THR T 43 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain 'T' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS T 86 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'T' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG T 307 " --> pdb=" O LYS T 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE T 213 " --> pdb=" O TYR T 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR T 222 " --> pdb=" O ILE T 213 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'T' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY T 253 " --> pdb=" O LEU T 240 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'U' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 25 through 27 current: chain 'U' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 68 through 75 current: chain 'U' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER U 170 " --> pdb=" O ASN U 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA U 155 " --> pdb=" O THR U 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR U 168 " --> pdb=" O ALA U 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL U 157 " --> pdb=" O ARG U 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG U 166 " --> pdb=" O VAL U 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 173 current: chain 'U' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 260 through 268 current: chain 'U' and resid 331 through 337 Processing sheet with id=102, first strand: chain 'U' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER U 64 " --> pdb=" O ASN U 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR U 43 " --> pdb=" O ASN U 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN U 62 " --> pdb=" O THR U 43 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'U' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS U 86 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'U' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG U 307 " --> pdb=" O LYS U 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE U 213 " --> pdb=" O TYR U 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR U 222 " --> pdb=" O ILE U 213 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'U' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY U 253 " --> pdb=" O LEU U 240 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3654 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: 25.21 Time building geometry restraints manager: 13.36 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: 20433 1.34 - 1.46: 14018 1.46 - 1.58: 27604 1.58 - 1.70: 0 1.70 - 1.81: 315 Bond restraints: 62370 Sorted by residual: bond pdb=" CA ILE G 250 " pdb=" C ILE G 250 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.05e-02 9.07e+03 1.31e+00 bond pdb=" CA ILE I 250 " pdb=" C ILE I 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.29e+00 bond pdb=" CA ILE S 250 " pdb=" C ILE S 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.27e+00 bond pdb=" CA ILE J 250 " pdb=" C ILE J 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.23e+00 bond pdb=" CA ILE A 250 " pdb=" C ILE A 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.23e+00 ... (remaining 62365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 77856 1.19 - 2.37: 5809 2.37 - 3.56: 1133 3.56 - 4.75: 210 4.75 - 5.94: 42 Bond angle restraints: 85050 Sorted by residual: angle pdb=" C LEU P 351 " pdb=" N GLY P 352 " pdb=" CA GLY P 352 " ideal model delta sigma weight residual 121.65 119.55 2.10 6.80e-01 2.16e+00 9.52e+00 angle pdb=" C LEU K 351 " pdb=" N GLY K 352 " pdb=" CA GLY K 352 " ideal model delta sigma weight residual 121.65 119.56 2.09 6.80e-01 2.16e+00 9.48e+00 angle pdb=" C LEU Q 351 " pdb=" N GLY Q 352 " pdb=" CA GLY Q 352 " ideal model delta sigma weight residual 121.65 119.56 2.09 6.80e-01 2.16e+00 9.40e+00 angle pdb=" C LEU F 351 " pdb=" N GLY F 352 " pdb=" CA GLY F 352 " ideal model delta sigma weight residual 121.65 119.57 2.08 6.80e-01 2.16e+00 9.38e+00 angle pdb=" C LEU I 351 " pdb=" N GLY I 352 " pdb=" CA GLY I 352 " ideal model delta sigma weight residual 121.65 119.57 2.08 6.80e-01 2.16e+00 9.36e+00 ... (remaining 85045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 33028 14.16 - 28.31: 3033 28.31 - 42.47: 815 42.47 - 56.62: 215 56.62 - 70.78: 37 Dihedral angle restraints: 37128 sinusoidal: 