Starting phenix.real_space_refine on Sat Sep 28 03:56:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/09_2024/8dan_27271.cif" } resolution = 4.74 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= 0.004 sd= 0.067 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: 5 Type Number sf(0) Gaussians S 216 5.16 5 C 22136 2.51 5 N 6060 2.21 5 O 6588 1.98 5 H 33968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 68968 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "B" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "C" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4203 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: F, I, L, E, H, K, D, G, J Time building chain proxies: 28.97, per 1000 atoms: 0.42 Number of scatterers: 68968 At special positions: 0 Unit cell: (196.8, 166.8, 180, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 O 6588 8.00 N 6060 7.00 C 22136 6.00 H 33968 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.02 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.04 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 280 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG B 501 " - " ASN B 199 " " NAG D 501 " - " ASN D 139 " " NAG E 501 " - " ASN E 199 " " NAG G 501 " - " ASN G 139 " " NAG H 501 " - " ASN H 199 " " NAG J 501 " - " ASN J 139 " " NAG K 501 " - " ASN K 199 " Time building additional restraints: 13.57 Conformation dependent library (CDL) restraints added in 4.3 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8360 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 92 sheets defined 14.1% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.516A pdb=" N ASN A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.685A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.636A pdb=" N TYR B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 399 Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.200A pdb=" N ARG C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.662A pdb=" N ALA C 163 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.516A pdb=" N ASN D 246 " --> pdb=" O MET D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.686A pdb=" N CYS D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 416 through 438 removed outlier: 3.503A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.636A pdb=" N TYR E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 399 Processing helix chain 'E' and resid 411 through 419 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 104 through 109 removed outlier: 4.201A pdb=" N ARG F 108 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.661A pdb=" N ALA F 163 " --> pdb=" O LYS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG F 241 " --> pdb=" O PRO F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.515A pdb=" N ASN G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.687A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 403 through 414 Processing helix chain 'G' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG G 438 " --> pdb=" O LEU G 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 358 through 365 removed outlier: 3.637A pdb=" N TYR H 362 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 399 Processing helix chain 'H' and resid 411 through 419 Processing helix chain 'I' and resid 55 through 59 Processing helix chain 'I' and resid 104 through 109 removed outlier: 4.201A pdb=" N ARG I 108 " --> pdb=" O TYR I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 Processing helix chain 'I' and resid 160 through 164 removed outlier: 3.660A pdb=" N ALA I 163 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 removed outlier: 3.524A pdb=" N ARG I 241 " --> pdb=" O PRO I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 254 Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.515A pdb=" N ASN J 246 " --> pdb=" O MET J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.686A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 287 Processing helix chain 'J' and resid 403 through 414 Processing helix chain 'J' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG J 438 " --> pdb=" O LEU J 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 84 No H-bonds generated for 'chain 'K' and resid 82 through 84' Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'K' and resid 358 through 365 removed outlier: 3.637A pdb=" N TYR K 362 " --> pdb=" O ILE K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 399 Processing helix chain 'K' and resid 411 through 419 Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.200A pdb=" N ARG L 108 " --> pdb=" O TYR L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 119 Processing helix chain 'L' and resid 160 through 164 removed outlier: 3.661A pdb=" N ALA L 163 " --> pdb=" O LYS L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG L 241 " --> pdb=" O PRO L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 254 Processing helix chain 'L' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE A 162 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL A 19 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG A 21 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 132 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 132 