Starting phenix.real_space_refine on Wed Nov 20 07:44:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/11_2024/7kzo_23084.cif" } resolution = 3.3 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= 0.003 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: 6 Type Number sf(0) Gaussians P 37 5.49 5 Mg 7 5.21 5 S 404 5.16 5 C 33902 2.51 5 N 9336 2.21 5 O 10424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54110 Number of models: 1 Model: "" Number of chains: 34 Chain: "A1" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A2" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3339 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 410} Chain breaks: 1 Chain: "A3" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A4" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3318 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "A5" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A6" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3335 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Chain: "A7" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "B1" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 399} Chain breaks: 1 Chain: "B2" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3204 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 393} Chain breaks: 2 Chain: "B3" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3227 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 391} Chain breaks: 2 Chain: "B4" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3193 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 391} Chain breaks: 2 Chain: "B5" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "B6" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3318 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "B7" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1771 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 985 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 223 Chain: "Y" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 844 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "X1" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1178 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "Y1" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1185 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "Z" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "A1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A3" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A5" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A7" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B3" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B5" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B7" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.51, per 1000 atoms: 0.55 Number of scatterers: 54110 At special positions: 0 Unit cell: (142.8, 148.24, 334.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 404 16.00 P 37 15.00 Mg 7 11.99 O 10424 8.00 N 9336 7.00 C 33902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.83 Conformation dependent library (CDL) restraints added in 7.0 seconds 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12752 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 28 sheets defined 58.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A1' and resid 10 through 28 Processing helix chain 'A1' and resid 43 through 47 removed outlier: 3.980A pdb=" N ARGA1 46 " --> pdb=" O GLNA1 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEA1 47 " --> pdb=" O LEUA1 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A1' and resid 43 through 47' Processing helix chain 'A1' and resid 69 through 79 removed outlier: 3.945A pdb=" N META1 73 " --> pdb=" O GLUA1 69 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VALA1 76 " --> pdb=" O THRA1 72 " (cutoff:3.500A) Processing helix chain 'A1' and resid 86 through 90 Processing helix chain 'A1' and resid 100 through 106 Processing helix chain 'A1' and resid 108 through 126 removed outlier: 3.603A pdb=" N LEUA1 112 " --> pdb=" O GLUA1 108 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASPA1 114 " --> pdb=" O ALAA1 110 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SERA1 115 " --> pdb=" O GLUA1 111 " (cutoff:3.500A) Processing helix chain 'A1' and resid 144 through 159 Processing helix chain 'A1' and resid 180 through 196 removed outlier: 4.108A pdb=" N LEUA1 187 " --> pdb=" O TYRA1 183 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLUA1 194 " --> pdb=" O HISA1 190 " (cutoff:3.500A) Processing helix chain 'A1' and resid 204 through 214 Processing helix chain 'A1' and resid 221 through 237 removed outlier: 3.552A pdb=" N LEUA1 225 " --> pdb=" O THRA1 221 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THRA1 237 " --> pdb=" O META1 233 " (cutoff:3.500A) Processing helix chain 'A1' and resid 237 through 242 removed outlier: 3.896A pdb=" N ARGA1 241 " --> pdb=" O THRA1 237 " (cutoff:3.500A) Processing helix chain 'A1' and resid 249 through 258 Processing helix chain 'A1' and resid 278 through 282 removed outlier: 3.966A pdb=" N ARGA1 282 " --> pdb=" O GLNA1 279 " (cutoff:3.500A) Processing helix chain 'A1' and resid 285 through 294 removed outlier: 3.534A pdb=" N GLNA1 292 " --> pdb=" O GLUA1 288 " (cutoff:3.500A) Processing helix chain 'A1' and resid 295 through 299 Processing helix chain 'A1' and resid 304 through 308 Processing helix chain 'A1' and resid 322 through 337 removed outlier: 4.012A pdb=" N ASNA1 337 " --> pdb=" O VALA1 333 " (cutoff:3.500A) Processing helix chain 'A1' and resid 373 through 390 removed outlier: 4.214A pdb=" N META1 377 " --> pdb=" O ALAA1 373 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLNA1 384 " --> pdb=" O ARGA1 380 " (cutoff:3.500A) Processing helix chain 'A1' and resid 395 through 400 Processing helix chain 'A1' and resid 404 through 426 removed outlier: 4.007A pdb=" N PHEA1 408 " --> pdb=" O ASPA1 404 " (cutoff:3.500A) Processing helix chain 'A2' and resid 10 through 28 removed outlier: 3.755A pdb=" N GLUA2 22 " --> pdb=" O ASNA2 18 " (cutoff:3.500A) Processing helix chain 'A2' and resid 47 through 51 removed outlier: 3.738A pdb=" N THRA2 51 " --> pdb=" O ALAA2 48 " (cutoff:3.500A) Processing helix chain 'A2' and resid 71 through 80 removed outlier: 4.544A pdb=" N VALA2 75 " --> pdb=" O GLUA2 71 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VALA2 78 " --> pdb=" O VALA2 74 " (cutoff:3.500A) Processing helix chain 'A2' and resid 88 through 92 Processing helix chain 'A2' and resid 102 through 108 Processing helix chain 'A2' and resid 110 through 129 removed outlier: 4.955A pdb=" N ASPA2 116 " --> pdb=" O LYSA2 112 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEUA2 117 " --> pdb=" O GLUA2 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYSA2 124 " --> pdb=" O ASPA2 120 " (cutoff:3.500A) Processing helix chain 'A2' and resid 147 through 161 Processing helix chain 'A2' and resid 182 through 198 removed outlier: 4.286A pdb=" N SERA2 193 " --> pdb=" O LEUA2 189 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLUA2 196 " --> pdb=" O HISA2 192 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THRA2 198 " --> pdb=" O LEUA2 194 " (cutoff:3.500A) Processing helix chain 'A2' and resid 206 through 216 Processing helix chain 'A2' and resid 223 through 244 removed outlier: 3.850A pdb=" N LEUA2 227 " --> pdb=" O THRA2 223 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SERA2 241 " --> pdb=" O SERA2 237 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEUA2 242 " --> pdb=" O LEUA2 238 " (cutoff:3.500A) Processing helix chain 'A2' and resid 254 through 259 Processing helix chain 'A2' and resid 277 through 284 removed outlier: 4.028A pdb=" N TYRA2 282 " --> pdb=" O ALAA2 278 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HISA2 283 " --> pdb=" O GLUA2 279 " (cutoff:3.500A) Processing helix chain 'A2' and resid 287 through 295 Processing helix chain 'A2' and resid 297 through 301 removed outlier: 3.606A pdb=" N META2 301 " --> pdb=" O PROA2 298 " (cutoff:3.500A) Processing helix chain 'A2' and resid 306 through 310 Processing helix chain 'A2' and resid 324 through 338 removed outlier: 3.782A pdb=" N VALA2 328 " --> pdb=" O VALA2 324 " (cutoff:3.500A) Processing helix chain 'A2' and resid 383 through 400 removed outlier: 3.599A pdb=" N ILEA2 387 " --> pdb=" O ALAA2 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYSA2 394 " --> pdb=" O ARGA2 390 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N META2 398 " --> pdb=" O LYSA2 394 " (cutoff:3.500A) Processing helix chain 'A2' and resid 404 through 412 removed outlier: 4.090A pdb=" N TYRA2 408 " --> pdb=" O PHEA2 404 " (cutoff:3.500A) Processing helix chain 'A2' and resid 414 through 437 removed outlier: 4.439A pdb=" N PHEA2 418 " --> pdb=" O GLUA2 414 " (cutoff:3.500A) Processing helix chain 'A3' and resid 10 through 29 Processing helix chain 'A3' and resid 40 through 45 removed outlier: 4.108A pdb=" N LEUA3 44 " --> pdb=" O SERA3 40 " (cutoff:3.500A) Processing helix chain 'A3' and resid 69 through 79 removed outlier: 4.177A pdb=" N META3 73 " --> pdb=" O GLUA3 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLYA3 79 " --> pdb=" O SERA3 75 " (cutoff:3.500A) Processing helix chain 'A3' and resid 86 through 88 No H-bonds generated for 'chain 'A3' and resid 86 through 88' Processing helix chain 'A3' and resid 100 through 106 Processing helix chain 'A3' and resid 108 through 126 removed outlier: 3.524A pdb=" N LEUA3 112 " --> pdb=" O GLUA3 108 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASPA3 114 " --> pdb=" O ALAA3 110 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SERA3 115 " --> pdb=" O GLUA3 111 " (cutoff:3.500A) Processing helix chain 'A3' and resid 144 through 159 Processing helix chain 'A3' and resid 180 through 196 removed outlier: 3.575A pdb=" N LEUA3 187 " --> pdb=" O TYRA3 183 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLUA3 194 " --> pdb=" O HISA3 190 " (cutoff:3.500A) Processing helix chain 'A3' and resid 204 through 214 Processing helix chain 'A3' and resid 221 through 237 removed outlier: 3.759A pdb=" N LEUA3 225 " --> pdb=" O THRA3 221 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THRA3 237 " --> pdb=" O META3 233 " (cutoff:3.500A) Processing helix chain 'A3' and resid 237 through 242 removed outlier: 3.740A pdb=" N ARGA3 241 " --> pdb=" O THRA3 237 " (cutoff:3.500A) Processing helix chain 'A3' and resid 249 through 258 Processing helix chain 'A3' and resid 285 through 294 removed outlier: 3.557A pdb=" N GLNA3 292 " --> pdb=" O GLUA3 288 " (cutoff:3.500A) Processing helix chain 'A3' and resid 304 through 308 Processing helix chain 'A3' and resid 322 through 337 removed outlier: 3.954A pdb=" N ASNA3 337 " --> pdb=" O VALA3 333 " (cutoff:3.500A) Processing helix chain 'A3' and resid 374 through 390 removed outlier: 3.589A pdb=" N PHEA3 378 " --> pdb=" O ILEA3 374 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLNA3 384 " --> pdb=" O ARGA3 380 " (cutoff:3.500A) Processing helix chain 'A3' and resid 395 through 400 Processing helix chain 'A3' and resid 404 through 426 removed outlier: 4.254A pdb=" N PHEA3 408 " --> pdb=" O ASPA3 404 " (cutoff:3.500A) Processing helix chain 'A4' and resid 10 through 29 removed outlier: 3.507A pdb=" N GLUA4 22 " --> pdb=" O ASNA4 18 " (cutoff:3.500A) Processing helix chain 'A4' and resid 47 through 51 removed outlier: 4.006A pdb=" N THRA4 51 " --> pdb=" O ALAA4 48 " (cutoff:3.500A) Processing helix chain 'A4' and resid 71 through 79 removed outlier: 4.562A pdb=" N VALA4 75 " --> pdb=" O GLUA4 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUA4 77 " --> pdb=" O THRA4 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VALA4 78 " --> pdb=" O VALA4 74 " (cutoff:3.500A) Processing helix chain 'A4' and resid 80 through 86 removed outlier: 6.283A pdb=" N TYRA4 83 " --> pdb=" O THRA4 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARGA4 84 " --> pdb=" O GLYA4 81 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLNA4 85 " --> pdb=" O THRA4 82 " (cutoff:3.500A) Processing helix chain 'A4' and resid 88 through 92 Processing helix chain 'A4' and resid 102 through 108 Processing helix chain 'A4' and resid 110 through 129 removed outlier: 3.799A pdb=" N ILEA4 114 " --> pdb=" O ILEA4 110 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASPA4 116 " --> pdb=" O LYSA4 112 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEUA4 117 " --> pdb=" O GLUA4 113 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYSA4 124 " --> pdb=" O ASPA4 120 " (cutoff:3.500A) Processing helix chain 'A4' and resid 147 through 161 Processing helix chain 'A4' and resid 182 through 198 removed outlier: 3.963A pdb=" N SERA4 193 " --> pdb=" O LEUA4 189 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLUA4 196 " --> pdb=" O HISA4 192 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THRA4 198 " --> pdb=" O LEUA4 194 " (cutoff:3.500A) Processing helix chain 'A4' and resid 206 through 216 Processing helix chain 'A4' and resid 223 through 244 removed outlier: 3.935A pdb=" N LEUA4 227 " --> pdb=" O THRA4 223 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SERA4 241 " --> pdb=" O SERA4 237 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEUA4 242 " --> pdb=" O LEUA4 238 " (cutoff:3.500A) Processing helix chain 'A4' and resid 253 through 259 removed outlier: 3.932A pdb=" N THRA4 257 " --> pdb=" O THRA4 253 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEUA4 259 " --> pdb=" O PHEA4 255 " (cutoff:3.500A) Processing helix chain 'A4' and resid 279 through 284 Processing helix chain 'A4' and resid 287 through 295 removed outlier: 3.616A pdb=" N ILEA4 291 " --> pdb=" O SERA4 287 " (cutoff:3.500A) Processing helix chain 'A4' and resid 297 through 301 removed outlier: 3.605A pdb=" N META4 301 " --> pdb=" O PROA4 298 " (cutoff:3.500A) Processing helix chain 'A4' and resid 324 through 338 removed outlier: 4.065A pdb=" N VALA4 328 " --> pdb=" O VALA4 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASNA4 329 " --> pdb=" O PROA4 325 " (cutoff:3.500A) Processing helix chain 'A4' and resid 383 through 400 removed outlier: 3.660A pdb=" N ILEA4 387 " --> pdb=" O ALAA4 383 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYSA4 394 " --> pdb=" O ARGA4 390 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N META4 398 " --> pdb=" O LYSA4 394 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAA4 400 " --> pdb=" O ASPA4 396 " (cutoff:3.500A) Processing helix chain 'A4' and resid 404 through 412 removed outlier: 4.205A pdb=" N TYRA4 408 " --> pdb=" O PHEA4 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLYA4 412 " --> pdb=" O TYRA4 408 " (cutoff:3.500A) Processing helix chain 'A4' and resid 415 through 437 removed outlier: 3.539A pdb=" N SERA4 419 " --> pdb=" O GLUA4 415 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALAA4 437 " --> pdb=" O GLUA4 433 " (cutoff:3.500A) Processing helix chain 'A5' and resid 10 through 28 Processing helix chain 'A5' and resid 40 through 44 Processing helix chain 'A5' and resid 69 through 79 removed outlier: 4.199A pdb=" N META5 73 " --> pdb=" O GLUA5 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLYA5 79 " --> pdb=" O SERA5 75 " (cutoff:3.500A) Processing helix chain 'A5' and resid 86 through 90 Processing helix chain 'A5' and resid 100 through 106 Processing helix chain 'A5' and resid 108 through 126 removed outlier: 5.389A pdb=" N ASPA5 114 " --> pdb=" O ALAA5 110 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SERA5 115 " --> pdb=" O GLUA5 111 " (cutoff:3.500A) Processing helix chain 'A5' and resid 144 through 157 Processing helix chain 'A5' and resid 180 through 196 removed outlier: 4.016A pdb=" N LEUA5 187 " --> pdb=" O TYRA5 183 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLUA5 194 " --> pdb=" O HISA5 190 " (cutoff:3.500A) Processing helix chain 'A5' and resid 204 through 214 Processing helix chain 'A5' and resid 221 through 237 removed outlier: 3.808A pdb=" N LEUA5 225 " --> pdb=" O THRA5 221 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THRA5 237 " --> pdb=" O META5 233 " (cutoff:3.500A) Processing helix chain 'A5' and resid 237 through 242 removed outlier: 3.868A pdb=" N ARGA5 241 " --> pdb=" O THRA5 237 " (cutoff:3.500A) Processing helix chain 'A5' and resid 249 through 258 Processing helix chain 'A5' and resid 278 through 282 removed outlier: 3.883A pdb=" N ARGA5 282 " --> pdb=" O GLNA5 279 " (cutoff:3.500A) Processing helix chain 'A5' and resid 285 through 294 removed outlier: 3.507A pdb=" N GLNA5 292 " --> pdb=" O GLUA5 288 " (cutoff:3.500A) Processing helix chain 'A5' and resid 295 through 299 Processing helix chain 'A5' and resid 304 through 308 