14364 harmonic: 22764 Sorted by residual: dihedral pdb=" CA ARG N 56 " pdb=" C ARG N 56 " pdb=" N GLY N 57 " pdb=" CA GLY N 57 " ideal model delta harmonic sigma weight residual 180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ARG U 56 " pdb=" C ARG U 56 " pdb=" N GLY U 57 " pdb=" CA GLY U 57 " ideal model delta harmonic sigma weight residual -180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ARG B 56 " pdb=" C ARG B 56 " pdb=" N GLY B 57 " pdb=" CA GLY B 57 " ideal model delta harmonic sigma weight residual -180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 ... (remaining 37125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7347 0.048 - 0.096: 2072 0.096 - 0.143: 430 0.143 - 0.191: 0 0.191 - 0.239: 21 Chirality restraints: 9870 Sorted by residual: chirality pdb=" CB ILE G 199 " pdb=" CA ILE G 199 " pdb=" CG1 ILE G 199 " pdb=" CG2 ILE G 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE U 199 " pdb=" CA ILE U 199 " pdb=" CG1 ILE U 199 " pdb=" CG2 ILE U 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE E 199 " pdb=" CA ILE E 199 " pdb=" CG1 ILE E 199 " pdb=" CG2 ILE E 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 9867 not shown) Planarity restraints: 11088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 92 " 0.013 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR J 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR J 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR J 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 92 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR J 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 92 " 0.013 2.00e-02 2.50e+03 1.17e-02 2.73e+00 pdb=" CG TYR Q 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 92 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR Q 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 92 " -0.013 2.00e-02 2.50e+03 1.17e-02 2.72e+00 pdb=" CG TYR N 92 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR N 92 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR N 92 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR N 92 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 92 " 0.002 2.00e-02 2.50e+03 ... (remaining 11085 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1736 2.68 - 3.24: 62418 3.24 - 3.79: 97067 3.79 - 4.35: 121805 4.35 - 4.90: 200026 Nonbonded interactions: 483052 Sorted by model distance: nonbonded pdb=" O ALA F 127 " pdb=" NH2 ARG M 53 " model vdw 2.127 3.120 nonbonded pdb=" O ALA G 127 " pdb=" NH2 ARG N 53 " model vdw 2.127 3.120 nonbonded pdb=" NH2 ARG F 53 " pdb=" O ALA T 127 " model vdw 2.127 3.120 nonbonded pdb=" O ALA K 127 " pdb=" NH2 ARG R 53 " model vdw 2.127 3.120 nonbonded pdb=" NH2 ARG D 53 " pdb=" O ALA R 127 " model vdw 2.127 3.120 ... (remaining 483047 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.050 Extract box with map and model: 1.650 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 91.900 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.035 62370 Z= 0.215 Angle : 0.702 5.937 85050 Z= 0.415 Chirality : 0.045 0.239 9870 Planarity : 0.004 0.040 11088 Dihedral : 12.326 70.779 22512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.99 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.09), residues: 7812 helix: 1.54 (0.17), residues: 861 sheet: 0.80 (0.11), residues: 2604 loop : -1.89 (0.08), residues: 4347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 70 HIS 0.002 0.001 HIS P 129 PHE 0.025 0.002 PHE S 353 TYR 0.027 0.002 TYR J 92 ARG 0.008 0.001 ARG N 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.250 Fit side-chains REVERT: A 216 MET cc_start: 0.8878 (mmm) cc_final: 0.8571 (mmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1751 time to fit residues: 5.5285 Evaluate side-chains 20 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 656 optimal weight: 6.9990 chunk 588 optimal weight: 5.9990 chunk 326 optimal weight: 0.0270 chunk 201 optimal weight: 0.3980 chunk 397 optimal weight: 6.9990 chunk 314 optimal weight: 0.0970 chunk 609 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 453 optimal weight: 0.9990 chunk 705 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 62370 Z= 0.142 Angle : 0.550 8.264 85050 Z= 0.294 Chirality : 0.045 0.164 9870 Planarity : 0.004 0.036 11088 Dihedral : 