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 removed outlier: 3.725A pdb=" N GLN A 204 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 214 " --> pdb=" O GLN A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL A 299 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A 319 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.675A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB2, first strand: chain 'B' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 107 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG B 96 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.602A pdb=" N GLN B 53 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 removed outlier: 4.246A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB9, first strand: chain 'B' and resid 278 through 279 removed outlier: 4.031A pdb=" N THR B 278 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 310 through 314 Processing sheet with id=AC2, first strand: chain 'C' and resid 34 through 41 removed outlier: 7.785A pdb=" N ILE C 287 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 38 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN C 289 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN C 40 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 210 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 222 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC4, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.213A pdb=" N ARG C 99 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 91 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TRP C 74 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP C 91 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 72 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR C 93 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 70 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 173 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.545A pdb=" N ILE D 162 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL D 19 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 27 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 21 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 35 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 132 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 132 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 35 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR D 107 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR D 107 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.724A pdb=" N GLN D 204 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 214 " --> pdb=" O GLN D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'D' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL D 299 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN D 319 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS D 301 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY D 326 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AD7, first strand: chain 'E' and resid 34 through 38 removed outlier: 4.588A pdb=" N ASN E 36 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN E 107 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG E 96 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN E 53 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.245A pdb=" N ASP E 112 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 151 through 158 Processing sheet with id=AE2, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AE3, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AE4, first strand: chain 'E' and resid 210 through 215 Processing sheet with id=AE5, first strand: chain 'E' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR E 278 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 310 through 314 Processing sheet with id=AE7, first strand: chain 'F' and resid 34 through 41 removed outlier: 7.785A pdb=" N ILE F 287 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL F 38 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN F 289 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN F 40 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG F 210 " --> pdb=" O ARG F 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG F 222 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 4.212A pdb=" N ARG F 99 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP F 91 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP F 74 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP F 91 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 72 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR F 93 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG F 70 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA F 173 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE G 162 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL G 19 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 132 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 132 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 203 through 204 removed outlier: 3.724A pdb=" N GLN G 204 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 214 " --> pdb=" O GLN G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AF9, first