Processing helix chain 'A5' and resid 322 through 337 removed outlier: 3.929A pdb=" N ASNA5 337 " --> pdb=" O VALA5 333 " (cutoff:3.500A) Processing helix chain 'A5' and resid 338 through 341 Processing helix chain 'A5' and resid 374 through 390 removed outlier: 3.757A pdb=" N PHEA5 378 " --> pdb=" O ILEA5 374 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLNA5 384 " --> pdb=" O ARGA5 380 " (cutoff:3.500A) Processing helix chain 'A5' and resid 395 through 400 Processing helix chain 'A5' and resid 404 through 426 removed outlier: 4.232A pdb=" N PHEA5 408 " --> pdb=" O ASPA5 404 " (cutoff:3.500A) Processing helix chain 'A6' and resid 10 through 26 removed outlier: 3.883A pdb=" N GLUA6 22 " --> pdb=" O ASNA6 18 " (cutoff:3.500A) Processing helix chain 'A6' and resid 47 through 51 removed outlier: 3.576A pdb=" N THRA6 51 " --> pdb=" O ALAA6 48 " (cutoff:3.500A) Processing helix chain 'A6' and resid 72 through 81 removed outlier: 3.531A pdb=" N GLUA6 77 " --> pdb=" O THRA6 73 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VALA6 78 " --> pdb=" O VALA6 74 " (cutoff:3.500A) Processing helix chain 'A6' and resid 88 through 92 Processing helix chain 'A6' and resid 102 through 108 Processing helix chain 'A6' and resid 110 through 129 removed outlier: 4.071A pdb=" N ILEA6 114 " --> pdb=" O ILEA6 110 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASPA6 116 " --> pdb=" O LYSA6 112 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEUA6 117 " --> pdb=" O GLUA6 113 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYSA6 124 " --> pdb=" O ASPA6 120 " (cutoff:3.500A) Processing helix chain 'A6' and resid 147 through 161 Processing helix chain 'A6' and resid 182 through 197 removed outlier: 3.919A pdb=" N SERA6 193 " --> pdb=" O LEUA6 189 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLUA6 196 " --> pdb=" O HISA6 192 " (cutoff:3.500A) Processing helix chain 'A6' and resid 206 through 216 Processing helix chain 'A6' and resid 223 through 244 removed outlier: 3.703A pdb=" N LEUA6 227 " --> pdb=" O THRA6 223 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SERA6 241 " --> pdb=" O SERA6 237 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEUA6 242 " --> pdb=" O LEUA6 238 " (cutoff:3.500A) Processing helix chain 'A6' and resid 254 through 259 removed outlier: 3.607A pdb=" N LEUA6 259 " --> pdb=" O PHEA6 255 " (cutoff:3.500A) Processing helix chain 'A6' and resid 277 through 283 Processing helix chain 'A6' and resid 287 through 295 removed outlier: 3.961A pdb=" N ILEA6 291 " --> pdb=" O SERA6 287 " (cutoff:3.500A) Processing helix chain 'A6' and resid 297 through 301 removed outlier: 3.614A pdb=" N META6 301 " --> pdb=" O PROA6 298 " (cutoff:3.500A) Processing helix chain 'A6' and resid 324 through 338 removed outlier: 3.998A pdb=" N VALA6 328 " --> pdb=" O VALA6 324 " (cutoff:3.500A) Processing helix chain 'A6' and resid 382 through 400 removed outlier: 3.912A pdb=" N GLUA6 386 " --> pdb=" O THRA6 382 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHEA6 388 " --> pdb=" O ILEA6 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SERA6 389 " --> pdb=" O GLYA6 385 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGA6 390 " --> pdb=" O GLUA6 386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYSA6 394 " --> pdb=" O ARGA6 390 " (cutoff:3.500A) Processing helix chain 'A6' and resid 404 through 412 removed outlier: 4.010A pdb=" N TYRA6 408 " --> pdb=" O PHEA6 404 " (cutoff:3.500A) Processing helix chain 'A6' and resid 415 through 437 Processing helix chain 'A7' and resid 10 through 28 Processing helix chain 'A7' and resid 40 through 44 removed outlier: 3.745A pdb=" N GLNA7 43 " --> pdb=" O SERA7 40 " (cutoff:3.500A) Processing helix chain 'A7' and resid 69 through 79 removed outlier: 4.098A pdb=" N META7 73 " --> pdb=" O GLUA7 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLYA7 79 " --> pdb=" O SERA7 75 " (cutoff:3.500A) Processing helix chain 'A7' and resid 86 through 88 No H-bonds generated for 'chain 'A7' and resid 86 through 88' Processing helix chain 'A7' and resid 100 through 106 Processing helix chain 'A7' and resid 108 through 126 removed outlier: 5.257A pdb=" N ASPA7 114 " --> pdb=" O ALAA7 110 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SERA7 115 " --> pdb=" O GLUA7 111 " (cutoff:3.500A) Processing helix chain 'A7' and resid 144 through 159 Processing helix chain 'A7' and resid 180 through 196 removed outlier: 3.834A pdb=" N LEUA7 187 " --> pdb=" O TYRA7 183 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLUA7 194 " --> pdb=" O HISA7 190 " (cutoff:3.500A) Processing helix chain 'A7' and resid 203 through 214 Processing helix chain 'A7' and resid 221 through 242 removed outlier: 3.747A pdb=" N LEUA7 225 " --> pdb=" O THRA7 221 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYSA7 239 " --> pdb=" O GLYA7 235 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEUA7 240 " --> pdb=" O ILEA7 236 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARGA7 241 " --> pdb=" O THRA7 237 " (cutoff:3.500A) Processing helix chain 'A7' and resid 249 through 258 Processing helix chain 'A7' and resid 285 through 294 Processing helix chain 'A7' and resid 304 through 308 Processing helix chain 'A7' and resid 322 through 337 removed outlier: 3.836A pdb=" N ASNA7 337 " --> pdb=" O VALA7 333 " (cutoff:3.500A) Processing helix chain 'A7' and resid 374 through 390 removed outlier: 3.702A pdb=" N PHEA7 378 " --> pdb=" O ILEA7 374 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLNA7 384 " --> pdb=" O ARGA7 380 " (cutoff:3.500A) Processing helix chain 'A7' and resid 395 through 400 Processing helix chain 'A7' and resid 404 through 426 removed outlier: 4.076A pdb=" N PHEA7 408 " --> pdb=" O ASPA7 404 " (cutoff:3.500A) Processing helix chain 'B1' and resid 10 through 28 Processing helix chain 'B1' and resid 41 through 46 removed outlier: 3.943A pdb=" N GLUB1 45 " --> pdb=" O ASPB1 41 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARGB1 46 " --> pdb=" O LEUB1 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 41 through 46' Processing helix chain 'B1' and resid 69 through 79 removed outlier: 4.131A pdb=" N METB1 73 " --> pdb=" O GLUB1 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLYB1 79 " --> pdb=" O SERB1 75 " (cutoff:3.500A) Processing helix chain 'B1' and resid 86 through 90 Processing helix chain 'B1' and resid 100 through 106 Processing helix chain 'B1' and resid 108 through 126 removed outlier: 3.500A pdb=" N LEUB1 112 " --> pdb=" O GLUB1 108 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASPB1 114 " --> pdb=" O ALAB1 110 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SERB1 115 " --> pdb=" O GLUB1 111 " (cutoff:3.500A) Processing helix chain 'B1' and resid 144 through 159 Processing helix chain 'B1' and resid 180 through 196 removed outlier: 3.889A pdb=" N LEUB1 187 " --> pdb=" O TYRB1 183 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLUB1 194 " --> pdb=" O HISB1 190 " (cutoff:3.500A) Processing helix chain 'B1' and resid 204 through 214 Processing helix chain 'B1' and resid 221 through 237 removed outlier: 3.692A pdb=" N LEUB1 225 " --> pdb=" O THRB1 221 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THRB1 237 " --> pdb=" O METB1 233 " (cutoff:3.500A) Processing helix chain 'B1' and resid 237 through 242 removed outlier: 3.602A pdb=" N ARGB1 241 " --> pdb=" O THRB1 237 " (cutoff:3.500A) Processing helix chain 'B1' and resid 249 through 258 Processing helix chain 'B1' and resid 285 through 294 Processing helix chain 'B1' and resid 295 through 299 removed outlier: 3.742A pdb=" N METB1 299 " --> pdb=" O ALAB1 296 " (cutoff:3.500A) Processing helix chain 'B1' and resid 304 through 308 Processing helix chain 'B1' and resid 322 through 337 removed outlier: 3.635A pdb=" N VALB1 326 " --> pdb=" O SERB1 322 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASNB1 337 " --> pdb=" O VALB1 333 " (cutoff:3.500A) Processing helix chain 'B1' and resid 373 through 391 removed outlier: 4.210A pdb=" N METB1 377 " --> pdb=" O ALAB1 373 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLNB1 384 " --> pdb=" O ARGB1 380 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARGB1 391 " --> pdb=" O ALAB1 387 " (cutoff:3.500A) Processing helix chain 'B1' and resid 395 through 400 Processing helix chain 'B1' and resid 404 through 426 removed outlier: 4.079A pdb=" N PHEB1 408 " --> pdb=" O ASPB1 404 " (cutoff:3.500A) Processing helix chain 'B2' and resid 10 through 28 removed outlier: 3.754A pdb=" N GLUB2 22 " --> pdb=" O ASNB2 18 " (cutoff:3.500A) Processing helix chain 'B2' and resid 47 through 52 removed outlier: 3.861A pdb=" N THRB2 51 " --> pdb=" O ALAB2 48 " (cutoff:3.500A) Processing helix chain 'B2' and resid 71 through 81 removed outlier: 4.506A pdb=" N VALB2 75 " --> pdb=" O GLUB2 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALB2 78 " --> pdb=" O VALB2 74 " (cutoff:3.500A) Processing helix chain 'B2' and resid 88 through 92 Processing helix chain 'B2' and resid 110 through 129 removed outlier: 3.679A pdb=" N ILEB2 114 " --> pdb=" O ILEB2 110 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASPB2 116 " --> pdb=" O LYSB2 112 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUB2 117 " --> pdb=" O GLUB2 113 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYSB2 124 " --> pdb=" O ASPB2 120 " (cutoff:3.500A) Processing helix chain 'B2' and resid 147 through 161 Processing helix chain 'B2' and resid 182 through 198 removed outlier: 4.421A pdb=" N SERB2 193 " --> pdb=" O LEUB2 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLUB2 196 " --> pdb=" O HISB2 192 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THRB2 198 " --> pdb=" O LEUB2 194 " (cutoff:3.500A) Processing helix chain 'B2' and resid 206 through 216 Processing helix chain 'B2' and resid 223 through 244 removed outlier: 3.711A pdb=" N LEUB2 227 " --> pdb=" O THRB2 223 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SERB2 241 " --> pdb=" O SERB2 237 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEUB2 242 " --> pdb=" O LEUB2 238 " (cutoff:3.500A) Processing helix chain 'B2' and resid 251 through 259 removed outlier: 4.273A pdb=" N PHEB2 255 " --> pdb=" O ASPB2 251 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLNB2 256 " --> pdb=" O ILEB2 252 " (cutoff:3.500A) Processing helix chain 'B2' and resid 277 through 284 removed outlier: 3.715A pdb=" N TYRB2 282 " --> pdb=" O ALAB2 278 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HISB2 283 " --> pdb=" O GLUB2 279 " (cutoff:3.500A) Processing helix chain 'B2' and resid 287 through 295 Processing helix chain 'B2' and resid 296 through 301 removed outlier: 6.207A pdb=" N ALAB2 299 " --> pdb=" O PHEB2 296 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N METB2 301 " --> pdb=" O PROB2 298 " (cutoff:3.500A) Processing helix chain 'B2' and resid 306 through 310 Processing helix chain 'B2' and resid 324 through 338 removed outlier: 3.848A pdb=" N VALB2 328 " --> pdb=" O VALB2 324 " (cutoff:3.500A) Processing helix chain 'B2' and resid 382 through 401 removed outlier: 3.582A pdb=" N GLUB2 386 " --> pdb=" O THRB2 382 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SERB2 389 " --> pdb=" O GLYB2 385 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYSB2 394 " --> pdb=" O ARGB2 390 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N METB2 398 " --> pdb=" O LYSB2 394 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYSB2 401 " --> pdb=" O LEUB2 397 " (cutoff:3.500A) Processing helix chain 'B2' and resid 404 through 412 removed outlier: 4.293A pdb=" N TYRB2 408 " --> pdb=" O PHEB2 404 " (cutoff:3.500A) Processing helix chain 'B2' and resid 415 through 436 removed outlier: 4.068A pdb=" N SERB2 419 " --> pdb=" O GLUB2 415 " (cutoff:3.500A) Processing helix chain 'B3' and resid 10 through 28 Processing helix chain 'B3' and resid 40 through 44 removed outlier: 3.597A pdb=" N GLNB3 43 " --> pdb=" O SERB3 40 " (cutoff:3.500A) Processing helix chain 'B3' and resid 69 through 79 removed outlier: 4.079A pdb=" N METB3 73 " --> pdb=" O GLUB3 69 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLYB3 79 " --> pdb=" O SERB3 75 " (cutoff:3.500A) Processing helix chain 'B3' and resid 86 through 88 No H-bonds generated for 'chain 'B3' and resid 86 through 88' Processing helix chain 'B3' and resid 100 through 106 Processing helix chain 'B3' and resid 108 through 126 removed outlier: 5.265A pdb=" N ASPB3 114 " --> pdb=" O ALAB3 110 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SERB3 115 " --> pdb=" O GLUB3 111 " (cutoff:3.500A) Processing helix chain 'B3' and resid 144 through 159 Processing helix chain 'B3' and resid 180 through 196 removed outlier: 3.799A pdb=" N LEUB3 187 " --> pdb=" O TYRB3 183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLNB3 191 " --> pdb=" O LEUB3 187 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLUB3 194 " --> pdb=" O HISB3 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALAB3 196 " --> pdb=" O LEUB3 192 " (cutoff:3.500A) Processing helix chain 'B3' and resid 203 through 214 removed outlier: 3.627A pdb=" N LEUB3 207 " --> pdb=" O ASPB3 203 " (cutoff:3.500A) Processing helix chain 'B3' and resid 221 through 237 removed outlier: 3.669A pdb=" N LEUB3 225 " --> pdb=" O THRB3 221 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THRB3 237 " --> pdb=" O METB3 233 " (cutoff:3.500A) Processing helix chain 'B3' and resid 237 through 242 removed outlier: 3.713A pdb=" N ARGB3 241 " --> pdb=" O THRB3 237 " (cutoff:3.500A) Processing helix chain 'B3' and resid 249 through 258 Processing helix chain 'B3' and resid 285 through 294 removed outlier: 3.635A pdb=" N GLNB3 292 " --> pdb=" O GLUB3 288 " (cutoff:3.500A) Processing helix chain 'B3' and resid 295 through 299 removed outlier: 3.662A pdb=" N METB3 299 " --> pdb=" O ALAB3 296 " (cutoff:3.500A) Processing helix chain 'B3' and resid 304 through 308 Processing helix chain 'B3' and resid 322 through 337 removed outlier: 3.648A pdb=" N ASNB3 337 " --> pdb=" O VALB3 333 " (cutoff:3.500A) Processing helix chain 'B3' and resid 374 through 391 removed outlier: 3.641A pdb=" N PHEB3 378 " --> pdb=" O ILEB3 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLNB3 384 " --> pdb=" O ARGB3 380 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARGB3 391 " --> pdb=" O ALAB3 387 " (cutoff:3.500A) Processing helix chain 'B3' and resid 395 through 400 Processing helix chain 'B3' and resid 404 through 426 removed outlier: 4.277A pdb=" N PHEB3 408 " --> pdb=" O ASPB3 404 " (cutoff:3.500A) Processing helix chain 'B4' and resid 10 through 28 removed outlier: 3.583A pdb=" N GLNB4 15 " --> pdb=" O GLNB4 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLUB4 22 " --> pdb=" O ASNB4 18 " (cutoff:3.500A) Processing helix chain 'B4' and resid 47 through 52 removed outlier: 3.852A pdb=" N THRB4 51 " --> pdb=" O ALAB4 48 " (cutoff:3.500A) Processing helix chain 'B4' and resid 71 through 81 removed outlier: 4.698A pdb=" N VALB4 75 " --> pdb=" O GLUB4 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VALB4 78 " --> pdb=" O VALB4 74 " (cutoff:3.500A) Processing helix chain 'B4' and resid 110 through 129 removed outlier: 3.966A pdb=" N ILEB4 114 " --> pdb=" O ILEB4 110 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASPB4 116 " --> pdb=" O LYSB4 112 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEUB4 117 " --> pdb=" O GLUB4 113 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYSB4 124 " --> pdb=" O ASPB4 120 " (cutoff:3.500A) Processing helix chain 'B4' and resid 147 through 161 Processing helix chain 'B4' and resid 182 through 198 removed outlier: 4.533A pdb=" N SERB4 193 " --> pdb=" O LEUB4 189 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLUB4 196 " --> pdb=" O HISB4 192 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THRB4 198 " --> pdb=" O LEUB4 194 " (cutoff:3.500A) Processing helix chain 'B4' and resid 206 through 216 Processing helix chain 'B4' and resid 223 through 244 removed outlier: 3.635A pdb=" N LEUB4 227 " --> pdb=" O THRB4 223 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SERB4 241 " --> pdb=" O SERB4 237 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEUB4 242 " --> pdb=" O LEUB4 238 " (cutoff:3.500A) Processing helix chain 'B4' and resid 251 through 259 removed outlier: 3.847A pdb=" N PHEB4 255 " --> pdb=" O ASPB4 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLNB4 256 " --> pdb=" O ILEB4 252 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THRB4 257 " --> pdb=" O THRB4 253 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEUB4 259 " --> pdb=" O PHEB4 255 " (cutoff:3.500A) Processing helix chain 'B4' and resid 277 through 284 removed