5.336 20.971 8358 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -0.58 (0.09), residues: 7812 helix: 1.30 (0.17), residues: 840 sheet: 1.11 (0.11), residues: 2457 loop : -1.70 (0.08), residues: 4515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 70 HIS 0.002 0.001 HIS T 129 PHE 0.012 0.001 PHE P 231 TYR 0.012 0.001 TYR O 268 ARG 0.006 0.001 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.252 Fit side-chains REVERT: I 197 MET cc_start: 0.9411 (tpp) cc_final: 0.8965 (tpp) REVERT: I 216 MET cc_start: 0.8383 (mmm) cc_final: 0.7530 (mmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1315 time to fit residues: 4.3275 Evaluate side-chains 23 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 392 optimal weight: 0.0000 chunk 218 optimal weight: 8.9990 chunk 587 optimal weight: 3.9990 chunk 480 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 706 optimal weight: 0.6980 chunk 763 optimal weight: 0.1980 chunk 629 optimal weight: 9.9990 chunk 700 optimal weight: 0.1980 chunk 240 optimal weight: 0.0670 chunk 567 optimal weight: 8.9990 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 62370 Z= 0.129 Angle : 0.522 6.755 85050 Z= 0.280 Chirality : 0.044 0.145 9870 Planarity : 0.004 0.038 11088 Dihedral : 5.017 18.884 8358 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.57 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -0.88 (0.09), residues: 7812 helix: 1.34 (0.17), residues: 840 sheet: 0.62 (0.11), residues: 2499 loop : -1.79 (0.08), residues: 4473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 144 HIS 0.002 0.001 HIS J 96 PHE 0.012 0.001 PHE Q 231 TYR 0.010 0.001 TYR K 268 ARG 0.004 0.001 ARG S 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.256 Fit side-chains REVERT: P 5 LEU cc_start: 0.8495 (mt) cc_final: 0.7996 (tt) REVERT: P 6 LEU cc_start: 0.8749 (tp) cc_final: 0.7914 (mp) REVERT: P 163 ASP cc_start: 0.7678 (t0) cc_final: 0.7343 (t0) REVERT: P 216 MET cc_start: 0.8931 (mmm) cc_final: 0.8553 (mmm) REVERT: P 347 ASP cc_start: 0.8737 (t70) cc_final: 0.8203 (m-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1520 time to fit residues: 5.9047 Evaluate side-chains 25 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 698 optimal weight: 20.0000 chunk 531 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 337 optimal weight: 5.9990 chunk 474 optimal weight: 7.9990 chunk 709 optimal weight: 4.9990 chunk 751 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 672 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 62370 Z= 0.200 Angle : 0.547 6.970 85050 Z= 0.292 Chirality : 0.043 0.165 9870 Planarity : 0.004 0.037 11088 Dihedral : 5.048 20.027 8358 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -1.03 (0.09), residues: 7812 helix: 1.25 (0.17), residues: 882 sheet: 0.49 (0.11), residues: 2646 loop : -1.98 (0.08), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 144 HIS 0.002 0.001 HIS G 318 PHE 0.009 0.001 PHE B 259 TYR 0.007 0.001 TYR Q 92 ARG 0.010 0.001 ARG M 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: I 6 LEU cc_start: 0.8697 (tp) cc_final: 0.7955 (mp) REVERT: I 197 MET cc_start: 0.9197 (tpp) cc_final: 0.8887 (tpp) REVERT: I 269 LEU cc_start: 0.8445 (mm) cc_final: 0.8226 (tp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0998 time to fit residues: 3.5100 Evaluate side-chains 19 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 625 optimal weight: 5.9990 chunk 426 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 559 optimal weight: 0.7980 chunk 309 optimal weight: 8.9990 chunk 640 optimal weight: 2.9990 chunk 519 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 383 optimal weight: 6.9990 chunk 674 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 62370 Z= 0.171 Angle : 0.514 5.804 85050 Z= 0.278 Chirality : 0.043 0.149 9870 Planarity : 0.004 0.037 11088 Dihedral : 4.874 19.192 8358 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.31 % Allowed : 2.15 % Favored : 97.54 % 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: -0.97 (0.09), residues: 7812 helix: 1.52 (0.17), residues: 882 sheet: 0.39 (0.11), residues: 2646 loop : -1.90 (0.08), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 70 HIS 0.002 0.001 HIS B 318 PHE 0.018 0.001 PHE B 259 TYR 0.013 0.001 TYR S 92 ARG 0.008 0.001 ARG T 