strand: chain 'G' and resid 296 through 302 removed outlier: 4.327A pdb=" N VAL G 299 " --> pdb=" O GLN G 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN G 319 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS G 301 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR G 317 " --> pdb=" O CYS G 301 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY G 326 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG4, first strand: chain 'H' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN H 107 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG H 96 " --> pdb=" O GLN H 107 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN H 53 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 86 through 89 removed outlier: 4.245A pdb=" N ASP H 112 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 151 through 158 Processing sheet with id=AG8, first strand: chain 'H' and resid 169 through 171 Processing sheet with id=AG9, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AH1, first strand: chain 'H' and resid 210 through 215 Processing sheet with id=AH2, first strand: chain 'H' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR H 278 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 34 through 41 removed outlier: 7.786A pdb=" N ILE I 287 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL I 38 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN I 289 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN I 40 " --> pdb=" O GLN I 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG I 210 " --> pdb=" O ARG I 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG I 222 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AH5, first strand: chain 'I' and resid 99 through 100 removed outlier: 4.213A pdb=" N ARG I 99 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP I 91 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP I 74 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP I 91 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL I 72 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR I 93 " --> pdb=" O ARG I 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG I 70 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA I 173 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AH7, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE J 162 " --> pdb=" O SER J 279 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL J 19 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU J 27 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG J 21 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 132 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.742A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 132 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.677A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.677A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 203 through 204 removed outlier: 3.723A pdb=" N GLN J 204 " --> pdb=" O VAL J 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL J 214 " --> pdb=" O GLN J 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI5, first strand: chain 'J' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL J 299 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN J 319 " --> pdb=" O VAL J 299 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS J 301 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR J 317 " --> pdb=" O CYS J 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY J 326 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI9, first strand: chain 'K' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN K 107 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG K 96 " --> pdb=" O GLN K 107 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN K 53 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 86 through 89 removed outlier: 4.246A pdb=" N ASP K 112 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 151 through 158 Processing sheet with id=AJ4, first strand: chain 'K' and resid 169 through 171 Processing sheet with id=AJ5, first strand: chain 'K' and resid 183 through 184 Processing sheet with id=AJ6, first strand: chain 'K' and resid 210 through 215 Processing sheet with id=AJ7, first strand: chain 'K' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR K 278 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 34 through 41 removed outlier: 7.784A pdb=" N ILE L 287 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL L 38 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN L 289 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN L 40 " --> pdb=" O GLN L 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG L 210 " --> pdb=" O ARG L 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG L 222 " --> pdb=" O ARG L 210 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 49 through 51 Processing sheet with id=AK1, first strand: chain 'L' and resid 99 through 100 removed outlier: 4.212A pdb=" N ARG L 99 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP L 91 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TRP L 74 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP L 91 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL L 72 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR L 93 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG L 70 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA L 173 " --> pdb=" O LYS L 152 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 123 through 125 1188 hydrogen bonds defined for protein. 