outlier: 3.704A pdb=" N ALAB4 281 " --> pdb=" O SERB4 277 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYRB4 282 " --> pdb=" O ALAB4 278 " (cutoff:3.500A) Processing helix chain 'B4' and resid 287 through 295 removed outlier: 3.637A pdb=" N ILEB4 291 " --> pdb=" O SERB4 287 " (cutoff:3.500A) Processing helix chain 'B4' and resid 297 through 301 removed outlier: 3.777A pdb=" N METB4 301 " --> pdb=" O PROB4 298 " (cutoff:3.500A) Processing helix chain 'B4' and resid 324 through 338 removed outlier: 3.947A pdb=" N VALB4 328 " --> pdb=" O VALB4 324 " (cutoff:3.500A) Processing helix chain 'B4' and resid 383 through 401 removed outlier: 3.899A pdb=" N ILEB4 387 " --> pdb=" O ALAB4 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHEB4 388 " --> pdb=" O ILEB4 384 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERB4 389 " --> pdb=" O GLYB4 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HISB4 393 " --> pdb=" O SERB4 389 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYSB4 394 " --> pdb=" O ARGB4 390 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYSB4 401 " --> pdb=" O LEUB4 397 " (cutoff:3.500A) Processing helix chain 'B4' and resid 404 through 412 removed outlier: 3.925A pdb=" N TYRB4 408 " --> pdb=" O PHEB4 404 " (cutoff:3.500A) Processing helix chain 'B4' and resid 414 through 437 removed outlier: 4.134A pdb=" N PHEB4 418 " --> pdb=" O GLUB4 414 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALAB4 437 " --> pdb=" O GLUB4 433 " (cutoff:3.500A) Processing helix chain 'B5' and resid 10 through 28 Processing helix chain 'B5' and resid 40 through 44 removed outlier: 3.575A pdb=" N GLNB5 43 " --> pdb=" O SERB5 40 " (cutoff:3.500A) Processing helix chain 'B5' and resid 69 through 79 removed outlier: 4.182A pdb=" N METB5 73 " --> pdb=" O GLUB5 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLYB5 79 " --> pdb=" O SERB5 75 " (cutoff:3.500A) Processing helix chain 'B5' and resid 86 through 88 No H-bonds generated for 'chain 'B5' and resid 86 through 88' Processing helix chain 'B5' and resid 100 through 106 Processing helix chain 'B5' and resid 108 through 125 removed outlier: 3.654A pdb=" N LEUB5 112 " --> pdb=" O GLUB5 108 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASPB5 114 " --> pdb=" O ALAB5 110 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SERB5 115 " --> pdb=" O GLUB5 111 " (cutoff:3.500A) Processing helix chain 'B5' and resid 144 through 159 Processing helix chain 'B5' and resid 180 through 196 removed outlier: 3.718A pdb=" N LEUB5 187 " --> pdb=" O TYRB5 183 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLUB5 194 " --> pdb=" O HISB5 190 " (cutoff:3.500A) Processing helix chain 'B5' and resid 203 through 214 removed outlier: 3.581A pdb=" N LEUB5 207 " --> pdb=" O ASPB5 203 " (cutoff:3.500A) Processing helix chain 'B5' and resid 221 through 237 removed outlier: 3.536A pdb=" N LEUB5 225 " --> pdb=" O THRB5 221 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THRB5 237 " --> pdb=" O METB5 233 " (cutoff:3.500A) Processing helix chain 'B5' and resid 237 through 242 removed outlier: 4.200A pdb=" N ARGB5 241 " --> pdb=" O THRB5 237 " (cutoff:3.500A) Processing helix chain 'B5' and resid 249 through 258 Processing helix chain 'B5' and resid 275 through 279 removed outlier: 3.644A pdb=" N GLNB5 279 " --> pdb=" O ARGB5 276 " (cutoff:3.500A) Processing helix chain 'B5' and resid 285 through 294 Processing helix chain 'B5' and resid 295 through 299 removed outlier: 3.856A pdb=" N METB5 299 " --> pdb=" O ALAB5 296 " (cutoff:3.500A) Processing helix chain 'B5' and resid 304 through 308 Processing helix chain 'B5' and resid 322 through 337 removed outlier: 3.746A pdb=" N ASNB5 337 " --> pdb=" O VALB5 333 " (cutoff:3.500A) Processing helix chain 'B5' and resid 374 through 390 removed outlier: 3.798A pdb=" N PHEB5 378 " --> pdb=" O ILEB5 374 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLNB5 384 " --> pdb=" O ARGB5 380 " (cutoff:3.500A) Processing helix chain 'B5' and resid 395 through 400 Processing helix chain 'B5' and resid 404 through 426 removed outlier: 3.941A pdb=" N PHEB5 408 " --> pdb=" O ASPB5 404 " (cutoff:3.500A) Processing helix chain 'B6' and resid 10 through 29 Processing helix chain 'B6' and resid 47 through 51 removed outlier: 4.093A pdb=" N THRB6 51 " --> pdb=" O ALAB6 48 " (cutoff:3.500A) Processing helix chain 'B6' and resid 71 through 80 removed outlier: 4.694A pdb=" N VALB6 75 " --> pdb=" O GLUB6 71 " (cutoff:3.500A) Processing helix chain 'B6' and resid 102 through 108 Processing helix chain 'B6' and resid 110 through 129 removed outlier: 3.848A pdb=" N ILEB6 114 " --> pdb=" O ILEB6 110 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASPB6 116 " --> pdb=" O LYSB6 112 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEUB6 117 " --> pdb=" O GLUB6 113 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYSB6 124 " --> pdb=" O ASPB6 120 " (cutoff:3.500A) Processing helix chain 'B6' and resid 144 through 161 Processing helix chain 'B6' and resid 182 through 195 removed outlier: 4.539A pdb=" N SERB6 193 " --> pdb=" O LEUB6 189 " (cutoff:3.500A) Processing helix chain 'B6' and resid 205 through 216 removed outlier: 3.863A pdb=" N ILEB6 209 " --> pdb=" O ASPB6 205 " (cutoff:3.500A) Processing helix chain 'B6' and resid 223 through 244 removed outlier: 3.711A pdb=" N LEUB6 227 " --> pdb=" O THRB6 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SERB6 241 " --> pdb=" O SERB6 237 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEUB6 242 " --> pdb=" O LEUB6 238 " (cutoff:3.500A) Processing helix chain 'B6' and resid 252 through 260 removed outlier: 4.193A pdb=" N GLNB6 256 " --> pdb=" O ILEB6 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALB6 260 " --> pdb=" O GLNB6 256 " (cutoff:3.500A) Processing helix chain 'B6' and resid 277 through 284 removed outlier: 3.659A pdb=" N HISB6 283 " --> pdb=" O GLUB6 279 " (cutoff:3.500A) Processing helix chain 'B6' and resid 287 through 295 Processing helix chain 'B6' and resid 297 through 301 removed outlier: 3.700A pdb=" N METB6 301 " --> pdb=" O PROB6 298 " (cutoff:3.500A) Processing helix chain 'B6' and resid 306 through 310 Processing helix chain 'B6' and resid 324 through 338 removed outlier: 3.613A pdb=" N VALB6 328 " --> pdb=" O VALB6 324 " (cutoff:3.500A) Processing helix chain 'B6' and resid 383 through 401 removed outlier: 3.657A pdb=" N SERB6 389 " --> pdb=" O GLYB6 385 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSB6 394 " --> pdb=" O ARGB6 390 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N METB6 398 " --> pdb=" O LYSB6 394 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYSB6 401 " --> pdb=" O LEUB6 397 " (cutoff:3.500A) Processing helix chain 'B6' and resid 404 through 412 removed outlier: 3.974A pdb=" N TYRB6 408 " --> pdb=" O PHEB6 404 " (cutoff:3.500A) Processing helix chain 'B6' and resid 414 through 436 removed outlier: 4.441A pdb=" N PHEB6 418 " --> pdb=" O GLUB6 414 " (cutoff:3.500A) Processing helix chain 'B7' and resid 10 through 29 Processing helix chain 'B7' and resid 40 through 47 removed outlier: 3.855A pdb=" N GLUB7 45 " --> pdb=" O LEUB7 42 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARGB7 46 " --> pdb=" O GLNB7 43 " (cutoff:3.500A) Processing helix chain 'B7' and resid 69 through 79 removed outlier: 4.175A pdb=" N METB7 73 " --> pdb=" O GLUB7 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SERB7 75 " --> pdb=" O GLYB7 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALB7 76 " --> pdb=" O THRB7 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLYB7 79 " --> pdb=" O SERB7 75 " (cutoff:3.500A) Processing helix chain 'B7' and resid 86 through 90 Processing helix chain 'B7' and resid 100 through 106 Processing helix chain 'B7' and resid 108 through 125 removed outlier: 3.742A pdb=" N LEUB7 112 " --> pdb=" O GLUB7 108 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASPB7 114 " --> pdb=" O ALAB7 110 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SERB7 115 " --> pdb=" O GLUB7 111 " (cutoff:3.500A) Processing helix chain 'B7' and resid 144 through 159 Processing helix chain 'B7' and resid 180 through 196 removed outlier: 3.820A pdb=" N LEUB7 187 " --> pdb=" O TYRB7 183 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLUB7 194 " --> pdb=" O HISB7 190 " (cutoff:3.500A) Processing helix chain 'B7' and resid 204 through 214 Processing helix chain 'B7' and resid 221 through 237 removed outlier: 3.913A pdb=" N LEUB7 225 " --> pdb=" O THRB7 221 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THRB7 237 " --> pdb=" O METB7 233 " (cutoff:3.500A) Processing helix chain 'B7' and resid 237 through 242 removed outlier: 3.746A pdb=" N ARGB7 241 " --> pdb=" O THRB7 237 " (cutoff:3.500A) Processing helix chain 'B7' and resid 249 through 258 Processing helix chain 'B7' and resid 285 through 294 removed outlier: 3.629A pdb=" N GLNB7 292 " --> pdb=" O GLUB7 288 " (cutoff:3.500A) Processing helix chain 'B7' and resid 295 through 299 removed outlier: 3.804A pdb=" N METB7 299 " --> pdb=" O ALAB7 296 " (cutoff:3.500A) Processing helix chain 'B7' and resid 304 through 308 Processing helix chain 'B7' and resid 322 through 337 removed outlier: 3.875A pdb=" N ASNB7 337 " --> pdb=" O VALB7 333 " (cutoff:3.500A) Processing helix chain 'B7' and resid 338 through 341 removed outlier: 3.651A pdb=" N PHEB7 341 " --> pdb=" O SERB7 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B7' and resid 338 through 341' Processing helix chain 'B7' and resid 373 through 390 removed outlier: 4.293A pdb=" N METB7 377 " --> pdb=" O ALAB7 373 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLNB7 384 " --> pdb=" O ARGB7 380 " (cutoff:3.500A) Processing helix chain 'B7' and resid 395 through 400 Processing helix chain 'B7' and resid 404 through 426 removed outlier: 3.964A pdb=" N PHEB7 408 " --> pdb=" O ASPB7 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 removed outlier: 3.573A pdb=" N LEU C 300 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.750A pdb=" N GLN C 309 " --> pdb=" O PRO C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 330 removed outlier: 4.037A pdb=" N GLU C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 339 through 362 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 414 through 440 removed outlier: 4.054A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.745A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 506 removed outlier: 4.275A pdb=" N ASP C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 486 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 278 removed outlier: 3.792A pdb=" N GLU X 254 " --> pdb=" O GLN X 250 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU X 255 " --> pdb=" O ALA X 251 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA X 256 " --> pdb=" O GLU X 252 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG X 257 " --> pdb=" O ARG X 253 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 346 removed outlier: 3.957A pdb=" N TYR X 322 " --> pdb=" O GLU X 318 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA X 330 " --> pdb=" O VAL X 326 " (cutoff:3.500A) Proline residue: X 331 - end of helix Processing helix chain 'X' and resid 350 through 382 Processing helix chain 'Y' and resid 176 through 247 Processing helix chain 'Y' and resid 268 through 281 Processing helix chain 'Y' and resid 283 through 314 removed outlier: 3.972A pdb=" N LYS Y 295 " --> pdb=" O VAL Y 291 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL Y 296 " --> pdb=" O ALA Y 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET Y 298 " --> pdb=" O GLU Y 294 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN Y 301 " --> pdb=" O GLU Y 297 " (cutoff:3.500A) Processing helix chain 'X1' and resid 120 through 167 removed outlier: 3.825A pdb=" N ARGX1 130 " --> pdb=" O LYSX1 126 " (cutoff:3.500A) Processing helix chain 'X1' and resid 171 through 261 removed outlier: 4.390A pdb=" N TYRX1 177 " --> pdb=" O GLUX1 173 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSX1 219 " --> pdb=" O ALAX1 215 " (cutoff:3.500A) Processing helix chain 'Y1' and resid 68 through 115 removed outlier: 3.622A pdb=" N ASNY1 74 " --> pdb=" O GLNY1 70 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLNY1 99 " --> pdb=" O LYSY1 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLNY1 100 " --> pdb=" O METY1 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SERY1 102 " --> pdb=" O ASPY1 98 " (cutoff:3.500A) Processing helix chain 'Y1' and resid 119 through 213 removed outlier: 3.814A pdb=" N METY1 169 " --> pdb=" O ARGY1 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 27 removed outlier: 5.246A pdb=" N ASN Z 17 " --> pdb=" O LYS Z 13 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG Z 21 " --> pdb=" O ASN Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 47 removed outlier: 3.532A pdb=" N LEU Z 39 " --> pdb=" O ASP Z 35 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR Z 40 " --> pdb=" O ALA Z 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 63 removed outlier: 3.786A pdb=" N VAL Z 62 " --> pdb=" O MET Z 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP Z 63 " --> pdb=" O ILE Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 84 Processing helix chain 'Z' and resid 92 through 103 removed outlier: 3.731A pdb=" N ASN Z 96 " --> pdb=" O ARG Z 92 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL Z 97 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 122 removed outlier: 3.986A pdb=" N ALA Z 116 " --> pdb=" O THR Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 133 removed outlier: 3.519A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 162 removed outlier: 3.724A pdb=" N LEU Z 148 " --> pdb=" O SER Z 144 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU Z 150 " --> pdb=" O LYS Z 146 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR Z 151 " --> pdb=" O ILE Z 147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Z 162 " --> pdb=" O HIS Z 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A1' and resid 63 through 66 removed outlier: 9.040A pdb=" N ILEA1 64 " --> pdb=" O ILEA1 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HISA1 6 " --> pdb=" O ILEA1 64 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N META1 66 " --> pdb=" O HISA1 6 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLNA1 8 " --> pdb=" O META1 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLUA1 3 " --> pdb=" O GLNA1 131 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N PHEA1 133 " --> pdb=" O GLUA1 3 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VALA1 5 " --> pdb=" O PHEA1 133 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VALA1 135 " --> pdb=" O VALA1 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILEA1 7 " --> pdb=" O VALA1 135 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HISA1 137 " --> pdb=" O ILEA1 7 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLYA1 9 " --> pdb=" O HISA1 137 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N META1 163 " --> pdb=" O CYSA1 129 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLNA1 131 " --> pdb=" O META1 163 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEUA1 165 " --> pdb=" O GLNA1 131 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHEA1 133 " --> pdb=" O LEUA1 165 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHEA1 167 " --> pdb=" O PHEA1 133 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VALA1 135 " --> pdb=" O PHEA1 167 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VALA1 169 " --> pdb=" O VALA1 135 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N HISA1 137 " --> pdb=" O VALA1 169 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N META1 164 " --> pdb=" O GLUA1 198 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N META1 200 " --> pdb=" O META1 164 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THRA1 166 " --> pdb=" O META1 200 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEUA1 202 " --> pdb=" O THRA1 166 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SERA1 168 " --> pdb=" O LEUA1 202 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N CYSA1 199 " --> pdb=" O PHEA1 266 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VALA1 268 " --> pdb=" O CYSA1 199 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VALA1 201 " --> pdb=" O VALA1 268 " (cutoff:3.500A) removed outlier: 10.982A pdb=" N PHEA1 270 " --> pdb=" O VALA1 201 " (cutoff:3.500A) removed outlier: 14.438A pdb=" N ASPA1 203 " --> pdb=" O PHEA1 270 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHEA1 265 " --> pdb=" O SERA1 371 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SERA1 371 " --> pdb=" O