Starting phenix.real_space_refine on Tue Dec 12 04:47:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/12_2023/8do4_27590_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 132 5.16 5 C 12773 2.51 5 N 3303 2.21 5 O 3955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "E TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20163 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3348 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3393 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain: "C" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Chain: "D" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3393 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain: "E" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Chain: "G" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Time building chain proxies: 12.21, per 1000 atoms: 0.61 Number of scatterers: 20163 At special positions: 0 Unit cell: (156.04, 145.7, 99.64, 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 132 16.00 O 3955 8.00 N 3303 7.00 C 12773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.02 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.36 Conformation dependent library (CDL) restraints added in 4.1 seconds 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4958 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 33 sheets defined 38.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.933A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.590A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.944A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 211 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.933A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.587A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.981A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.657A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 5.035A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 71 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 4.115A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.694A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 191 through 211 removed outlier: 3.514A pdb=" N THR B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.762A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.926A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.937A pdb=" N CYS C 71 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 72' Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.679A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.872A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.550A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 191 through 211 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.896A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.827A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.556A pdb=" N LEU D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 74 through 99 Proline residue: D 89 - end of helix removed outlier: 3.586A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 147 removed outlier: 3.595A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.360A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.773A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 358 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.862A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.562A pdb=" N LYS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.815A pdb=" N SER E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS E 71 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.643A pdb=" N ASN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 3.540A pdb=" N ILE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.940A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 191 through 212 removed outlier: 4.003A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 removed outlier: 3.595A pdb=" N GLY E 236 " --> pdb=" O GLN E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.780A pdb=" N LEU E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 358 through 363 removed outlier: 5.482A pdb=" N GLU E 361 " --> pdb=" O GLY E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 452 through 468 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.608A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.562A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.654A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.995A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 188 removed outlier: 4.778A pdb=" N VAL G 184 " --> pdb=" O ASN G 180 " (cutoff:3.500A) Proline residue: G 185 - end of helix removed outlier: 4.333A pdb=" N ASP G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 211 removed outlier: 3.927A pdb=" N SER G 198 " --> pdb=" O GLN G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.826A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 349 through 356 Processing helix chain 'G' and resid 357 through 358 No H-bonds generated for 'chain 'G' and resid 357 through 358' Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.736A pdb=" N LYS G 362 " --> pdb=" O SER G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 Processing helix chain 'G' and resid 452 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.765A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.067A pdb=" N ILE A 266 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG A 279 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 268 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.654A pdb=" N LEU G 383 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.268A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.082A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.506A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.619A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB1, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.337A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.546A pdb=" N HIS B 102 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B 113 " --> pdb=" O ILE E 426 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER E 428 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 394 removed outlier: 6.671A pdb=" N ILE B 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 162 removed outlier: 17.003A pdb=" N THR C 168 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N THR C 54 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 11.309A pdb=" N TYR C 170 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP C 56 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE C 172 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 58 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C 46 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N SER C 50 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLU C 287 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N LEU C 285 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR C 54 