2976 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: 25.76 Time building geometry restraints manager: 16.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 33964 1.04 - 1.24: 4652 1.24 - 1.44: 11024 1.44 - 1.64: 19964 1.64 - 1.84: 272 Bond restraints: 69876 Sorted by residual: bond pdb=" N PHE D 1 " pdb=" H3 PHE D 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N ASN F 32 " pdb=" H3 ASN F 32 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PHE J 1 " pdb=" H2 PHE J 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE E 5 " pdb=" H3 ILE E 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ASN C 32 " pdb=" H2 ASN C 32 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 69871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.54: 126092 19.54 - 39.08: 16 39.08 - 58.62: 4 58.62 - 78.16: 0 78.16 - 97.71: 4 Bond angle restraints: 126116 Sorted by residual: angle pdb=" H1 ILE E 5 " pdb=" N ILE E 5 " pdb=" H2 ILE E 5 " ideal model delta sigma weight residual 109.47 11.76 97.71 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE K 5 " pdb=" N ILE K 5 " pdb=" H2 ILE K 5 " ideal model delta sigma weight residual 109.47 11.77 97.70 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE H 5 " pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 109.47 11.80 97.67 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE B 5 " pdb=" N ILE B 5 " pdb=" H2 ILE B 5 " ideal model delta sigma weight residual 109.47 11.82 97.65 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 PHE J 1 " pdb=" N PHE J 1 " pdb=" H2 PHE J 1 " ideal model delta sigma weight residual 109.47 56.67 52.80 3.00e+00 1.11e-01 3.10e+02 ... (remaining 126111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 30174 17.83 - 35.67: 2380 35.67 - 53.50: 733 53.50 - 71.33: 143 71.33 - 89.16: 41 Dihedral angle restraints: 33471 sinusoidal: 17939 harmonic: 15532 Sorted by residual: dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.66 78.34 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 68 " pdb=" SG CYS A 68 " pdb=" SG CYS A 78 " pdb=" CB CYS A 78 " ideal model delta sinusoidal sigma weight residual 93.00 162.61 -69.61 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CA TYR E 403 " pdb=" C TYR E 403 " pdb=" N ALA E 404 " pdb=" CA ALA E 404 " ideal model delta harmonic sigma weight residual 180.00 146.99 33.01 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 33468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4911 0.072 - 0.145: 577 0.145 - 0.217: 4 0.217 - 0.290: 0 0.290 - 0.362: 4 Chirality restraints: 5496 Sorted by residual: chirality pdb=" CA LEU K 405 " pdb=" N LEU K 405 " pdb=" C LEU K 405 " pdb=" CB LEU K 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU E 405 " pdb=" N LEU E 405 " pdb=" C LEU E 405 " pdb=" CB LEU E 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU B 405 " pdb=" N LEU B 405 " pdb=" C LEU B 405 " pdb=" CB LEU B 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 5493 not shown) Planarity restraints: 10480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 401 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 402 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 401 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO K 402 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 402 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 402 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 401 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO H 402 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 402 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 402 " -0.021 5.00e-02 4.00e+02 ... (remaining 10477 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 2718 2.15 - 2.76: 131108 2.76 - 3.37: 190148 3.37 - 3.99: 237727 3.99 - 4.60: 356985 Nonbonded interactions: 918686 Sorted by model distance: nonbonded pdb=" O THR K 164 " pdb=" HE ARG L 64 " model vdw 1.532 2.450 nonbonded pdb=" H SER G 57 " pdb=" OD1 ASN H 242 " model vdw 1.592 2.450 nonbonded pdb=" H VAL A 330 " pdb=" O ALA A 342 " model vdw 1.600 2.450 nonbonded pdb=" H VAL G 330 " pdb=" O ALA G 342 " model vdw 1.600 2.450 nonbonded pdb=" H VAL D 330 " pdb=" O ALA D 342 " model vdw 1.600 2.450 ... (remaining 918681 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.970 Extract box with map and model: 2.080 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 116.680 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.140 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:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 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 0.045 35908 Z= 0.171 Angle : 0.526 6.045 48900 Z= 0.279 Chirality : 0.044 0.362 5496 Planarity : 0.003 0.038 6264 Dihedral : 13.829 89.165 13120 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.75 (0.13), residues: 4448 helix: 0.96 (0.27), residues: 428 sheet: -0.63 (0.14), residues: 1532 loop : -0.59 (0.13), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 