PHEA1 265 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THRA1 312 " --> pdb=" O ASNA1 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A1' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A2' and resid 65 through 68 removed outlier: 6.855A pdb=" N SERA2 6 " --> pdb=" O ILEA2 66 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEUA2 68 " --> pdb=" O SERA2 6 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N HISA2 8 " --> pdb=" O LEUA2 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILEA2 5 " --> pdb=" O GLYA2 134 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALAA2 140 " --> pdb=" O ILEA2 9 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHEA2 135 " --> pdb=" O LEUA2 167 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHEA2 169 " --> pdb=" O PHEA2 135 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VALA2 137 " --> pdb=" O PHEA2 169 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VALA2 171 " --> pdb=" O VALA2 137 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASNA2 139 " --> pdb=" O VALA2 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VALA2 200 " --> pdb=" O LYSA2 166 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SERA2 270 " --> pdb=" O META2 203 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALAA2 314 " --> pdb=" O ASNA2 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A2' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A3' and resid 90 through 92 removed outlier: 3.929A pdb=" N ASPA3 67 " --> pdb=" O VALA3 91 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLUA3 3 " --> pdb=" O LEUA3 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLYA3 132 " --> pdb=" O GLUA3 3 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VALA3 5 " --> pdb=" O GLYA3 132 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SERA3 138 " --> pdb=" O GLYA3 9 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N META3 163 " --> pdb=" O CYSA3 129 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLNA3 131 " --> pdb=" O META3 163 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEUA3 165 " --> pdb=" O GLNA3 131 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHEA3 133 " --> pdb=" O LEUA3 165 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHEA3 167 " --> pdb=" O PHEA3 133 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALA3 135 " --> pdb=" O PHEA3 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VALA3 169 " --> pdb=" O VALA3 135 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HISA3 137 " --> pdb=" O VALA3 169 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N META3 164 " --> pdb=" O GLUA3 198 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N META3 200 " --> pdb=" O META3 164 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THRA3 166 " --> pdb=" O META3 200 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEUA3 202 " --> pdb=" O THRA3 166 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SERA3 168 " --> pdb=" O LEUA3 202 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VALA3 268 " --> pdb=" O VALA3 201 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASPA3 203 " --> pdb=" O VALA3 268 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N PHEA3 270 " --> pdb=" O ASPA3 203 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHEA3 265 " --> pdb=" O SERA3 371 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SERA3 371 " --> pdb=" O PHEA3 265 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYSA3 350 " --> pdb=" O LEUA3 311 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALAA3 313 " --> pdb=" O LYSA3 350 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SERA3 352 " --> pdb=" O ALAA3 313 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALAA3 315 " --> pdb=" O SERA3 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYSA3 354 " --> pdb=" O ALAA3 315 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHEA3 317 " --> pdb=" O CYSA3 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A3' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'A4' and resid 65 through 68 removed outlier: 9.237A pdb=" N ILEA4 66 " --> pdb=" O VALA4 4 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SERA4 6 " --> pdb=" O ILEA4 66 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEUA4 68 " --> pdb=" O SERA4 6 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HISA4 8 " --> pdb=" O LEUA4 68 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLUA4 3 " --> pdb=" O GLNA4 133 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHEA4 135 " --> pdb=" O GLUA4 3 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILEA4 5 " --> pdb=" O PHEA4 135 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VALA4 137 " --> pdb=" O ILEA4 5 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILEA4 7 " --> pdb=" O VALA4 137 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASNA4 139 " --> pdb=" O ILEA4 7 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILEA4 9 " --> pdb=" O ASNA4 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SERA4 165 " --> pdb=" O GLNA4 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASNA4 139 " --> pdb=" O PHEA4 169 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYSA4 166 " --> pdb=" O VALA4 200 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VALA4 202 " --> pdb=" O LYSA4 166 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLYA4 168 " --> pdb=" O VALA4 202 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEUA4 204 " --> pdb=" O GLYA4 168 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THRA4 170 " --> pdb=" O LEUA4 204 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERA4 270 " --> pdb=" O META4 203 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALAA4 314 " --> pdb=" O ASNA4 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A4' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A5' and resid 63 through 66 removed outlier: 5.340A pdb=" N GLUA5 3 " --> pdb=" O LEUA5 130 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SERA5 138 " --> pdb=" O GLYA5 9 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N META5 163 " --> pdb=" O CYSA5 129 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLNA5 131 " --> pdb=" O META5 163 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEUA5 165 " --> pdb=" O GLNA5 131 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHEA5 133 " --> pdb=" O LEUA5 165 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHEA5 167 " --> pdb=" O PHEA5 133 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VALA5 135 " --> pdb=" O PHEA5 167 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VALA5 169 " --> pdb=" O VALA5 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HISA5 137 " --> pdb=" O VALA5 169 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N META5 164 " --> pdb=" O GLUA5 198 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N META5 200 " --> pdb=" O META5 164 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THRA5 166 " --> pdb=" O META5 200 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEUA5 202 " --> pdb=" O THRA5 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SERA5 168 " --> pdb=" O LEUA5 202 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VALA5 268 " --> pdb=" O VALA5 201 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASPA5 203 " --> pdb=" O VALA5 268 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N PHEA5 270 " --> pdb=" O ASPA5 203 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHEA5 265 " --> pdb=" O SERA5 371 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SERA5 371 " --> pdb=" O PHEA5 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A5' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'A6' and resid 65 through 68 removed outlier: 8.844A pdb=" N ILEA6 66 " --> pdb=" O VALA6 4 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SERA6 6 " --> pdb=" O ILEA6 66 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEUA6 68 " --> pdb=" O SERA6 6 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HISA6 8 " --> pdb=" O LEUA6 68 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLUA6 3 " --> pdb=" O GLNA6 133 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHEA6 135 " --> pdb=" O GLUA6 3 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILEA6 5 " --> pdb=" O PHEA6 135 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VALA6 137 " --> pdb=" O ILEA6 5 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILEA6 7 " --> pdb=" O VALA6 137 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASNA6 139 " --> pdb=" O ILEA6 7 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILEA6 9 " --> pdb=" O ASNA6 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SERA6 165 " --> pdb=" O GLNA6 133 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VALA6 200 " --> pdb=" O LYSA6 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A6' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A6' and resid 269 through 273 removed outlier: 3.816A pdb=" N ALAA6 314 " --> pdb=" O ASNA6 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A7' and resid 90 through 92 removed outlier: 7.952A pdb=" N VALA7 91 " --> pdb=" O ALAA7 63 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEUA7 65 " --> pdb=" O VALA7 91 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLUA7 3 " --> pdb=" O LEUA7 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALA7 5 " --> pdb=" O GLYA7 132 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SERA7 138 " --> pdb=" O GLYA7 9 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLNA7 131 " --> pdb=" O META7 163 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEUA7 165 " --> pdb=" O GLNA7 131 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHEA7 133 " --> pdb=" O LEUA7 165 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHEA7 167 " --> pdb=" O PHEA7 133 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VALA7 135 " --> pdb=" O PHEA7 167 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VALA7 169 " --> pdb=" O VALA7 135 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N HISA7 137 " --> pdb=" O VALA7 169 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N META7 164 " --> pdb=" O GLUA7 198 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N META7 200 " --> pdb=" O META7 164 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THRA7 166 " --> pdb=" O META7 200 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEUA7 202 " --> pdb=" O THRA7 166 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SERA7 168 " --> pdb=" O LEUA7 202 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYSA7 199 " --> pdb=" O PHEA7 266 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VALA7 268 " --> pdb=" O CYSA7 199 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VALA7 201 " --> pdb=" O VALA7 268 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N PHEA7 270 " --> pdb=" O VALA7 201 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHEA7 265 " --> pdb=" O SERA7 371 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SERA7 371 " --> pdb=" O PHEA7 265 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LYSA7 350 " --> pdb=" O LEUA7 311 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALAA7 313 " --> pdb=" O LYSA7 350 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SERA7 352 " --> pdb=" O ALAA7 313 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALAA7 315 " --> pdb=" O SERA7 352 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N CYSA7 354 " --> pdb=" O ALAA7 315 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHEA7 317 " --> pdb=" O CYSA7 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A7' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B1' and resid 63 through 66 removed outlier: 6.770A pdb=" N GLUB1 3 " --> pdb=" O GLNB1 131 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHEB1 133 " --> pdb=" O GLUB1 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VALB1 5 " --> pdb=" O PHEB1 133 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VALB1 135 " --> pdb=" O VALB1 5 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILEB1 7 " --> pdb=" O VALB1 135 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HISB1 137 " --> pdb=" O ILEB1 7 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLYB1 9 " --> pdb=" O HISB1 137 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALB1 169 " --> pdb=" O HISB1 137 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLUB1 198 " --> pdb=" O METB1 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THRB1 166 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYSB1 199 " --> pdb=" O PHEB1 266 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VALB1 268 " --> pdb=" O CYSB1 199 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VALB1 201 " --> pdb=" O VALB1 268 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N PHEB1 270 " --> pdb=" O VALB1 201 " (cutoff:3.500A) removed outlier: 14.137A pdb=" N ASPB1 203 " --> pdb=" O PHEB1 270 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHEB1 265 " --> pdb=" O SERB1 371 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SERB1 371 " --> pdb=" O PHEB1 265 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SERB1 364 " --> pdb=" O PHEB1 317 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHEB1 317 " --> pdb=" O SERB1 364 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THRB1 366 " --> pdb=" O ALAB1 315 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALAB1 315 " --> pdb=" O THRB1 366 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILEB1 368 " --> pdb=" O ALAB1 313 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALAB1 313 " --> pdb=" O ILEB1 368 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASNB1 370 " --> pdb=" O LEUB1 311 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LYSB1 350 " --> pdb=" O LEUB1 311 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALAB1 313 " --> pdb=" O LYSB1 350 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SERB1 352 " --> pdb=" O ALAB1 313 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALAB1 315 " --> pdb=" O SERB1 352 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYSB1 354 " --> pdb=" O ALAB1 315 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHEB1 317 " --> pdb=" O CYSB1 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B2' and resid 93 through 94 removed outlier: 7.589A pdb=" N ILEB2 93 " --> pdb=" O CYSB2 65 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHEB2 67 " --> pdb=" O ILEB2 93 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ILEB2 66 " --> pdb=" O VALB2 4 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SERB2 6 " --> pdb=" O ILEB2 66 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEUB2 68 " --> pdb=" O SERB2 6 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HISB2 8 " --> pdb=" O LEUB2 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLUB2 3 " --> pdb=" O GLNB2 133 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHEB2 135 " --> pdb=" O GLUB2 3 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILEB2 5 " --> pdb=" O PHEB2 135 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VALB2 137 " --> pdb=" O ILEB2 5 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEB2 7 " --> pdb=" O VALB2 137 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASNB2 139 " --> pdb=" O ILEB2 7 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILEB2 9 " --> pdb=" O ASNB2 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SERB2 165 " --> pdb=" O GLNB2 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALB2 200 " --> pdb=" O LYSB2 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B2' and resid 269 through 273 removed outlier: 3.745A pdb=" N ALAB2 314 " --> pdb=" O ASNB2 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 90 through 92 removed outlier: 3.976A pdb=" N ASPB3 67 " --> pdb=" O VALB3 91 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLUB3 3 " --> pdb=" O GLNB3 131 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHEB3 133 " --> pdb=" O GLUB3 3 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VALB3 5 " --> pdb=" O PHEB3 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VALB3 135 " --> pdb=" O VALB3 5 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILEB3 7 " --> pdb=" O VALB3 135 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HISB3 137 " --> pdb=" O ILEB3 7 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLYB3 9 " --> pdb=" O HISB3 137 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VALB3 169 " --> pdb=" O HISB3 137 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N METB3 164 " --> pdb=" O GLUB3 198 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N METB3 200 " --> pdb=" O METB3 164 