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N ASP C 56 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N TYR C 281 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL C 58 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG C 279 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS C 60 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ILE C 277 " --> pdb=" O LYS C 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 298 current: chain 'C' and resid 332 through 333 Processing sheet with id=AB8, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.256A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ILE C 277 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS C 60 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG C 279 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL C 58 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N TYR C 281 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N ASP C 56 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR C 54 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N LEU C 285 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLU C 287 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N SER C 50 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C 46 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 322 through 326 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.070A pdb=" N ARG C 365 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 401 removed outlier: 4.452A pdb=" N CYS C 392 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 393 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 426 " --> pdb=" O MET E 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 158 through 164 removed outlier: 6.292A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N THR D 168 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP D 56 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AC4, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.231A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AC5, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'D' and resid 399 through 401 removed outlier: 4.513A pdb=" N CYS D 392 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.441A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC9, first strand: chain 'E' and resid 266 through 270 removed outlier: 6.094A pdb=" N ILE E 266 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG E 279 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 268 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AD1, first strand: chain 'E' and resid 226 through 227 removed outlier: 4.132A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 301 through 303 Processing sheet with id=AD3, first strand: chain 'G' and resid 158 through 162 removed outlier: 17.062A pdb=" N THR G 168 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N THR G 54 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N TYR G 170 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP G 56 " --> pdb=" O TYR G 170 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE G 172 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 58 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 333 Processing sheet with id=AD4, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.060A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AD5, first strand: chain 'G' and resid 301 through 303 removed outlier: 6.021A pdb=" N ARG G 365 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 392 through 394 removed outlier: 4.619A pdb=" N CYS G 392 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG G 399 " --> pdb=" O CYS G 394 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2223 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: 8.18 Time building geometry restraints manager: 9.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6162 1.34 - 1.46: 3796 1.46 - 1.58: 10309 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 20459 Sorted by residual: bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.34e+01 bond pdb=" N ILE C 326 " pdb=" CA ILE C 326 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N VAL D 113 " pdb=" CA VAL D 113 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.95e+00 bond pdb=" CA ASN B 51 " pdb=" CB ASN B 51 " ideal model delta sigma weight residual 1.522 1.543 -0.021 7.00e-03 2.04e+04 9.12e+00 bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.73e+00 ... (remaining 20454 not shown) Histogram of bond angle deviations from ideal: 93.39 - 101.51: 57 101.51 - 109.62: 2163 109.62 - 117.73: 13586 117.73 - 125.85: 11850 125.85 - 133.96: 147 Bond angle restraints: 27803 Sorted by residual: angle pdb=" N ALA B 111 " pdb=" CA ALA B 111 " pdb=" C ALA B 111 " ideal model delta sigma weight residual 110.35 115.91 -5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" OE1 GLN D 162 " pdb=" CD GLN D 162 " pdb=" NE2 GLN D 162 " ideal model delta sigma weight residual 122.60 118.80 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" OE1 GLN D 289 " pdb=" CD GLN D 289 " pdb=" NE2 GLN D 289 " ideal model delta sigma weight residual 122.60 118.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" N VAL G 369 " pdb=" CA VAL G 369 " pdb=" C VAL G 369 " ideal model delta sigma weight residual 112.29 108.78 3.51 9.40e-01 1.13e+00 1.40e+01 angle pdb=" N ILE B 328 " pdb=" CA ILE B 328 " pdb=" CB ILE B 328 " ideal model delta sigma weight residual 111.23 105.13 6.10 1.65e+00 3.67e-01 1.37e+01 ... (remaining 27798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11029 17.97 - 35.94: 1159 35.94 - 53.91: 325 53.91 - 71.89: 68 71.89 - 89.86: 30 Dihedral angle restraints: 12611 sinusoidal: 4930 harmonic: 7681 Sorted by residual: dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -158.24 72.24 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -17.40 -68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS G 71 " pdb=" SG CYS G 71 " pdb=" SG CYS G 192 " pdb=" CB CYS G 192 " ideal model delta sinusoidal sigma weight residual -86.00 -152.23 66.23 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 12608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2206 0.043 - 0.087: 764 0.087 - 0.130: 339 0.130 - 0.173: 75 0.173 - 0.217: 19 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3400 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 240 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C GLU D 240 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU D 240 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 241 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 350 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ASN A 350 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 350 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 351 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 96 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ILE B 96 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE B 96 