407 HIS 0.005 0.001 HIS D 275 PHE 0.010 0.001 PHE D 398 TYR 0.012 0.001 TYR K 403 ARG 0.005 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 SER cc_start: 0.5512 (t) cc_final: 0.5023 (m) REVERT: A 117 ASP cc_start: 0.6717 (t0) cc_final: 0.6306 (t0) REVERT: A 120 VAL cc_start: 0.6472 (t) cc_final: 0.6189 (t) REVERT: A 203 ILE cc_start: 0.8081 (mm) cc_final: 0.7765 (mm) REVERT: A 246 ASN cc_start: 0.7748 (m-40) cc_final: 0.6819 (t0) REVERT: A 375 THR cc_start: 0.6769 (m) cc_final: 0.6409 (m) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2818 time to fit residues: 49.2932 Evaluate side-chains 101 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.386 Evaluate side-chains 145 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.8559 (pt) cc_final: 0.8342 (pt) REVERT: B 114 VAL cc_start: 0.9001 (p) cc_final: 0.8746 (m) REVERT: B 152 LEU cc_start: 0.8458 (mm) cc_final: 0.7731 (mp) REVERT: B 288 LEU cc_start: 0.8056 (mm) cc_final: 0.7824 (mm) REVERT: B 312 GLU cc_start: 0.5523 (tt0) cc_final: 0.5289 (tt0) REVERT: B 331 TYR cc_start: 0.6288 (t80) cc_final: 0.5865 (t80) REVERT: B 358 ILE cc_start: 0.6934 (mm) cc_final: 0.6577 (mp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3063 time to fit residues: 51.6305 Evaluate side-chains 105 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.386 Evaluate side-chains 73 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASN cc_start: 0.6979 (p0) cc_final: 0.6765 (p0) REVERT: C 193 ILE cc_start: 0.7751 (tt) cc_final: 0.7386 (tp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3027 time to fit residues: 24.7659 Evaluate side-chains 53 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 3.9990 chunk 333 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 344 optimal weight: 0.0370 chunk 133 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS D 125 HIS D 275 HIS D 362 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS E 289 HIS E 321 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN L 98 GLN L 154 GLN L 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35908 Z= 0.224 Angle : 0.568 7.995 48900 Z= 0.301 Chirality : 0.045 0.369 5496 Planarity : 0.006 0.096 6264 Dihedral : 5.340 44.635 5136 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.21 % Allowed : 3.03 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4448 helix: 1.42 (0.28), residues: 400 sheet: -0.94 (0.13), residues: 1544 loop : -0.63 (0.13), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 74 HIS 0.009 0.001 HIS H 252 PHE 0.033 0.001 PHE A 257 TYR 0.025 0.001 TYR F 104 ARG 0.011 0.001 ARG I 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.7540 (mttt) cc_final: 0.7203 (mttt) REVERT: D 117 ASP cc_start: 0.7298 (t0) cc_final: 0.6630 (t0) REVERT: D 136 VAL cc_start: 0.8240 (t) cc_final: 0.7503 (t) REVERT: D 270 ASN cc_start: 0.5481 (t0) cc_final: 0.5264 (t0) REVERT: D 330 VAL cc_start: 0.8792 (m) cc_final: 0.8558 (m) REVERT: D 335 THR cc_start: 0.7592 (t) cc_final: 0.7339 (t) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2286 time to fit residues: 35.7154 Evaluate side-chains 95 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.395 Evaluate side-chains 123 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 LYS cc_start: 0.7504 (pttp) cc_final: 0.7228 (ptpp) REVERT: E 264 LEU cc_start: 0.8758 (tt) cc_final: 0.8480 (tt) REVERT: E 335 ASN cc_start: 0.7495 (m-40) cc_final: 0.7233 (m-40) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.2634 time to fit residues: 38.5752 Evaluate side-chains 89 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.965 Evaluate side-chains 70 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8537 (p0) cc_final: 0.8236 (t0) REVERT: L 150 THR cc_start: 0.6501 (p) cc_final: 0.6198 (p) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3252 time to fit residues: 25.3368 Evaluate side-chains 55 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 332 optimal weight: 0.0060 chunk 272 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 chunk 400 optimal weight: 0.3980 chunk 432 optimal weight: 0.0370 chunk 356 optimal weight: 0.0060 chunk 396 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 overall best weight: 0.0246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN E 76 HIS ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 35908 Z= 0.320 Angle : 0.713 16.051 48900 Z= 0.372 Chirality : 0.050 0.366 5496 Planarity : 0.010 0.284 6264 Dihedral : 5.558 43.471 5136 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.25 (0.13), residues: 4448 helix: 1.09 (0.28), residues: 400 sheet: -1.18 (0.13), residues: 1560 loop : -0.83 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 89 HIS 0.042 0.002 HIS A 52 PHE 0.030 0.003 PHE D 147 TYR 0.025 0.002 TYR H 21 ARG 0.089 0.003 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 136 VAL cc_start: 0.8157 (t) cc_final: 0.7504 (t) REVERT: D 270 ASN cc_start: 0.5473 (t0) cc_final: 0.5137 (t0) REVERT: D 362 GLN cc_start: 0.7402 (tp40) cc_final: 0.7116 (tp-100) REVERT: D 364 ASN cc_start: 0.7650 (p0) cc_final: 0.6195 (p0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1960 time to fit residues: 26.9791 Evaluate side-chains 90 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.395 