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THRB3 166 " --> pdb=" O METB3 200 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEUB3 202 " --> pdb=" O THRB3 166 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SERB3 168 " --> pdb=" O LEUB3 202 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VALB3 268 " --> pdb=" O VALB3 201 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHEB3 265 " --> pdb=" O SERB3 371 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SERB3 371 " --> pdb=" O PHEB3 265 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N LYSB3 350 " --> pdb=" O LEUB3 311 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALAB3 313 " --> pdb=" O LYSB3 350 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SERB3 352 " --> pdb=" O ALAB3 313 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALAB3 315 " --> pdb=" O SERB3 352 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N CYSB3 354 " --> pdb=" O ALAB3 315 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHEB3 317 " --> pdb=" O CYSB3 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B4' and resid 65 through 68 removed outlier: 4.828A pdb=" N ALAB4 140 " --> pdb=" O ILEB4 9 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASNB4 139 " --> pdb=" O PHEB4 169 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VALB4 200 " --> pdb=" O LYSB4 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B4' and resid 269 through 273 Processing sheet with id=AC4, first strand: chain 'B5' and resid 90 through 92 removed outlier: 3.504A pdb=" N VALB5 91 " --> pdb=" O LEUB5 65 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASPB5 67 " --> pdb=" O VALB5 91 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLUB5 3 " --> pdb=" O LEUB5 130 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SERB5 138 " --> pdb=" O GLYB5 9 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N METB5 163 " --> pdb=" O CYSB5 129 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLNB5 131 " --> pdb=" O METB5 163 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEUB5 165 " --> pdb=" O GLNB5 131 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHEB5 133 " --> pdb=" O LEUB5 165 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHEB5 167 " --> pdb=" O PHEB5 133 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VALB5 135 " --> pdb=" O PHEB5 167 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VALB5 169 " --> pdb=" O VALB5 135 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N HISB5 137 " --> pdb=" O VALB5 169 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N METB5 164 " --> pdb=" O GLUB5 198 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N METB5 200 " --> pdb=" O METB5 164 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THRB5 166 " --> pdb=" O METB5 200 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEUB5 202 " --> pdb=" O THRB5 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SERB5 168 " --> pdb=" O LEUB5 202 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYSB5 199 " --> pdb=" O PHEB5 266 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VALB5 268 " --> pdb=" O CYSB5 199 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VALB5 201 " --> pdb=" O VALB5 268 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHEB5 270 " --> pdb=" O VALB5 201 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHEB5 265 " --> pdb=" O SERB5 371 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SERB5 371 " --> pdb=" O PHEB5 265 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SERB5 364 " --> pdb=" O PHEB5 317 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHEB5 317 " --> pdb=" O SERB5 364 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THRB5 366 " --> pdb=" O ALAB5 315 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALAB5 315 " --> pdb=" O THRB5 366 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILEB5 368 " --> pdb=" O ALAB5 313 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALAB5 313 " --> pdb=" O ILEB5 368 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASNB5 370 " --> pdb=" O LEUB5 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B5' and resid 51 through 53 Processing sheet with id=AC6, first strand: chain 'B6' and resid 65 through 68 removed outlier: 9.029A pdb=" N ILEB6 66 " --> pdb=" O VALB6 4 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SERB6 6 " --> pdb=" O ILEB6 66 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEUB6 68 " --> pdb=" O SERB6 6 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HISB6 8 " --> pdb=" O LEUB6 68 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLUB6 3 " --> pdb=" O GLNB6 133 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHEB6 135 " --> pdb=" O GLUB6 3 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILEB6 5 " --> pdb=" O PHEB6 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VALB6 137 " --> pdb=" O ILEB6 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILEB6 7 " --> pdb=" O VALB6 137 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASNB6 139 " --> pdb=" O ILEB6 7 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILEB6 9 " --> pdb=" O ASNB6 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SERB6 165 " --> pdb=" O GLNB6 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASNB6 139 " --> pdb=" O PHEB6 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYSB6 166 " --> pdb=" O VALB6 200 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VALB6 202 " --> pdb=" O LYSB6 166 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLYB6 168 " --> pdb=" O VALB6 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B6' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'B6' and resid 269 through 273 removed outlier: 3.527A pdb=" N ALAB6 314 " --> pdb=" O ASNB6 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B7' and resid 63 through 66 removed outlier: 8.893A pdb=" N ILEB7 64 " --> pdb=" O ILEB7 4 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HISB7 6 " --> pdb=" O ILEB7 64 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N METB7 66 " --> pdb=" O HISB7 6 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLNB7 8 " --> pdb=" O METB7 66 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLUB7 3 " --> pdb=" O GLNB7 131 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHEB7 133 " --> pdb=" O GLUB7 3 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VALB7 5 " --> pdb=" O PHEB7 133 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VALB7 135 " --> pdb=" O VALB7 5 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILEB7 7 " --> pdb=" O VALB7 135 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HISB7 137 " --> pdb=" O ILEB7 7 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLYB7 9 " --> pdb=" O HISB7 137 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N METB7 163 " --> pdb=" O CYSB7 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLNB7 131 " --> pdb=" O METB7 163 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEUB7 165 " --> pdb=" O GLNB7 131 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHEB7 133 " --> pdb=" O LEUB7 165 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHEB7 167 " --> pdb=" O PHEB7 133 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VALB7 135 " --> pdb=" O PHEB7 167 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VALB7 169 " --> pdb=" O VALB7 135 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N HISB7 137 " --> pdb=" O VALB7 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLUB7 198 " --> pdb=" O METB7 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SERB7 168 " --> pdb=" O METB7 200 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N CYSB7 199 " --> pdb=" O PHEB7 266 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VALB7 268 " --> pdb=" O CYSB7 199 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VALB7 201 " --> pdb=" O VALB7 268 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N PHEB7 270 " --> pdb=" O VALB7 201 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N ASPB7 203 " --> pdb=" O PHEB7 270 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHEB7 265 " --> pdb=" O SERB7 371 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N SERB7 371 " --> pdb=" O PHEB7 265 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B7' and resid 51 through 53 2941 hydrogen bonds defined for protein. 8553 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: 21.44 Time building geometry restraints manager: 15.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10083 1.32 - 1.45: 13853 1.45 - 1.57: 30547 1.57 - 1.69: 59 1.69 - 1.82: 657 Bond restraints: 55199 Sorted by residual: bond pdb=" N VALA4 62 " pdb=" CA VALA4 62 " ideal model delta sigma weight residual 1.457 1.501 -0.044 9.00e-03 1.23e+04 2.34e+01 bond pdb=" C LEUX1 204 " pdb=" O LEUX1 204 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.31e-02 5.83e+03 1.29e+01 bond pdb=" N VALA2 74 " pdb=" CA VALA2 74 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.30e-02 5.92e+03 9.75e+00 bond pdb=" N LEUX1 204 " pdb=" CA LEUX1 204 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.33e+00 bond pdb=" CA SERA4 54 " pdb=" CB SERA4 54 " ideal model delta sigma weight residual 1.530 1.483 0.048 1.58e-02 4.01e+03 9.15e+00 ... (remaining 55194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 72478 2.22 - 4.44: 1933 4.44 - 6.66: 281 6.66 - 8.88: 64 8.88 - 11.10: 7 Bond angle restraints: 74763 Sorted by residual: angle pdb=" C LYS Z 86 " pdb=" N THR Z 87 " pdb=" CA THR Z 87 " ideal model delta sigma weight residual 122.08 111.91 10.17 1.50e+00 4.44e-01 4.60e+01 angle pdb=" N PRO X 331 " pdb=" CA PRO X 331 " pdb=" CB PRO X 331 " ideal model delta sigma weight residual 103.33 110.28 -6.95 1.10e+00 8.26e-01 3.99e+01 angle pdb=" N PRO X 352 " pdb=" CA PRO X 352 " pdb=" CB PRO X 352 " ideal model delta sigma weight residual 103.33 110.17 -6.84 1.10e+00 8.26e-01 3.87e+01 angle pdb=" N METX1 218 " pdb=" CA METX1 218 " pdb=" C METX1 218 " ideal model delta sigma weight residual 111.82 105.40 6.42 1.16e+00 7.43e-01 3.07e+01 angle pdb=" N LEUX1 205 " pdb=" CA LEUX1 205 " pdb=" C LEUX1 205 " ideal model delta sigma weight residual 111.28 105.34 5.94 1.09e+00 8.42e-01 2.97e+01 ... (remaining 74758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 32500 35.72 - 71.45: 513 71.45 - 107.17: 56 107.17 - 142.89: 15 142.89 - 178.61: 13 Dihedral angle restraints: 33097 sinusoidal: 13283 harmonic: 19814 Sorted by residual: dihedral pdb=" C5' GTPA1 501 " pdb=" O5' GTPA1 501 " pdb=" PA GTPA1 501 " pdb=" O3A GTPA1 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.12 -178.61 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTPA5 501 " pdb=" O5' GTPA5 501 " pdb=" PA GTPA5 501 " pdb=" O3A GTPA5 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.44 -178.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTPB5 501 " pdb=" O5' GTPB5 501 " pdb=" PA GTPB5 501 " pdb=" O3A GTPB5 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.23 -169.50 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 33094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 7038 0.074 - 0.149: 1096 0.149 - 0.223: 76 0.223 - 0.298: 9 0.298 - 0.372: 2 Chirality restraints: 8221 Sorted by residual: chirality pdb=" CA ARGA4 84 " pdb=" N ARGA4 84 " pdb=" C ARGA4 84 " pdb=" CB ARGA4 84 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA LEUX1 205 " pdb=" N LEUX1 205 " pdb=" C LEUX1 205 " pdb=" CB LEUX1 205 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILEB5 345 " pdb=" CA ILEB5 345 " pdb=" CG1 ILEB5 345 " pdb=" CG2 ILEB5 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 8218 not shown) Planarity restraints: 9726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALA4 363 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PROA4 364 " 0.230 5.00e-02 4.00e+02 pdb=" CA PROA4 364 " -0.072 5.00e-02 4.00e+02 pdb=" CD PROA4 364 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYRX1 203 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C TYRX1 203 " -0.076 2.00e-02 2.50e+03 pdb=" O TYRX1 203 " 0.028 2.00e-02 2.50e+03 pdb=" N LEUX1 204 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HISB2 88 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PROB2 89 " 0.189 5.00e-02 4.00e+02 pdb=" CA PROB2 89 " -0.058 5.00e-02 4.00e+02 pdb=" CD PROB2 89 " -0.059 5.00e-02 4.00e+02 ... (remaining 9723 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 4 1.30 - 2.20: 49 2.20 - 3.10: 40453 3.10 - 4.00: 140699 4.00 - 4.90: 259289 Warning: very small nonbonded interaction distances. Nonbonded interactions: 440494 Sorted by model distance: nonbonded pdb="MG MGA2 501 " pdb=" PB GTPA3 501 " model vdw 0.399 2.530 nonbonded pdb="MG MGA4 501 " pdb=" PB GTPA5 501 " model vdw 0.606 2.530 nonbonded pdb=" O1G GTPB2 501 " pdb="MG MGB3 501 " model vdw 1.056 2.170 nonbonded pdb="MG MGA4 501 " pdb=" O1B GTPA5 501 " model vdw 1.210 2.170 nonbonded pdb="MG MGA2 501 " pdb=" O3B GTPA3 501 " model vdw 1.323 2.170 ... (remaining 440489 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 'A1' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'A3' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'A5' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'A7' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'B1' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'B3' and (resid 1 through 51 or resid 60 through 426)) selection = (chain 'B5' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) selection = (chain 'B7' and (resid 1 through 29 or resid 39 through 51 or resid 60 through 4 \ 26)) } ncs_group { reference = (chain 'A2' and (resid 2 through 28 or resid 47 through 53 or resid 63 through 4 \ 37)) selection = (chain 'A4' and (resid 2 through 28 or resid 47 through 53 or resid 63 through 4 \ 37)) selection = (chain 'A6' and (resid 2 through 28 or resid 47 through 53 or resid 63 through 4 \ 37)) selection = (chain 'B2' and (resid 2 through 28 or resid 47 through 53 or resid 63 through 4 \ 37)) selection = (chain 'B4' and resid 2 through 437) selection = (chain 'B6' and (resid 2 through 28 or resid 47 through 53 or resid 63 through 4 \ 37)) } 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: 1.260 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: 0.040 Extract box with map and model: 1.840 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 112.450 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.210 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 0.082 55199 Z= 0.307 Angle : 0.862 11.101 74763 Z= 0.486 Chirality : 0.052 0.372 8221 Planarity : 0.005 0.133 9726 Dihedral : 15.081 178.613 20345 Min Nonbonded Distance : 0.399 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 0.29 % Allowed : 0.43 % Favored : 99.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.20 % 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: -1.81 (0.09), residues: 6799 helix: -0.38 (0.08), residues: 3359 sheet: -1.17 (0.16), residues: 910 loop : -2.24 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRPB7 397 HIS 0.029 0.002 HIS Z 158 PHE 0.026 0.002 PHEB1 92 TYR 0.041 0.002 TYRA5 425 ARG 0.041 0.001 ARG Z 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1016 time to evaluate : 6.