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.262 Fit side-chains REVERT: J 5 LEU cc_start: 0.8985 (mt) cc_final: 0.8419 (tt) REVERT: J 6 LEU cc_start: 0.8514 (tp) cc_final: 0.8214 (mm) REVERT: J 163 ASP cc_start: 0.7344 (t0) cc_final: 0.7139 (t0) REVERT: J 197 MET cc_start: 0.9159 (tpp) cc_final: 0.8943 (tpp) REVERT: J 216 MET cc_start: 0.9050 (mmp) cc_final: 0.8758 (mmm) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1267 time to fit residues: 4.6982 Evaluate side-chains 18 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 252 optimal weight: 10.0000 chunk 676 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 440 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 751 optimal weight: 5.9990 chunk 624 optimal weight: 0.0040 chunk 348 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 248 optimal weight: 0.2980 chunk 394 optimal weight: 4.9990 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 62370 Z= 0.156 Angle : 0.520 6.566 85050 Z= 0.278 Chirality : 0.043 0.134 9870 Planarity : 0.005 0.069 11088 Dihedral : 4.876 18.685 8358 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.94 (0.09), residues: 7812 helix: 1.70 (0.17), residues: 882 sheet: 0.32 (0.11), residues: 2646 loop : -1.85 (0.08), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 70 HIS 0.002 0.001 HIS K 318 PHE 0.007 0.001 PHE S 231 TYR 0.028 0.001 TYR O 92 ARG 0.009 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.249 Fit side-chains REVERT: J 5 LEU cc_start: 0.8985 (mt) cc_final: 0.8403 (tt) REVERT: J 6 LEU cc_start: 0.8460 (tp) cc_final: 0.8241 (mm) REVERT: J 163 ASP cc_start: 0.7345 (t0) cc_final: 0.7129 (t0) REVERT: J 197 MET cc_start: 0.9196 (tpp) cc_final: 0.8993 (tpp) REVERT: J 269 LEU cc_start: 0.8710 (mm) cc_final: 0.8277 (tp) REVERT: J 351 LEU cc_start: 0.9609 (mt) cc_final: 0.9323 (mt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1358 time to fit residues: 5.3773 Evaluate side-chains 20 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 724 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 428 optimal weight: 9.9990 chunk 548 optimal weight: 0.0370 chunk 425 optimal weight: 7.9990 chunk 632 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 748 optimal weight: 0.9990 chunk 468 optimal weight: 0.0000 chunk 456 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 overall best weight: 1.1466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 62370 Z= 0.123 Angle : 0.520 6.264 85050 Z= 0.275 Chirality : 0.043 0.136 9870 Planarity : 0.003 0.036 11088 Dihedral : 4.681 18.493 8358 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.87 (0.09), residues: 7812 helix: 1.64 (0.17), residues: 882 sheet: 0.32 (0.11), residues: 2646 loop : -1.73 (0.09), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 70 HIS 0.001 0.001 HIS J 96 PHE 0.008 0.001 PHE S 123 TYR 0.025 0.001 TYR N 92 ARG 0.008 0.001 ARG H 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.248 Fit side-chains REVERT: J 5 LEU cc_start: 0.8953 (mt) cc_final: 0.8378 (tt) REVERT: J 163 ASP cc_start: 0.7344 (t0) cc_final: 0.7120 (t0) REVERT: J 197 MET cc_start: 0.9193 (tpp) cc_final: 0.8985 (tpp) REVERT: J 269 LEU cc_start: 0.8621 (mm) cc_final: 0.8348 (tp) REVERT: J 351 LEU cc_start: 0.9584 (mt) cc_final: 0.9296 (mt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0957 time to fit residues: 3.8949 Evaluate side-chains 22 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 463 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 447 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 147 optimal weight: 0.0470 chunk 145 optimal weight: 4.9990 chunk 476 optimal weight: 4.9990 chunk 510 optimal weight: 7.9990 chunk 370 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 588 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 62370 Z= 0.161 Angle : 0.535 7.779 85050 Z= 0.280 Chirality : 0.043 0.128 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.697 16.961 8358 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.99 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.88 (0.10), residues: 7812 helix: 1.63 (0.17), residues: 882 sheet: 0.27 (0.11), residues: 2646 loop : -1.70 (0.09), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 70 HIS 0.002 0.001 HIS Q 318 PHE 0.008 0.001 PHE L 259 TYR 0.029 0.001 TYR E 92 ARG 0.003 