Evaluate side-chains 108 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 PHE cc_start: 0.6439 (t80) cc_final: 0.6080 (t80) REVERT: E 136 LYS cc_start: 0.7528 (pttp) cc_final: 0.7298 (ptpp) REVERT: E 152 LEU cc_start: 0.7494 (mm) cc_final: 0.6934 (mt) REVERT: E 171 MET cc_start: 0.2877 (mmm) cc_final: 0.2624 (mmm) REVERT: E 251 ASP cc_start: 0.8320 (p0) cc_final: 0.7855 (p0) REVERT: E 335 ASN cc_start: 0.7508 (m-40) cc_final: 0.7170 (m-40) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2927 time to fit residues: 37.7269 Evaluate side-chains 95 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.389 Evaluate side-chains 62 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8524 (p0) cc_final: 0.8112 (t0) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2923 time to fit residues: 20.5384 Evaluate side-chains 51 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5319 > 50: distance: 0 - 1: 41.519 distance: 0 - 7: 42.474 distance: 1 - 2: 10.657 distance: 1 - 4: 24.833 distance: 1 - 8: 8.863 distance: 2 - 3: 20.936 distance: 2 - 14: 43.855 distance: 4 - 5: 24.114 distance: 4 - 6: 10.513 distance: 5 - 10: 15.182 distance: 6 - 11: 22.695 distance: 6 - 12: 6.968 distance: 6 - 13: 7.589 distance: 14 - 15: 39.491 distance: 14 - 22: 32.463 distance: 15 - 16: 45.122 distance: 15 - 18: 51.988 distance: 15 - 23: 57.271 distance: 16 - 17: 46.404 distance: 16 - 33: 23.437 distance: 18 - 19: 26.319 distance: 18 - 20: 37.318 distance: 18 - 24: 43.021 distance: 19 - 21: 44.372 distance: 19 - 25: 29.316 distance: 19 - 26: 41.700 distance: 20 - 27: 21.076 distance: 20 - 28: 36.401 distance: 20 - 29: 38.663 distance: 21 - 31: 3.066 distance: 33 - 34: 33.043 distance: 33 - 41: 3.482 distance: 34 - 35: 23.921 distance: 34 - 37: 25.712 distance: 34 - 42: 15.610 distance: 35 - 36: 35.580 distance: 35 - 45: 25.292 distance: 37 - 38: 29.352 distance: 37 - 43: 23.957 distance: 37 - 44: 21.654 distance: 38 - 39: 17.347 distance: 38 - 40: 29.749 distance: 45 - 46: 11.627 distance: 45 - 55: 21.824 distance: 46 - 47: 37.013 distance: 46 - 49: 23.437 distance: 46 - 56: 6.201 distance: 47 - 48: 41.104 distance: 47 - 62: 8.911 distance: 49 - 50: 19.814 distance: 49 - 57: 25.964 distance: 49 - 58: 11.071 distance: 50 - 51: 27.294 distance: 50 - 52: 26.969 distance: 51 - 53: 4.920 distance: 52 - 54: 20.477 distance: 53 - 54: 41.579 distance: 53 - 60: 3.066 distance: 54 - 61: 19.224 distance: 62 - 63: 13.164 distance: 62 - 67: 18.991 distance: 63 - 64: 4.469 distance: 63 - 66: 39.175 distance: 63 - 68: 22.819 distance: 64 - 65: 21.991 distance: 64 - 72: 16.491 distance: 66 - 69: 11.221 distance: 66 - 70: 16.404 distance: 66 - 71: 43.299 distance: 72 - 73: 3.687 distance: 72 - 79: 11.552 distance: 73 - 74: 15.353 distance: 73 - 76: 6.587 distance: 73 - 80: 22.581 distance: 74 - 75: 26.169 distance: 74 - 88: 40.618 distance: 76 - 77: 23.372 distance: 76 - 78: 10.317 distance: 76 - 81: 19.236 distance: 77 - 82: 11.749 distance: 77 - 83: 12.952 distance: 77 - 84: 5.474 distance: 78 - 85: 22.631 distance: 78 - 86: 10.740 distance: 78 - 87: 10.623 distance: 88 - 89: 25.822 distance: 88 - 93: 18.437 distance: 89 - 90: 41.322 distance: 89 - 92: 31.483 distance: 89 - 94: 37.327 distance: 90 - 91: 42.641 distance: 90 - 98: 44.673 distance: 92 - 95: 35.782 distance: 92 - 96: 10.755 distance: 92 - 97: 23.821 distance: 98 - 99: 28.306 distance: 98 - 106: 42.406 distance: 99 - 100: 13.900 distance: 99 - 102: 22.167 distance: 99 - 107: 29.642 distance: 100 - 101: 14.032 distance: 100 - 117: 14.389 distance: 102 - 103: 7.896 distance: 102 - 108: 11.963 distance: 102 - 109: 18.126 distance: 103 - 104: 29.076 distance: 103 - 105: 17.501 distance: 103 - 110: 30.166 distance: 104 - 111: 8.960 distance: 104 - 112: 4.504 distance: 104 - 113: 3.989 distance: 105 - 116: 3.380 distance: 117 - 118: 23.938 distance: 117 - 126: 20.641 distance: 118 - 119: 24.419 distance: 118 - 121: 45.186 distance: 118 - 127: 42.608 distance: 119 - 120: 47.980 distance: 119 - 139: 9.991 distance: 121 - 122: 68.287 distance: 121 - 128: 6.685 distance: 121 - 129: 29.151 distance: 122 - 123: 31.376 distance: 122 - 130: 39.965 distance: 122 - 131: 51.986 distance: 123 - 124: 44.660 distance: 123 - 132: 38.443 distance: 123 - 133: 10.518 distance: 124 - 125: 16.849 distance: 124 - 134: 14.160 distance: 124 - 135: 14.347 distance: 125 - 136: 15.889 distance: 125 - 137: 8.848 distance: 125 - 138: 10.966 distance: 139 - 140: 9.132 distance: 140 - 141: 51.604 distance: 140 - 143: 32.866 distance: 140 - 147: 4.073 distance: 141 - 142: 41.656 distance: 141 - 155: 42.696 distance: 143 - 144: 40.819 distance: 143 - 145: 33.174 distance: 143 - 148: 11.520 distance: 144 - 149: 9.398 distance: 144 - 150: 10.054 distance: 144 - 151: 9.580 distance: 145 - 152: 17.821 distance: 145 - 153: 14.305 distance: 145 - 154: 14.593 distance: 155 - 156: 19.235 distance: 155 - 165: 11.875 distance: 156 - 157: 12.674 distance: 156 - 159: 17.898 distance: 156 - 166: 16.393 distance: 157 - 158: 18.973 distance: 159 - 160: 10.252 distance: 159 - 167: 14.545 distance: 160 - 161: 9.754 distance: 160 - 162: 9.723 distance: 161 - 163: 10.635 distance: 162 - 164: 4.029 distance: 163 - 164: 10.008