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 361 LEU cc_start: 0.5778 (tp) cc_final: 0.4697 (mp) REVERT: A2 230 LEU cc_start: 0.7430 (pp) cc_final: 0.7207 (pp) REVERT: A3 122 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8124 (tttt) REVERT: A3 282 ARG cc_start: 0.5819 (ptt180) cc_final: 0.5435 (tpp-160) REVERT: A3 299 MET cc_start: 0.6518 (mmm) cc_final: 0.6296 (mmm) REVERT: A3 330 MET cc_start: 0.5513 (mmp) cc_final: 0.5196 (mmp) REVERT: A4 62 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8787 (p) REVERT: A4 83 TYR cc_start: 0.8677 (m-80) cc_final: 0.8397 (m-80) REVERT: A4 123 ARG cc_start: 0.7619 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: A4 377 MET cc_start: 0.7482 (tmm) cc_final: 0.6034 (tmm) REVERT: A5 73 MET cc_start: 0.7574 (mmp) cc_final: 0.7249 (mmp) REVERT: A5 406 MET cc_start: 0.6636 (pmm) cc_final: 0.6389 (pmm) REVERT: A6 56 THR cc_start: 0.6542 (t) cc_final: 0.5932 (m) REVERT: A6 191 THR cc_start: 0.8268 (m) cc_final: 0.8053 (m) REVERT: A6 370 LYS cc_start: 0.7558 (tptt) cc_final: 0.6930 (pttt) REVERT: A6 401 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7586 (tptp) REVERT: A6 428 LEU cc_start: 0.8083 (tp) cc_final: 0.7863 (tp) REVERT: A7 285 THR cc_start: 0.5863 (p) cc_final: 0.5643 (t) REVERT: A7 294 TRP cc_start: 0.6069 (m100) cc_final: 0.3995 (t60) REVERT: A7 359 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7830 (mtmt) REVERT: B1 200 MET cc_start: 0.8103 (mpp) cc_final: 0.7860 (mpp) REVERT: B3 47 ILE cc_start: 0.8503 (pt) cc_final: 0.8112 (mt) REVERT: B3 330 MET cc_start: 0.8416 (mmm) cc_final: 0.8116 (mmm) REVERT: B4 71 GLU cc_start: 0.5658 (pt0) cc_final: 0.5216 (pm20) REVERT: B5 69 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5550 (tm-30) REVERT: B5 149 THR cc_start: 0.7563 (m) cc_final: 0.7116 (m) REVERT: B6 33 ASP cc_start: 0.7066 (p0) cc_final: 0.6520 (p0) REVERT: B6 123 ARG cc_start: 0.7621 (tpt90) cc_final: 0.7380 (tpt90) REVERT: B6 275 ILE cc_start: 0.8803 (mm) cc_final: 0.8522 (tp) REVERT: B6 388 PHE cc_start: 0.8315 (m-80) cc_final: 0.8077 (m-10) REVERT: B7 69 GLU cc_start: 0.7242 (tp30) cc_final: 0.6629 (tm-30) REVERT: B7 150 LEU cc_start: 0.7414 (pp) cc_final: 0.6568 (tp) REVERT: X 244 MET cc_start: 0.8103 (tmm) cc_final: 0.7825 (tmm) REVERT: X 248 LYS cc_start: 0.7652 (ptmm) cc_final: 0.6987 (pptt) REVERT: X 264 GLU cc_start: 0.6262 (pp20) cc_final: 0.5808 (pp20) REVERT: X 274 ARG cc_start: 0.4552 (mtt180) cc_final: 0.4199 (mmt-90) REVERT: Y 194 GLN cc_start: 0.7769 (mp10) cc_final: 0.6998 (mp10) REVERT: Y 209 MET cc_start: 0.6689 (mmm) cc_final: 0.6470 (ptt) REVERT: Y 213 LYS cc_start: 0.5994 (ttpp) cc_final: 0.5663 (tttt) REVERT: Y 221 GLN cc_start: 0.8612 (tt0) cc_final: 0.7235 (tm-30) REVERT: Y 271 LYS cc_start: 0.1149 (mtpt) cc_final: 0.0671 (tppp) REVERT: X1 121 GLN cc_start: 0.6895 (pt0) cc_final: 0.6662 (pm20) REVERT: X1 124 ASP cc_start: 0.7349 (m-30) cc_final: 0.6977 (m-30) REVERT: Y1 73 ILE cc_start: 0.8759 (mm) cc_final: 0.8558 (mm) REVERT: Y1 122 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7015 (mptt) REVERT: Y1 129 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8391 (tp40) REVERT: Y1 152 HIS cc_start: 0.7685 (t70) cc_final: 0.7129 (t-90) REVERT: Z 29 LYS cc_start: 0.6701 (ptpp) cc_final: 0.6339 (pttp) REVERT: Z 45 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6744 (tpt90) REVERT: Z 80 THR cc_start: 0.9138 (t) cc_final: 0.8774 (p) REVERT: Z 82 CYS cc_start: 0.6908 (t) cc_final: 0.5817 (t) REVERT: Z 120 MET cc_start: 0.6975 (ttm) cc_final: 0.6764 (tpp) REVERT: Z 170 THR cc_start: 0.6577 (p) cc_final: 0.5834 (p) outliers start: 17 outliers final: 2 residues processed: 1028 average time/residue: 0.7079 time to fit residues: 1195.2028 Evaluate side-chains 794 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 791 time to evaluate : 6.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 62 VAL Chi-restraints excluded: chain A4 residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 0.4980 chunk 513 optimal weight: 7.9990 chunk 284 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 346 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 530 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 394 optimal weight: 0.7980 chunk 614 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS A1 348 ASN A1 414 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 190 HIS ** A3 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 332 ASN A3 334 GLN A3 414 ASN A4 15 GLN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 329 ASN ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 227 HIS ** B1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 329 GLN B1 396 HIS B2 329 ASN B2 380 ASN B3 190 HIS B3 348 ASN B3 384 GLN B4 88 HIS ** B4 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 99 ASN B5 100 ASN B5 190 HIS B5 191 GLN B5 245 GLN B5 292 GLN ** B5 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 264 HIS B7 280 GLN C 392 GLN X 250 GLN Y 229 GLN X1 224 GLN X1 240 HIS Z 103 ASN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55199 Z= 0.235 Angle : 0.672 9.903 74763 Z= 0.345 Chirality : 0.045 0.205 8221 Planarity : 0.005 0.082 9726 Dihedral : 10.529 169.966 7618 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 9.10 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.60 (0.10), residues: 6799 helix: 0.64 (0.09), residues: 3448 sheet: -0.71 (0.17), residues: 906 loop : -1.73 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPB7 397 HIS 0.008 0.001 HISB3 190 PHE 0.023 0.002 PHEB5 92 TYR 0.018 0.001 TYRA5 425 ARG 0.007 0.001 ARG Z 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 882 time to evaluate : 6.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 3 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A1 294 TRP cc_start: 0.5851 (m100) cc_final: 0.4611 (t60) REVERT: A1 361 LEU cc_start: 0.6591 (tp) cc_final: 0.5900 (mp) REVERT: A1 363 MET cc_start: 0.6103 (ttm) cc_final: 0.5889 (ttt) REVERT: A1 401 GLU cc_------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 73 THR Chi-restraints excluded: chain A2 residue 384 ILE Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 62 VAL Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A5 residue 164 MET Chi-restraints excluded: chain A5 residue 219 THR Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 271 THR Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A6 residue 5 ILE Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A7 residue 354 CYS Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B3 residue 321 MET Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B4 residue 391 LEU Chi-restraints excluded: chain B4 residue 393 HIS Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 189 VAL Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B6 residue 76 ASP Chi-restraints excluded: chain B6 residue 177 VAL Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 132 LEU Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 217 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain X1 residue 240 HIS Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 511 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 615 optimal weight: 30.0000 chunk 665 optimal weight: 2.9990 chunk 548 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 494 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 6 HIS ** A1 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 227 HIS ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 195 ASN ** A3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 332 ASN A3 414 ASN A4 50 ASN ** A4 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 14 ASN A5 347 ASN A5 348 ASN A6 61 HIS ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 190 HIS A7 348 ASN B1 43 GLN ** B1 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 256 GLN B2 329 ASN B2 380 ASN B3 89 ASN B4 15 GLN ** B4 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 15 GLN B5 245 GLN ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 414 ASN ** B6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B6 258 ASN B6 266 HIS B6 283 HIS B7 37 HIS ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN X 224 GLN X 250 GLN Y 194 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 55199 Z= 0.476 Angle : 0.787 11.880 74763 Z= 0.405 Chirality : 0.050 0.290 8221 Planarity : 0.005 0.065 9726 Dihedral : 10.848 170.191 7618 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 13.65 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.49 (0.10), residues: 6799 helix: 0.67 (0.09), residues: 3432 sheet: -0.40 (0.17), residues: 861 loop : -1.66 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRPB2 21 HIS 0.012 0.002 HISB4 266 PHE 0.034 0.003 PHEA2 296 TYR 0.026 0.002 TYRA3 310 ARG 0.007 0.001 ARGA6 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 811 time to evaluate : 6.122 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: A1 3 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A1 163 MET cc_start: 0.6911 (mmm) cc_final: 0.6503 (tpp) REVERT: A1 294 TRP cc_start: 0.5970 (m100) cc_final: 0.4667 (t60) REVERT: A1 361 LEU cc_start: 0.6384 (tp) cc_final: 0.5682 (mp) REVERT: A1 401 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6370 (tm-30) REVERT: A3 197 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6429 (t0) REVERT: A3 282 ARG cc_start: 0.5860 (ptt180) cc_final: 0.5522 (tpp-160) REVERT: A3 293 MET cc_start: 0.6665 (ttt) cc_final: 0.6298 (ttm) REVERT: A3 294 TRP cc_start: 0.6491 (m100) cc_final: 0.4743 (t60) REVERT: A4 203 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (mpp) REVERT: A4 370 LYS cc_start: 0.7783 (tptt) cc_final: 0.6895 (pttt) REVERT: A4 377 MET cc_start: 0.7707 (tmm) cc_final: 0.6301 (tmm) REVERT: A5 293 MET cc_start: 0.6757 (ttp) cc_final: 0.6297 (ttm) REVERT: A5 415 MET cc_start: 0.5754 (ttt) cc_final: 0.5392 (ttt) REVERT: A5 422 TYR cc_start: 0.7177 (m-80) cc_final: 0.6961 (m-80) REVERT: A6 11 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: A6 56 THR cc_start: 0.7098 (t) cc_final: 0.6738 (m) REVERT: A6 370 LYS cc_start: 0.7790 (tptt) cc_final: 0.6947 (pttt) REVERT: A6 398 MET cc_start: 0.6632 (mtm) cc_final: 0.6384 (mtm) REVERT: A6 401 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7872 (tptt) REVERT: A7 163 MET cc_start: 0.8068 (mmm) cc_final: 0.7715 (mmm) REVERT: A7 200 MET cc_start: 0.8088 (mtp) cc_final: 0.7738 (mtt) REVERT: A7 251 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7243 (ttm170) REVERT: A7 294 TRP cc_start: 0.7129 (m100) cc_final: 0.4330 (t60) REVERT: A7 359 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7867 (mtmt) REVERT: A7 391 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6370 (tmt170) REVERT: B1 118 ASP cc_start: 0.8188 (m-30) cc_final: 0.7981 (m-30) REVERT: B2 5 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7922 (pt) REVERT: B2 90 GLU cc_start: 0.7421 (pt0) cc_final: 0.6875 (tm-30) REVERT: B2 318 MET cc_start: 0.7828 (mmm) cc_final: 0.7552 (mmm) REVERT: B2 428 LEU cc_start: 0.8043 (tt) cc_final: 0.7811 (tt) REVERT: B4 393 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.7135 (t-90) REVERT: B5 125 GLU cc_start: 0.6070 (pt0) cc_final: 0.5516 (pt0) REVERT: B5 276 ARG cc_start: 0.7648 (ttt180) cc_final: 0.6924 (ttm-80) REVERT: B6 268 MET cc_start: 0.8721 (mmm) cc_final: 0.8402 (mmt) REVERT: B7 3 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6893 (mp0) REVERT: B7 150 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7076 (tt) REVERT: X 258 MET cc_start: 0.7068 (mmm) cc_final: 0.6812 (mmp) REVERT: X 264 GLU cc_start: 0.5870 (pp20) cc_final: 0.5450 (pp20) REVERT: X 274 ARG cc_start: 0.5034 (mtt180) cc_final: 0.4388 (mmt-90) REVERT: Y 209 MET cc_start: 0.6504 (mmm) cc_final: 0.5890 (ptt) REVERT: Y 210 ASN cc_start: 0.7387 (m110) cc_final: 0.6760 (m110) REVERT: Y 213 LYS cc_start: 0.6054 (ttpp) cc_final: 0.5613 (tttt) REVERT: Y 221 GLN cc_start: 0.8670 (tt0) cc_final: 0.7297 (tm-30) REVERT: Y 271 LYS cc_start: 0.1375 (mtpt) cc_final: 0.0759 (tppp) REVERT: X1 124 ASP cc_start: 0.7541 (m-30) cc_final: 0.7256 (m-30) REVERT: X1 132 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7616 (mp) REVERT: X1 250 GLN cc_start: 0.6598 (tm-30) cc_final: 0.6276 (tt0) REVERT: X1 258 MET cc_start: 0.6619 (mmm) cc_final: 0.6349 (mmm) REVERT: Y1 73 ILE cc_start: 0.8706 (mm) cc_final: 0.8477 (mm) REVERT: Y1 152 HIS cc_start: 0.7989 (t70) cc_final: 0.7409 (t-90) REVERT: Y1 178 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: Y1 185 LYS cc_start: 0.7459 (ptmt) cc_final: 0.6858 (pttp) REVERT: Y1 191 MET cc_start: 0.5953 (tmm) cc_final: 0.5218 (tmm) REVERT: Z 29 LYS cc_start: 0.6465 (ptpp) cc_final: 0.5775 (pttp) REVERT: Z 51 LYS cc_start: 0.6681 (mtpp) cc_final: 0.6371 (mmtm) REVERT: Z 70 ILE cc_start: 0.8038 (mp) cc_final: 0.7786 (tt) REVERT: Z 80 THR cc_start: 0.9030 (t) cc_final: 0.8734 (p) REVERT: Z 90 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6328 (mm-30) REVERT: Z 131 MET cc_start: 0.5836 (tmm) cc_final: 0.5440 (tmm) outliers start: 163 outliers final: 101 residues processed: 910 average time/residue: 0.6894 time to fit residues: 1034.2657 Evaluate side-chains 866 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 757 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 50 TYR Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 263 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 345 ILE Chi-restraints excluded: chain A1 residue 349 VAL Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 73 THR Chi-restraints excluded: chain A2 residue 82 THR Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 286 LEU Chi-restraints excluded: chain A2 residue 384 ILE Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 126 SER Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 197 ASP Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 290 THR Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 203 MET Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A4 residue 368 LEU Chi-restraints excluded: chain A5 residue 155 ILE Chi-restraints excluded: chain A5 residue 164 MET Chi-restraints excluded: chain A5 residue 166 THR Chi-restraints excluded: chain A5 residue 202 LEU Chi-restraints excluded: chain A5 residue 219 THR Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A5 residue 321 MET Chi-restraints excluded: chain A5 residue 359 LYS Chi-restraints excluded: chain A6 residue 5 ILE Chi-restraints excluded: chain A6 residue 11 GLN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 182 VAL Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 418 PHE Chi-restraints excluded: chain A7 residue 120 VAL Chi-restraints excluded: chain A7 residue 147 MET Chi-restraints excluded: chain A7 residue 282 ARG Chi-restraints excluded: chain A7 residue 354 CYS Chi-restraints excluded: chain A7 residue 399 THR Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 238 CYS Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B2 residue 301 MET Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B3 residue 115 SER Chi-restraints excluded: chain B3 residue 126 SER Chi-restraints excluded: chain B3 residue 151 LEU Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B3 residue 321 MET Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 313 MET Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B4 residue 391 LEU Chi-restraints excluded: chain B4 residue 393 HIS Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 189 VAL Chi-restraints excluded: chain B5 residue 200 MET Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 119 LEU Chi-restraints excluded: chain B6 residue 136 LEU Chi-restraints excluded: chain B6 residue 182 VAL Chi-restraints excluded: chain B6 residue 191 THR Chi-restraints excluded: chain B6 residue 249 ASN Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 233 ASP Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 234 ILE Chi-restraints excluded: chain X1 residue 132 LEU Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 168 ILE Chi-restraints excluded: chain Y1 residue 178 GLU Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 6.9990 chunk 463 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 413 optimal weight: 0.6980 chunk 618 optimal weight: 8.9990 chunk 654 optimal weight: 0.8980 chunk 322 optimal weight: 0.0970 chunk 585 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS A1 348 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 332 ASN A4 11 GLN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 99 ASN A5 347 ASN A6 186 ASN ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 292 GLN B2 15 GLN B3 195 ASN B3 347 ASN B4 28 HIS B5 245 GLN ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 384 GLN ** B6 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 292 GLN C 341 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1 240 HIS ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55199 Z= 0.188 Angle : 0.608 11.127 74763 Z= 0.308 Chirality : 0.043 0.189 8221 Planarity : 0.004 0.056 9726 Dihedral : 10.393 160.934 7617 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.39 % Allowed : 15.69 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.04 (0.10), residues: 6799 helix: 1.16 (0.09), residues: 3412 sheet: -0.38 (0.17), residues: 914 loop : -1.39 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPB7 397 HIS 0.008 0.001 HIS Z 155 PHE 0.028 0.001 PHEB5 92 TYR 0.019 0.001 TYRB5 208 ARG 0.006 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 824 time to evaluate : 6.577 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: A1 3 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A1 163 MET cc_start: 0.6885 (mmm) cc_final: 0.6428 (tpp) REVERT: A1 294 TRP cc_start: 0.5850 (m100) cc_final: 0.5084 (t60) REVERT: A1 361 LEU cc_start: 0.6281 (tp) cc_final: 0.5593 (mp) REVERT: A2 77 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: A2 123 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7433 (tpm170) REVERT: A2 301 MET cc_start: 0.6561 (mmp) cc_final: 0.6248 (mmp) REVERT: A2 367 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: A3 282 ARG cc_start: 0.5713 (ptt180) cc_final: 0.5391 (tpm170) REVERT: A3 293 MET cc_start: 0.6618 (ttt) cc_final: 0.6290 (ttm) REVERT: A3 294 TRP cc_start: 0.6276 (m100) cc_final: 