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 97 " -0.015 2.00e-02 2.50e+03 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 275 2.62 - 3.19: 18680 3.19 - 3.76: 31827 3.76 - 4.33: 43626 4.33 - 4.90: 71235 Nonbonded interactions: 165643 Sorted by model distance: nonbonded pdb=" OG SER C 404 " pdb=" OE1 GLU C 406 " model vdw 2.056 2.440 nonbonded pdb=" O ASN B 182 " pdb=" OG1 THR B 186 " model vdw 2.110 2.440 nonbonded pdb=" OD1 ASP G 103 " pdb=" OH TYR G 135 " model vdw 2.151 2.440 nonbonded pdb=" NH2 ARG A 244 " pdb=" OD1 ASP D 200 " model vdw 2.169 2.520 nonbonded pdb=" OD1 ASN G 303 " pdb=" NH1 ARG G 365 " model vdw 2.173 2.520 ... (remaining 165638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 104 or resid 112 through 468)) selection = (chain 'B' and (resid 27 through 104 or resid 112 through 468)) selection = chain 'C' selection = (chain 'D' and (resid 27 through 104 or resid 112 through 468)) selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.510 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: 0.000 Extract box with map and model: 11.700 Check model and map are aligned: 0.240 Set scattering table: 0.180 Process input model: 59.790 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 87.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.005 0.073 20459 Z= 0.349 Angle : 0.811 7.507 27803 Z= 0.511 Chirality : 0.055 0.217 3403 Planarity : 0.004 0.060 3525 Dihedral : 16.405 89.857 7545 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.54 % Allowed : 21.78 % Favored : 76.67 % 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: -0.40 (0.16), residues: 2605 helix: 0.58 (0.18), residues: 833 sheet: 0.13 (0.24), residues: 430 loop : -0.92 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 308 HIS 0.005 0.001 HIS D 29 PHE 0.020 0.002 PHE C 253 TYR 0.025 0.002 TYR A 438 ARG 0.005 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 534 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 556 average time/residue: 0.3130 time to fit residues: 267.1903 Evaluate side-chains 320 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 314 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2017 time to fit residues: 5.4562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 265 GLN B 182 ASN B 229 GLN B 290 GLN B 320 ASN B 414 ASN C 51 ASN C 372 HIS C 407 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 140 ASN D 290 GLN E 265 GLN G 102 HIS G 180 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20459 Z= 0.228 Angle : 0.631 9.712 27803 Z= 0.329 Chirality : 0.048 0.224 3403 Planarity : 0.004 0.051 3525 Dihedral : 4.727 23.913 2785 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.60 % Allowed : 21.05 % Favored : 75.34 % 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: -0.21 (0.16), residues: 2605 helix: 1.05 (0.19), residues: 848 sheet: -0.17 (0.24), residues: 472 loop : -0.91 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 308 HIS 0.011 0.001 HIS B 372 PHE 0.015 0.002 PHE G 253 TYR 0.019 0.002 TYR B 206 ARG 0.007 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 319 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 42 residues processed: 387 average time/residue: 0.2817 time to fit residues: 176.1339 Evaluate side-chains 299 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1861 time to fit residues: 17.7477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 0.0050 chunk 65 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 255 optimal weight: 0.3980 chunk 210 optimal weight: 0.0870 chunk 234 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 140 ASN B 100 ASN B 303 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN E 29 HIS E 78 ASN G 217 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20459 Z= 0.175 Angle : 0.554 8.160 27803 Z= 0.289 Chirality : 0.046 0.190 3403 Planarity : 0.003 0.032 3525 Dihedral : 4.451 18.816 2785 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 2.14 % Allowed : 21.78 % Favored : 76.07 % 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: -0.05 (0.16), residues: 2605 helix: 1.34 (0.19), residues: 826 sheet: -0.17 (0.24), residues: 452 loop : -0.85 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 308 HIS 0.007 0.001 HIS B 372 PHE 0.016 0.001 PHE C 253 TYR 0.019 0.001 TYR B 438 ARG 0.006 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 331 average time/residue: 0.2999 time to fit residues: 161.9141 Evaluate side-chains 263 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1970 time to fit residues: 10.3410 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 57.6328 > 50: distance: 47 - 111: 18.340 distance: 56 - 97: 17.304 distance: 59 - 94: 9.951 distance: 79 - 82: 4.099 distance: 82 - 83: 4.488 distance: 83 - 84: 3.074 distance: 83 - 86: 5.583 distance: 84 - 85: 5.736 distance: 84 - 94: 8.224 distance: 86 - 87: 5.720 distance: 87 - 88: 7.604 distance: 87 - 89: 4.538 distance: 88 - 90: 12.361 distance: 90 - 92: 7.853 distance: 91 - 92: 3.264 distance: 92 - 93: 7.442 distance: 94 - 95: 7.389 distance: 95 - 96: 7.535 distance: 95 - 98: 9.549 distance: 96 - 97: 21.569 distance: 96 - 102: 6.843 distance: 98 - 99: 15.953 distance: 98 - 100: 31.292 distance: 102 - 103: 7.948 distance: 103 - 104: 27.944 distance: 103 - 106: 30.775 distance: 104 - 105: 7.748 distance: 104 - 111: 24.821 distance: 106 - 107: 10.682 distance: 107 - 108: 20.518 distance: 108 - 109: 12.232 distance: 108 - 110: 27.716 distance: 111 - 112: 11.900 distance: 112 - 113: 5.020 distance: 112 - 115: 5.045 distance: 113 - 114: 10.745 distance: 113 - 120: 7.191 distance: 115 - 116: 11.467 distance: 116 - 117: 19.854 distance: 117 - 118: 6.023 distance: 117 - 119: 11.950 distance: 120 - 121: 8.508 distance: 121 - 122: 9.227 distance: 121 - 124: 3.778 distance: 122 - 123: 7.609 distance: 122 - 128: 9.363 distance: 124 - 125: 9.408 distance: 125 - 126: 6.753 distance: 125 - 127: 6.047 distance: 128 - 129: 3.569 distance: 129 - 130: 10.205 distance: 129 - 132: 6.885 distance: 130 - 131: 7.235 distance: 130 - 136: 5.078 distance: 132 - 133: 18.882 distance: 133 - 134: 15.777 distance: 133 - 135: 13.436 distance: 136 - 142: 5.227 distance: 137 - 138: 11.115 distance: 137 - 140: 5.953 distance: 138 - 139: 11.599 distance: 138 - 143: 6.825 distance: 140 - 141: 5.206 distance: 141 - 142: 8.570 distance: 143 - 144: 3.547 distance: 144 - 145: 4.794 distance: 145 - 146: 6.764 distance: 145 - 150: 3.819 distance: 147 - 148: 4.824 distance: 147 - 149: 9.124 distance: 150 - 151: 5.400 distance: 151 - 152: 4.889 distance: 151 - 154: 4.330 distance: 152 - 153: 3.582 distance: 152 - 156: 7.148 distance: 154 - 155: 9.108 distance: 156 - 157: 4.888 distance: 156 - 190: 5.163 distance: 157 - 158: 13.482 distance: 157 - 160: 6.015 distance: 158 - 159: 20.413 distance: 158 - 167: 10.970 distance: 159 - 187: 13.461 distance: 160 - 161: 8.084 distance: 161 - 162: 7.442 distance: 161 - 163: 6.182 distance: 162 - 164: 3.734 distance: 165 - 166: 7.637