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: J 131 LEU cc_start: 0.8920 (tp) cc_final: 0.8599 (tp) REVERT: J 197 MET cc_start: 0.9228 (tpp) cc_final: 0.9020 (tpp) REVERT: J 351 LEU cc_start: 0.9610 (mt) cc_final: 0.9317 (mt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0726 time to fit residues: 2.5293 Evaluate side-chains 18 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 681 optimal weight: 9.9990 chunk 717 optimal weight: 0.1980 chunk 654 optimal weight: 10.0000 chunk 697 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 548 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 630 optimal weight: 20.0000 chunk 660 optimal weight: 7.9990 chunk 695 optimal weight: 0.0770 overall best weight: 2.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 62370 Z= 0.139 Angle : 0.501 4.259 85050 Z= 0.268 Chirality : 0.042 0.130 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.544 15.575 8358 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.10), residues: 7812 helix: 1.66 (0.17), residues: 882 sheet: 0.21 (0.10), residues: 2877 loop : -1.79 (0.09), residues: 4053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 70 HIS 0.002 0.001 HIS B 129 PHE 0.008 0.001 PHE B 259 TYR 0.031 0.001 TYR U 92 ARG 0.002 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: J 7 ARG cc_start: 0.5935 (ptm160) cc_final: 0.5585 (ttt180) REVERT: J 163 ASP cc_start: 0.7342 (t0) cc_final: 0.7136 (t0) REVERT: J 197 MET cc_start: 0.9241 (tpp) cc_final: 0.9027 (tpp) REVERT: J 245 MET cc_start: 0.6885 (pmm) cc_final: 0.6597 (pmm) REVERT: J 351 LEU cc_start: 0.9614 (mt) cc_final: 0.9298 (mt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1031 time to fit residues: 3.4812 Evaluate side-chains 19 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 458 optimal weight: 0.5980 chunk 737 optimal weight: 0.0070 chunk 450 optimal weight: 0.0040 chunk 350 optimal weight: 8.9990 chunk 513 optimal weight: 8.9990 chunk 774 optimal weight: 0.0170 chunk 712 optimal weight: 0.8980 chunk 616 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 476 optimal weight: 9.9990 chunk 377 optimal weight: 0.8980 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 62370 Z= 0.119 Angle : 0.513 5.284 85050 Z= 0.268 Chirality : 0.044 0.134 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.433 15.124 8358 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.88 (0.10), residues: 7812 helix: 1.56 (0.18), residues: 882 sheet: 0.24 (0.10), residues: 2877 loop : -1.77 (0.09), residues: 4053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 95 HIS 0.002 0.001 HIS N 96 PHE 0.008 0.001 PHE D 231 TYR 0.031 0.001 TYR Q 92 ARG 0.001 0.000 ARG U 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: J 163 ASP cc_start: 0.7443 (t0) cc_final: 0.7213 (t0) REVERT: J 197 MET cc_start: 0.9237 (tpp) cc_final: 0.9021 (tpp) REVERT: J 245 MET cc_start: 0.6951 (pmm) cc_final: 0.6696 (pmm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0725 time to fit residues: 2.6232 Evaluate side-chains 19 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 489 optimal weight: 4.9990 chunk 656 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 568 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 171 optimal weight: 0.0670 chunk 617 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 633 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.041266 restraints weight = 15192.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.042839 restraints weight = 8841.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.044010 restraints weight = 6040.307| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 62370 Z= 0.162 Angle : 0.523 8.953 85050 Z= 0.274 Chirality : 0.042 0.128 9870 Planarity : 0.003 0.038 11088 Dihedral : 4.505 15.203 8358 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.53 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.10), residues: 7812 helix: 1.67 (0.18), residues: 882 sheet: 0.22 (0.10), residues: 2877 loop : -1.78 (0.09), residues: 4053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 70 HIS 0.003 0.001 HIS H 129 PHE 0.007 0.001 PHE G 231 TYR 0.028 0.001 TYR B 92 ARG 0.002 0.000 ARG N 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4619.79 seconds wall clock time: 85 minutes 33.87 seconds (5133.87 seconds total)