0.4837 (t60) REVERT: A4 124 LYS cc_start: 0.7839 (ptpp) cc_final: 0.7564 (mtmm) REVERT: A4 370 LYS cc_start: 0.7790 (tptt) cc_final: 0.6952 (pttt) REVERT: A4 377 MET cc_start: 0.7645 (tmm) cc_final: 0.6035 (tmm) REVERT: A5 92 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6632 (t80) REVERT: A5 118 ASP cc_start: 0.6725 (t0) cc_final: 0.6452 (t0) REVERT: A5 122 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8112 (mmtm) REVERT: A5 293 MET cc_start: 0.6781 (ttp) cc_final: 0.6508 (ttm) REVERT: A5 337 ASN cc_start: 0.5337 (p0) cc_final: 0.4834 (p0) REVERT: A5 422 TYR cc_start: 0.6675 (m-80) cc_final: 0.6375 (m-80) REVERT: A6 11 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A6 101 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8449 (m-40) REVERT: A6 123 ARG cc_start: 0.7199 (tpp-160) cc_final: 0.6960 (mmm160) REVERT: A6 370 LYS cc_start: 0.7699 (tptt) cc_final: 0.6923 (pttt) REVERT: A6 401 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7756 (tptt) REVERT: A7 163 MET cc_start: 0.8081 (mmm) cc_final: 0.7681 (mmt) REVERT: A7 294 TRP cc_start: 0.7012 (m100) cc_final: 0.4683 (t60) REVERT: A7 299 MET cc_start: 0.7713 (mmp) cc_final: 0.7349 (mmp) REVERT: A7 300 MET cc_start: 0.6601 (mtt) cc_final: 0.6391 (mtm) REVERT: A7 359 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7837 (mtmt) REVERT: A7 391 ARG cc_start: 0.7112 (ttm170) cc_final: 0.6338 (tmt170) REVERT: B1 1 MET cc_start: 0.4814 (ttp) cc_final: 0.4502 (mtm) REVERT: B1 377 MET cc_start: 0.7683 (tmm) cc_final: 0.6981 (ptt) REVERT: B2 90 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: B2 123 ARG cc_start: 0.7583 (tpt90) cc_final: 0.7364 (tpt90) REVERT: B2 302 MET cc_start: 0.7789 (mmm) cc_final: 0.7488 (mtt) REVERT: B2 318 MET cc_start: 0.7893 (mmm) cc_final: 0.7555 (mmm) REVERT: B3 91 VAL cc_start: 0.8520 (p) cc_final: 0.8305 (m) REVERT: B4 24 TYR cc_start: 0.8244 (m-10) cc_final: 0.7666 (m-10) REVERT: B4 78 VAL cc_start: 0.8890 (t) cc_final: 0.8611 (t) REVERT: B4 203 MET cc_start: 0.7555 (mmm) cc_final: 0.7155 (mmm) REVERT: B4 302 MET cc_start: 0.8753 (mmm) cc_final: 0.8432 (mtp) REVERT: B5 212 PHE cc_start: 0.7023 (m-10) cc_final: 0.6742 (m-10) REVERT: B5 276 ARG cc_start: 0.7538 (ttt180) cc_final: 0.6882 (ttm-80) REVERT: B6 163 LYS cc_start: 0.7127 (mmmt) cc_final: 0.6890 (mmmt) REVERT: B6 268 MET cc_start: 0.8563 (mmm) cc_final: 0.8148 (mmt) REVERT: B7 150 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7175 (tt) REVERT: B7 164 MET cc_start: 0.7897 (tpp) cc_final: 0.7679 (tpp) REVERT: C 323 MET cc_start: 0.6035 (mtm) cc_final: 0.5469 (mtm) REVERT: C 392 GLN cc_start: 0.8371 (tt0) cc_final: 0.8040 (mp10) REVERT: X 245 ARG cc_start: 0.6084 (ttp80) cc_final: 0.5728 (ptm160) REVERT: X 248 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7178 (tmtt) REVERT: X 264 GLU cc_start: 0.5818 (pp20) cc_final: 0.5344 (pp20) REVERT: X 274 ARG cc_start: 0.4877 (mtt180) cc_final: 0.4209 (mmt-90) REVERT: Y 191 MET cc_start: 0.7035 (ppp) cc_final: 0.6534 (ppp) REVERT: Y 194 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: Y 209 MET cc_start: 0.6570 (mmm) cc_final: 0.6088 (tmm) REVERT: Y 210 ASN cc_start: 0.7527 (m110) cc_final: 0.6319 (m110) REVERT: Y 213 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5742 (tttt) REVERT: Y 221 GLN cc_start: 0.8644 (tt0) cc_final: 0.7288 (tm-30) REVERT: Y 271 LYS cc_start: 0.1368 (mtpt) cc_final: 0.0779 (tppp) REVERT: X1 124 ASP cc_start: 0.7503 (m-30) cc_final: 0.7297 (m-30) REVERT: X1 132 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (mp) REVERT: X1 204 LEU cc_start: 0.7929 (pp) cc_final: 0.7518 (mt) REVERT: X1 229 ASP cc_start: 0.7304 (p0) cc_final: 0.6857 (m-30) REVERT: X1 250 GLN cc_start: 0.6672 (tm-30) cc_final: 0.6142 (tt0) REVERT: X1 258 MET cc_start: 0.6566 (mmm) cc_final: 0.6264 (mmm) REVERT: Y1 73 ILE cc_start: 0.8588 (mm) cc_final: 0.8359 (mm) REVERT: Y1 152 HIS cc_start: 0.7924 (t70) cc_final: 0.7372 (t-90) REVERT: Y1 174 GLN cc_start: 0.6671 (mm110) cc_final: 0.5885 (mm110) REVERT: Y1 185 LYS cc_start: 0.7378 (ptmt) cc_final: 0.6873 (pttp) REVERT: Y1 191 MET cc_start: 0.6167 (tmm) cc_final: 0.5500 (tmm) REVERT: Z 23 PHE cc_start: 0.7632 (t80) cc_final: 0.7321 (t80) REVERT: Z 29 LYS cc_start: 0.6872 (ptpp) cc_final: 0.6153 (pttp) REVERT: Z 51 LYS cc_start: 0.6407 (mtpp) cc_final: 0.6014 (mmtm) REVERT: Z 70 ILE cc_start: 0.7978 (mp) cc_final: 0.7714 (tt) REVERT: Z 90 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6370 (mm-30) outliers start: 138 outliers final: 67 residues processed: 906 average time/residue: 0.6880 time to fit residues: 1030.3108 Evaluate side-chains 829 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 753 time to evaluate : 6.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 5 VAL Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 50 TYR Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 73 THR Chi-restraints excluded: chain A2 residue 77 GLU Chi-restraints excluded: chain A2 residue 110 ILE Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 303 VAL Chi-restraints excluded: chain A2 residue 367 ASP Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 166 THR Chi-restraints excluded: chain A5 residue 200 MET Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A5 residue 359 LYS Chi-restraints excluded: chain A6 residue 11 GLN Chi-restraints excluded: chain A6 residue 25 CYS Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 90 GLU Chi-restraints excluded: chain B2 residue 194 LEU Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B3 residue 321 MET Chi-restraints excluded: chain B4 residue 159 VAL Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 72 THR Chi-restraints excluded: chain B7 residue 149 THR Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 194 GLN Chi-restraints excluded: chain X1 residue 132 LEU Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 217 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 6.9990 chunk 371 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 487 optimal weight: 0.8980 chunk 270 optimal weight: 0.4980 chunk 558 optimal weight: 8.9990 chunk 452 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 587 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS A3 332 ASN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 14 ASN A5 347 ASN ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 423 GLN B3 329 GLN ** B3 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 15 GLN ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 107 HIS ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 GLN Z 108 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 55199 Z= 0.163 Angle : 0.588 11.327 74763 Z= 0.294 Chirality : 0.042 0.252 8221 Planarity : 0.004 0.052 9726 Dihedral : 10.086 160.707 7617 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.67 % Allowed : 16.42 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.33 (0.10), residues: 6799 helix: 1.39 (0.09), residues: 3428 sheet: -0.19 (0.17), residues: 912 loop : -1.28 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPB7 397 HIS 0.011 0.001 HIS Z 155 PHE 0.026 0.001 PHEB5 92 TYR 0.020 0.001 TYRB5 208 ARG 0.007 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 826 time to evaluate : 6.285 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: A1 3 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A1 163 MET cc_start: 0.6687 (mmm) cc_final: 0.6159 (tpp) REVERT: A1 294 TRP cc_start: 0.5858 (m100) cc_final: 0.5042 (t60) REVERT: A1 361 LEU cc_start: 0.6931 (tp) cc_final: 0.6412 (mp) REVERT: A2 123 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7453 (tpm170) REVERT: A2 301 MET cc_start: 0.6424 (mmp) cc_final: 0.6048 (mmp) REVERT: A2 313 MET cc_start: 0.6779 (mpp) cc_final: 0.6536 (mpp) REVERT: A2 431 ASP cc_start: 0.5080 (m-30) cc_final: 0.4716 (t0) REVERT: A3 282 ARG cc_start: 0.5739 (ptt180) cc_final: 0.5314 (tpm170) REVERT: A3 293 MET cc_start: 0.6642 (ttt) cc_final: 0.6313 (ttm) REVERT: A3 294 TRP cc_start: 0.6228 (m100) cc_final: 0.4850 (t60) REVERT: A4 370 LYS cc_start: 0.7737 (tptt) cc_final: 0.6885 (pttt) REVERT: A5 92 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6433 (t80) REVERT: A5 337 ASN cc_start: 0.5275 (p0) cc_final: 0.4792 (p0) REVERT: A5 422 TYR cc_start: 0.6571 (m-80) cc_final: 0.6291 (m-80) REVERT: A6 101 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (m-40) REVERT: A6 154 LEU cc_start: 0.8565 (mm) cc_final: 0.8337 (mm) REVERT: A6 370 LYS cc_start: 0.7683 (tptt) cc_final: 0.6890 (pttt) REVERT: A6 401 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7767 (tptt) REVERT: A7 163 MET cc_start: 0.7989 (mmm) cc_final: 0.7671 (mmt) REVERT: A7 294 TRP cc_start: 0.6953 (m100) cc_final: 0.4965 (t60) REVERT: A7 299 MET cc_start: 0.7656 (mmp) cc_final: 0.7161 (mmp) REVERT: A7 359 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7805 (mtmt) REVERT: A7 391 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6343 (tmt170) REVERT: B1 1 MET cc_start: 0.4808 (ttp) cc_final: 0.4588 (mtm) REVERT: B1 164 MET cc_start: 0.7896 (tpp) cc_final: 0.7437 (ttm) REVERT: B2 90 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6051 (pt0) REVERT: B2 301 MET cc_start: 0.7337 (mtt) cc_final: 0.6835 (mtt) REVERT: B2 379 SER cc_start: 0.7666 (p) cc_final: 0.7372 (t) REVERT: B4 24 TYR cc_start: 0.8169 (m-10) cc_final: 0.7650 (m-10) REVERT: B4 136 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6866 (pp) REVERT: B4 203 MET cc_start: 0.7567 (mmm) cc_final: 0.7203 (mmm) REVERT: B5 276 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6850 (ttm-80) REVERT: B6 163 LYS cc_start: 0.6967 (mmmt) cc_final: 0.6706 (mmmt) REVERT: B6 268 MET cc_start: 0.8517 (mmm) cc_final: 0.8145 (mmt) REVERT: B6 286 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7799 (mm) REVERT: B6 413 MET cc_start: 0.7613 (mtp) cc_final: 0.7133 (mtp) REVERT: B7 73 MET cc_start: 0.8572 (mmm) cc_final: 0.8322 (mmp) REVERT: B7 100 ASN cc_start: 0.7359 (t0) cc_final: 0.6915 (t0) REVERT: B7 150 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7176 (tt) REVERT: B7 340 TYR cc_start: 0.7374 (m-10) cc_final: 0.7138 (m-80) REVERT: C 295 LYS cc_start: 0.6505 (mmtt) cc_final: 0.6199 (tttt) REVERT: C 307 MET cc_start: 0.5604 (mpp) cc_final: 0.5331 (mmp) REVERT: C 432 ASP cc_start: 0.5890 (m-30) cc_final: 0.5215 (t0) REVERT: X 245 ARG cc_start: 0.6113 (ttp80) cc_final: 0.5747 (ptm160) REVERT: X 248 LYS cc_start: 0.7444 (tmtt) cc_final: 0.7215 (tmtt) REVERT: X 264 GLU cc_start: 0.5929 (pp20) cc_final: 0.5445 (pp20) REVERT: X 274 ARG cc_start: 0.5188 (mtt180) cc_final: 0.4464 (mmt-90) REVERT: Y 179 ARG cc_start: 0.7822 (ptp90) cc_final: 0.7568 (ptp-170) REVERT: Y 191 MET cc_start: 0.6979 (ppp) cc_final: 0.6760 (ppp) REVERT: Y 209 MET cc_start: 0.6615 (mmm) cc_final: 0.6026 (tmm) REVERT: Y 210 ASN cc_start: 0.7533 (m110) cc_final: 0.6338 (m110) REVERT: Y 213 LYS cc_start: 0.6270 (ttpp) cc_final: 0.5818 (tttt) REVERT: Y 221 GLN cc_start: 0.8643 (tt0) cc_final: 0.7290 (tm-30) REVERT: Y 271 LYS cc_start: 0.1354 (mtpt) cc_final: 0.0782 (tppp) REVERT: X1 204 LEU cc_start: 0.7865 (pp) cc_final: 0.7571 (mt) REVERT: X1 229 ASP cc_start: 0.7407 (p0) cc_final: 0.6961 (p0) REVERT: X1 240 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.5859 (t-90) REVERT: X1 258 MET cc_start: 0.6678 (mmm) cc_final: 0.6355 (mmm) REVERT: Y1 152 HIS cc_start: 0.7843 (t70) cc_final: 0.7310 (t-90) REVERT: Y1 174 GLN cc_start: 0.6581 (mm110) cc_final: 0.6229 (mm110) REVERT: Y1 185 LYS cc_start: 0.7400 (ptmt) cc_final: 0.6981 (pttp) REVERT: Y1 191 MET cc_start: 0.6324 (tmm) cc_final: 0.5711 (tmm) REVERT: Z 29 LYS cc_start: 0.6869 (ptpp) cc_final: 0.6173 (pttp) REVERT: Z 51 LYS cc_start: 0.6727 (mtpp) cc_final: 0.6313 (mmtm) REVERT: Z 70 ILE cc_start: 0.7970 (mp) cc_final: 0.7699 (tt) REVERT: Z 90 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6348 (mm-30) outliers start: 154 outliers final: 87 residues processed: 928 average time/residue: 0.6763 time to fit residues: 1037.6121 Evaluate side-chains 856 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 762 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 5 VAL Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 50 TYR Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 415 MET Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 110 ILE Chi-restraints excluded: chain A2 residue 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 303 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 163 MET Chi-restraints excluded: chain A3 residue 200 MET Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 68 LEU Chi-restraints excluded: chain A4 residue 102 ASN Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A4 residue 368 LEU Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 166 THR Chi-restraints excluded: chain A5 residue 200 MET Chi-restraints excluded: chain A5 residue 202 LEU Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A5 residue 359 LYS Chi-restraints excluded: chain A6 residue 25 CYS Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 269 LEU Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 345 ASP Chi-restraints excluded: chain A7 residue 65 LEU Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain A7 residue 354 CYS Chi-restraints excluded: chain B1 residue 95 THR Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 90 GLU Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 194 LEU Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 328 VAL Chi-restraints excluded: chain B2 residue 344 VAL Chi-restraints excluded: chain B3 residue 126 SER Chi-restraints excluded: chain B3 residue 143 THR Chi-restraints excluded: chain B3 residue 151 LEU Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B4 residue 4 VAL Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 364 SER Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B6 residue 119 LEU Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 149 THR Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 184 LEU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 217 ASP Chi-restraints excluded: chain X1 residue 218 MET Chi-restraints excluded: chain X1 residue 240 HIS Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 0.3980 chunk 589 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 655 optimal weight: 0.6980 chunk 543 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 216 optimal weight: 0.1980 chunk 343 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS A3 332 ASN A4 31 GLN A4 50 ASN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 347 ASN ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 423 GLN ** B1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 348 ASN ** B6 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B7 14 ASN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN Y 194 GLN Z 132 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55199 Z= 0.182 Angle : 0.590 11.505 74763 Z= 0.295 Chirality : 0.042 0.194 8221 Planarity : 0.004 0.051 9726 Dihedral : 9.943 164.215 7617 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 17.63 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.48 (0.10), residues: 6799 helix: 1.51 (0.09), residues: 3411 sheet: -0.10 (0.17), residues: 918 loop : -1.22 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPB7 397 HIS 0.006 0.001 HIS Z 155 PHE 0.024 0.001 PHEB5 92 TYR 0.016 0.001 TYRB5 208 ARG 0.008 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 794 time to evaluate : 6.320 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: A1 3 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A1 163 MET cc_start: 0.6656 (mmm) cc_final: 0.6182 (tpp) REVERT: A1 294 TRP cc_start: 0.5551 (m100) cc_final: 0.5120 (t60) REVERT: A1 361 LEU cc_start: 0.6928 (tp) cc_final: 0.6430 (mp) REVERT: A2 301 MET cc_start: 0.6422 (mmp) cc_final: 0.6078 (mmp) REVERT: A2 367 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: A2 413 MET cc_start: 0.6298 (mtp) cc_final: 0.5829 (ttm) REVERT: A3 282 ARG cc_start: 0.5820 (ptt180) cc_final: 0.5312 (tpm170) REVERT: A3 293 MET cc_start: 0.6667 (ttt) cc_final: 0.6339 (ttm) REVERT: A3 294 TRP cc_start: 0.6252 (m100) cc_final: 0.4878 (t60) REVERT: A4 370 LYS cc_start: 0.7740 (tptt) cc_final: 0.6876 (pttt) REVERT: A5 92 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A5 118 ASP cc_start: 0.6582 (t0) cc_final: 0.6161 (t0) REVERT: A5 122 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8045 (mmtm) REVERT: A5 337 ASN cc_start: 0.5302 (p0) cc_final: 0.4814 (p0) REVERT: A6 101 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: A6 123 ARG cc_start: 0.7564 (tpp-160) cc_final: 0.6917 (mmm160) REVERT: A6 154 LEU cc_start: 0.8568 (mm) cc_final: 0.8326 (mm) REVERT: A6 370 LYS cc_start: 0.7678 (tptt) cc_final: 0.6872 (pttt) REVERT: A6 401 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7773 (tptt) REVERT: A7 163 MET cc_start: 0.7955 (mmm) cc_final: 0.7648 (mmt) REVERT: A7 294 TRP cc_start: 0.6958 (m100) cc_final: 0.4968 (t60) REVERT: A7 299 MET cc_start: 0.7688 (mmp) cc_final: 0.7167 (mmp) REVERT: A7 359 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7849 (mtmt) REVERT: A7 391 ARG cc_start: 0.6913 (ttm170) cc_final: 0.6256 (tmt170) REVERT: B1 321 MET cc_start: 0.7497 (mpp) cc_final: 0.7161 (mpp) REVERT: B1 377 MET cc_start: 0.7561 (tmm) cc_final: 0.6900 (ptt) REVERT: B2 301 MET cc_start: 0.7340 (mtt) cc_final: 0.6962 (mtt) REVERT: B2 379 SER cc_start: 0.7669 (p) cc_final: 0.7373 (t) REVERT: B4 24 TYR cc_start: 0.8197 (m-10) cc_final: 0.7578 (m-10) REVERT: B4 136 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6831 (pp) REVERT: B4 203 MET cc_start: 0.7579 (mmm) cc_final: 0.7181 (mmm) REVERT: B5 276 ARG cc_start: 0.7455 (ttt180) cc_final: 0.6804 (ttm-80) REVERT: B5 297 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7966 (mppt) REVERT: B6 268 MET cc_start: 0.8456 (mmm) cc_final: 0.8074 (mmt) REVERT: B6 286 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7894 (mm) REVERT: B6 413 MET cc_start: 0.7516 (mtp) cc_final: 0.7113 (mtp) REVERT: B7 73 MET cc_start: 0.8579 (mmm) cc_final: 0.8357 (mmp) REVERT: B7 147 MET cc_start: 0.7709 (ttp) cc_final: 0.7455 (ttp) REVERT: B7 150 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7156 (tt) REVERT: C 295 LYS cc_start: 0.6374 (mmtt) cc_final: 0.6097 (ttmt) REVERT: C 307 MET cc_start: 0.5558 (mpp) cc_final: 0.5276 (mmp) REVERT: C 432 ASP cc_start: 0.6001 (m-30) cc_final: 0.5350 (t0) REVERT: X 248 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7134 (pttm) REVERT: X 254 GLU cc_start: 0.4054 (OUTLIER) cc_final: 0.3287 (tt0) REVERT: X 264 GLU cc_start: 0.5976 (pp20) cc_final: 0.5503 (pp20) REVERT: X 274 ARG cc_start: 0.5196 (mtt180) cc_final: 0.4380 (mmp80) REVERT: Y 191 MET cc_start: 0.6878 (ppp) cc_final: 0.6429 (ppp) REVERT: Y 194 GLN cc_start: 0.7645 (mt0) cc_final: 0.7243 (mp10) REVERT: Y 209 MET cc_start: 0.6600 (mmm) cc_final: 0.5904 (tmm) REVERT: Y 210 ASN cc_start: 0.7576 (m110) cc_final: 0.6346 (m110) REVERT: Y 213 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5858 (tttt) REVERT: Y 221 GLN cc_start: 0.8649 (tt0) cc_final: 0.7293 (tm-30) REVERT: Y 271 LYS cc_start: 0.1347 (mtpt) cc_final: 0.0791 (tppp) REVERT: X1 218 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7335 (mmt) REVERT: X1 229 ASP cc_start: 0.7370 (p0) cc_final: 0.7033 (p0) REVERT: X1 240 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5867 (t-90) REVERT: X1 250 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6158 (tt0) REVERT: X1 258 MET cc_start: 0.6840 (mmm) cc_final: 0.6526 (mmm) REVERT: Y1 152 HIS cc_start: 0.7804 (t70) cc_final: 0.7250 (t-90) REVERT: Y1 174 GLN cc_start: 0.6673 (mm110) cc_final: 0.6453 (mm110) REVERT: Y1 185 LYS cc_start: 0.7427 (ptmt) cc_final: 0.7019 (pttp) REVERT: Y1 191 MET cc_start: 0.6787 (tmm) cc_final: 0.6263 (tmm) REVERT: Z 29 LYS cc_start: 0.6873 (ptpp) cc_final: 0.6143 (pttp) REVERT: Z 45 ARG cc_start: 0.7649 (mtp180) cc_final: 0.7390 (ttt90) REVERT: Z 51 LYS cc_start: 0.6741 (mtpp) cc_final: 0.6311 (mmtm) REVERT: Z 70 ILE cc_start: 0.7963 (mp) cc_final: 0.7686 (tt) REVERT: Z 90 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6369 (mm-30) REVERT: Z 132 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6121 (pm20) outliers start: 148 outliers final: 101 residues processed: 889 average time/residue: 0.6943 time to fit residues: 1022.3004 Evaluate side-chains 861 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 750 time to evaluate : 6.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 5 VAL Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 50 TYR Chi-restraints excluded: chain A1 residue 60 VAL Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 415 MET Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 110 ILE Chi-restraints excluded: chain A2 residue 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 303 VAL Chi-restraints excluded: chain A2 residue 367 ASP Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 126 SER Chi-restraints excluded: chain A3 residue 163 MET Chi-restraints excluded: chain A3 residue 200 MET Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 333 VAL Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 68 LEU Chi-restraints excluded: chain A4 residue 102 ASN Chi-restraints excluded: chain A4 residue 149 LEU Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A4 residue 368 LEU Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 166 THR Chi-restraints excluded: chain A5 residue 200 MET Chi-restraints excluded: chain A5 residue 202 LEU Chi-restraints excluded: chain A5 residue 219 THR Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A5 residue 359 LYS Chi-restraints excluded: chain A5 residue 406 MET Chi-restraints excluded: chain A6 residue 25 CYS Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 341 ILE Chi-restraints excluded: chain A6 residue 409 VAL Chi-restraints excluded: chain A7 residue 44 LEU Chi-restraints excluded: chain A7 residue 65 LEU Chi-restraints excluded: chain A7 residue 147 MET Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain A7 residue 354 CYS Chi-restraints excluded: chain A7 residue 388 MET Chi-restraints excluded: chain B1 residue 95 THR Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 194 LEU Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 328 VAL Chi-restraints excluded: chain B2 residue 341 ILE Chi-restraints excluded: chain B2 residue 344 VAL Chi-restraints excluded: chain B3 residue 94 GLN Chi-restraints excluded: chain B3 residue 126 SER Chi-restraints excluded: chain B3 residue 143 THR Chi-restraints excluded: chain B3 residue 151 LEU Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B3 residue 205 GLU Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 200 MET Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 72 THR Chi-restraints excluded: chain B7 residue 149 THR Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 184 LEU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 217 ASP Chi-restraints excluded: chain X1 residue 218 MET Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain X1 residue 240 HIS Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 132 GLN Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 50.0000 chunk 73 optimal weight: 0.7980 chunk 373 optimal weight: 3.9990 chunk 478 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 551 optimal weight: 0.0870 chunk 365 optimal weight: 0.7980 chunk 652 optimal weight: 0.8980 chunk 408 optimal weight: 0.6980 chunk 397 optimal weight: 0.6980 chunk 301 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 6 HIS A1 227 HIS A2 329 ASN A3 195 ASN A3 332 ASN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 347 ASN ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 423 GLN ** B1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 101 ASN B6 102 ASN ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B6 226 ASN B6 256 GLN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 55199 Z= 0.160 Angle : 0.582 12.830 74763 Z= 0.288 Chirality : 0.042 0.190 8221 Planarity : 0.004 0.050 9726 Dihedral : 9.757 173.425 7617 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.46 % Allowed : 18.05 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.61 (0.10), residues: 6799 helix: 1.61 (0.09), residues: 3422 sheet: -0.02 (0.17), residues: 919 loop : -1.16 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPB7 397 HIS 0.015 0.001 HISA1 227 PHE 0.034 0.001 PHEB5 92 TYR 0.018 0.001 TYR C 389 ARG 0.009 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 797 time to evaluate : 6.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 3 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A1 163 MET cc_start: 0.6545 (mmm) cc_final: 0.6105 (tpp) REVERT: A1 292 GLN cc_start: 0.7875 (tt0) cc_final: 0.7619 (tt0) REVERT: A1 294 TRP cc_start: 0.5590 (m100) cc_final: 0.5085 (t60) REVERT: A1 361 LEU cc_start: 0.6928 (tp) cc_final: 0.6433 (mp) REVERT: A2 77 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: A2 136 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6841 (pp) REVERT: A2 264 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6816 (ttp-170) REVERT: A2 301 MET cc_start: 0.6378 (mmp) cc_final: 0.6009 (mmp) REVERT: A2 367 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: A2 413 MET cc_start: 0.6208 (mtp) cc_final: 0.5898 (ttm) REVERT: A3 30 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7319 (mt) REVERT: A3 282 ARG cc_start: 0.5781 (ptt180) cc_final: 0.5343 (tpm170) REVERT: A3 293 MET cc_start: 0.6626 (ttt) cc_final: 0.6304 (ttm) REVERT: A3 294 TRP cc_start: 0.6209 (m100) cc_final: 0.4893 (t60) REVERT: A4 370 LYS cc_start: 0.7727 (tptt) cc_final: 0.6869 (pttt) REVERT: A5 92 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A5 94 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7483 (tp40) REVERT: A5 337 ASN cc_start: 0.5249 (p0) cc_final: 0.4788 (p0) REVERT: A6 101 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7939 (m-40) REVERT: A6 154 LEU cc_start: 0.8549 (mm) cc_final: 0.8297 (mm) REVERT: A6 370 LYS cc_start: 0.7621 (tptt) cc_final: 0.6826 (pttt) REVERT: A6 391 LEU cc_start: 0.8132 (pp) cc_final: 0.7189 (mt) REVERT: A6 401 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7751 (tptt) REVERT: A7 163 MET cc_start: 0.8007 (mmm) cc_final: 0.7671 (mmt) REVERT: A7 294 TRP cc_start: 0.6877 (m100) cc_final: 0.4912 (t60) REVERT: A7 299 MET cc_start: 0.7628 (mmp) cc_final: 0.7082 (mmp) REVERT: A7 300 MET cc_start: 0.6570 (mtt) cc_final: 0.6364 (mtm) REVERT: A7 359 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7886 (mtmt) REVERT: A7 391 ARG cc_start: 0.6849 (ttm170) cc_final: 0.6207 (tmt170) REVERT: B1 377 MET cc_start: 0.7686 (tmm) cc_final: 0.7076 (ptt) REVERT: B2 228 ASN cc_start: 0.8718 (m-40) cc_final: 0.8277 (m110) REVERT: B2 379 SER cc_start: 0.7636 (p) cc_final: 0.7333 (t) REVERT: B4 24 TYR cc_start: 0.8167 (m-10) cc_final: 0.7596 (m-10) REVERT: B4 203 MET cc_start: 0.7599 (mmm) cc_final: 0.7232 (mmm) REVERT: B5 276 ARG cc_start: 0.7513 (ttt180) cc_final: 0.6849 (ttm-80) REVERT: B5 297 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7917 (mppt) REVERT: B6 268 MET cc_start: 0.8434 (mmm) cc_final: 0.8044 (mmt) REVERT: B6 286 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B6 413 MET cc_start: 0.7486 (mtp) cc_final: 0.7187 (mtp) REVERT: B7 73 MET cc_start: 0.8576 (mmm) cc_final: 0.8360 (mmp) REVERT: B7 150 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 295 LYS cc_start: 0.6380 (mmtt) cc_final: 0.6103 (ttmt) REVERT: C 307 MET cc_start: 0.5675 (mpp) cc_final: 0.5368 (mmp) REVERT: C 432 ASP cc_start: 0.5949 (m-30) cc_final: 0.5335 (t0) REVERT: X 228 LYS cc_start: 0.7399 (pptt) cc_final: 0.6807 (ptmt) REVERT: X 264 GLU cc_start: 0.5979 (pp20) cc_final: 0.5552 (pp20) REVERT: X 274 ARG cc_start: 0.5300 (mtt180) cc_final: 0.4431 (mmp80) REVERT: Y 188 MET cc_start: 0.5783 (mpp) cc_final: 0.4211 (mpp) REVERT: Y 209 MET cc_start: 0.6466 (mmm) cc_final: 0.5824 (ptt) REVERT: Y 210 ASN cc_start: 0.7591 (m110) cc_final: 0.7021 (m110) REVERT: Y 213 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5859 (tttt) REVERT: Y 221 GLN cc_start: 0.8636 (tt0) cc_final: 0.7291 (tm-30) REVERT: Y 271 LYS cc_start: 0.1368 (mtpt) cc_final: 0.0857 (tppp) REVERT: X1 218 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7348 (mmm) REVERT: X1 229 ASP cc_start: 0.7299 (p0) cc_final: 0.7026 (p0) REVERT: X1 240 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.5860 (t-90) REVERT: X1 250 GLN cc_start: 0.6818 (tm-30) cc_final: 0.6152 (tt0) REVERT: X1 258 MET cc_start: 0.6745 (mmm) cc_final: 0.6361 (mmm) REVERT: Y1 152 HIS cc_start: 0.7802 (t70) cc_final: 0.7260 (t-90) REVERT: Y1 185 LYS cc_start: 0.7460 (ptmt) cc_final: 0.6986 (pttp) REVERT: Y1 188 MET cc_start: 0.5156 (mmt) cc_final: 0.4940 (mmm) REVERT: Y1 191 MET cc_start: 0.6957 (tmm) cc_final: 0.6462 (tmm) REVERT: Y1 193 GLN cc_start: 0.6918 (mm110) cc_final: 0.6713 (mm-40) REVERT: Z 29 LYS cc_start: 0.6935 (ptpp) cc_final: 0.6210 (pttp) REVERT: Z 45 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7290 (mmm-85) REVERT: Z 51 LYS cc_start: 0.6784 (mtpp) cc_final: 0.6323 (mmtm) REVERT: Z 70 ILE cc_start: 0.7959 (mp) cc_final: 0.7675 (tt) REVERT: Z 90 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6462 (mm-30) REVERT: Z 132 GLN cc_start: 0.6555 (pm20) cc_final: 0.6227 (pm20) outliers start: 142 outliers final: 104 residues processed: 887 average time/residue: 0.7183 time to fit residues: 1056.5533 Evaluate side-chains 869 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 755 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 5 VAL Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 50 TYR Chi-restraints excluded: chain A1 residue 60 VAL Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 94 GLN Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE Chi-restraints excluded: chain A1 residue 415 MET Chi-restraints excluded: chain A1 residue 421 GLU Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 77 GLU Chi-restraints excluded: chain A2 residue 110 ILE Chi-restraints excluded: chain A2 residue 136 LEU Chi-restraints excluded: chain A2 residue 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 367 ASP Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 30 ILE Chi-restraints excluded: chain A3 residue 126 SER Chi-restraints excluded: chain A3 residue 163 MET Chi-restraints excluded: chain A3 residue 195 ASN Chi-restraints excluded: chain A3 residue 200 MET Chi-restraints excluded: chain A3 residue 267 MET Chi-restraints excluded: chain A3 residue 289 LEU Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 333 VAL Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 102 ASN Chi-restraints excluded: chain A4 residue 149 LEU Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A4 residue 368 LEU Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 166 THR Chi-restraints excluded: chain A5 residue 200 MET Chi-restraints excluded: chain A5 residue 202 LEU Chi-restraints excluded: chain A5 residue 219 THR Chi-restraints excluded: chain A5 residue 267 MET Chi-restraints excluded: chain A5 residue 274 THR Chi-restraints excluded: chain A5 residue 359 LYS Chi-restraints excluded: chain A5 residue 406 MET Chi-restraints excluded: chain A6 residue 9 ILE Chi-restraints excluded: chain A6 residue 25 CYS Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 341 ILE Chi-restraints excluded: chain A7 residue 44 LEU Chi-restraints excluded: chain A7 residue 65 LEU Chi-restraints excluded: chain A7 residue 147 MET Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain A7 residue 354 CYS Chi-restraints excluded: chain A7 residue 388 MET Chi-restraints excluded: chain B1 residue 95 THR Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 194 LEU Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 328 VAL Chi-restraints excluded: chain B2 residue 341 ILE Chi-restraints excluded: chain B2 residue 344 VAL Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 94 GLN Chi-restraints excluded: chain B3 residue 143 THR Chi-restraints excluded: chain B3 residue 151 LEU Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B3 residue 205 GLU Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 326 LYS Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 406 MET Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 24 VAL Chi-restraints excluded: chain B7 residue 72 THR Chi-restraints excluded: chain B7 residue 149 THR Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 166 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 184 LEU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 171 LEU Chi-restraints excluded: chain X1 residue 217 ASP Chi-restraints excluded: chain X1 residue 218 MET Chi-restraints excluded: chain X1 residue 240 HIS Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 0.0040 chunk 260 optimal weight: 1.9990 chunk 389 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 414 optimal weight: 4.9990 chunk 444 optimal weight: 0.5980 chunk 322 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 512 optimal weight: 3.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS A3 332 ASN A4 50 ASN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 347 ASN A6 28 HIS ** A7 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 105 HIS B2 11 GLN ** B2 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 245 GLN ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3408 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: