Starting phenix.real_space_refine on Sun Mar 10 22:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/03_2024/7kzo_23084_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/03_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_23084/03_2024/7kzo_23084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/03_2024/7kzo_23084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/03_2024/7kzo_23084_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzo_23084/03_2024/7kzo_23084_updated.pdb" } 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 Residue "A1 ARG 58": "NH1" <-> "NH2" Residue "A1 ARG 77": "NH1" <-> "NH2" Residue "A1 GLU 125": "OE1" <-> "OE2" Residue "A2 ARG 64": "NH1" <-> "NH2" Residue "A2 GLU 71": "OE1" <-> "OE2" Residue "A2 ARG 79": "NH1" <-> "NH2" Residue "A2 GLU 97": "OE1" <-> "OE2" Residue "A2 GLU 113": "OE1" <-> "OE2" Residue "A2 GLU 279": "OE1" <-> "OE2" Residue "A2 GLU 434": "OE1" <-> "OE2" Residue "A3 GLU 22": "OE1" <-> "OE2" Residue "A3 GLU 45": "OE1" <-> "OE2" Residue "A3 ARG 58": "NH1" <-> "NH2" Residue "A3 GLU 69": "OE1" <-> "OE2" Residue "A3 GLU 157": "OE1" <-> "OE2" Residue "A3 GLU 194": "OE1" <-> "OE2" Residue "A3 ARG 391": "NH1" <-> "NH2" Residue "A3 GLU 405": "OE1" <-> "OE2" Residue "A4 GLU 27": "OE1" <-> "OE2" Residue "A4 PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 ARG 64": "NH1" <-> "NH2" Residue "A4 ARG 79": "NH1" <-> "NH2" Residue "A4 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 GLU 90": "OE1" <-> "OE2" Residue "A4 GLU 183": "OE1" <-> "OE2" Residue "A4 GLU 279": "OE1" <-> "OE2" Residue "A4 GLU 411": "OE1" <-> "OE2" Residue "A4 GLU 415": "OE1" <-> "OE2" Residue "A4 GLU 420": "OE1" <-> "OE2" Residue "A4 GLU 433": "OE1" <-> "OE2" Residue "A5 GLU 45": "OE1" <-> "OE2" Residue "A5 ARG 58": "NH1" <-> "NH2" Residue "A5 GLU 158": "OE1" <-> "OE2" Residue "A5 GLU 194": "OE1" <-> "OE2" Residue "A5 GLU 412": "OE1" <-> "OE2" Residue "A6 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ARG 64": "NH1" <-> "NH2" Residue "A6 ARG 79": "NH1" <-> "NH2" Residue "A6 GLU 97": "OE1" <-> "OE2" Residue "A6 GLU 155": "OE1" <-> "OE2" Residue "A6 GLU 220": "OE1" <-> "OE2" Residue "A6 GLU 279": "OE1" <-> "OE2" Residue "A6 GLU 284": "OE1" <-> "OE2" Residue "A6 ARG 390": "NH1" <-> "NH2" Residue "A6 PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 415": "OE1" <-> "OE2" Residue "A6 GLU 434": "OE1" <-> "OE2" Residue "A6 GLU 438": "OE1" <-> "OE2" Residue "A7 GLU 22": "OE1" <-> "OE2" Residue "A7 ARG 58": "NH1" <-> "NH2" Residue "A7 GLU 194": "OE1" <-> "OE2" Residue "A7 GLU 376": "OE1" <-> "OE2" Residue "A7 GLU 401": "OE1" <-> "OE2" Residue "A7 GLU 407": "OE1" <-> "OE2" Residue "A7 GLU 412": "OE1" <-> "OE2" Residue "B1 ASP 26": "OD1" <-> "OD2" Residue "B1 GLU 125": "OE1" <-> "OE2" Residue "B1 GLU 157": "OE1" <-> "OE2" Residue "B1 GLU 383": "OE1" <-> "OE2" Residue "B1 GLU 405": "OE1" <-> "OE2" Residue "B2 ARG 64": "NH1" <-> "NH2" Residue "B2 GLU 71": "OE1" <-> "OE2" Residue "B2 GLU 77": "OE1" <-> "OE2" Residue "B2 ARG 79": "NH1" <-> "NH2" Residue "B2 GLU 155": "OE1" <-> "OE2" Residue "B2 GLU 411": "OE1" <-> "OE2" Residue "B3 GLU 69": "OE1" <-> "OE2" Residue "B3 GLU 123": "OE1" <-> "OE2" Residue "B3 GLU 125": "OE1" <-> "OE2" Residue "B3 GLU 157": "OE1" <-> "OE2" Residue "B3 GLU 401": "OE1" <-> "OE2" Residue "B3 GLU 405": "OE1" <-> "OE2" Residue "B3 GLU 412": "OE1" <-> "OE2" Residue "B4 GLU 27": "OE1" <-> "OE2" Residue "B4 ARG 64": "NH1" <-> "NH2" Residue "B4 GLU 71": "OE1" <-> "OE2" Residue "B4 ARG 79": "NH1" <-> "NH2" Residue "B4 GLU 284": "OE1" <-> "OE2" Residue "B4 GLU 433": "OE1" <-> "OE2" Residue "B4 GLU 434": "OE1" <-> "OE2" Residue "B5 ARG 58": "NH1" <-> "NH2" Residue "B5 GLU 125": "OE1" <-> "OE2" Residue "B5 GLU 194": "OE1" <-> "OE2" Residue "B5 GLU 343": "OE1" <-> "OE2" Residue "B5 ARG 391": "NH1" <-> "NH2" Residue "B5 GLU 401": "OE1" <-> "OE2" Residue "B6 ARG 64": "NH1" <-> "NH2" Residue "B6 GLU 77": "OE1" <-> "OE2" Residue "B6 ARG 79": "NH1" <-> "NH2" Residue "B6 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 417": "OE1" <-> "OE2" Residue "B7 GLU 3": "OE1" <-> "OE2" Residue "B7 GLU 22": "OE1" <-> "OE2" Residue "B7 GLU 27": "OE1" <-> "OE2" Residue "B7 GLU 45": "OE1" <-> "OE2" Residue "B7 ARG 58": "NH1" <-> "NH2" Residue "B7 GLU 157": "OE1" <-> "OE2" Residue "B7 GLU 288": "OE1" <-> "OE2" Residue "B7 GLU 407": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "X ARG 245": "NH1" <-> "NH2" Residue "X GLU 249": "OE1" <-> "OE2" Residue "X GLU 254": "OE1" <-> "OE2" Residue "X GLU 275": "OE1" <-> "OE2" Residue "Y ARG 241": "NH1" <-> "NH2" Residue "Y ARG 243": "NH1" <-> "NH2" Residue "X1 ARG 130": "NH1" <-> "NH2" Residue "X1 GLU 133": "OE1" <-> "OE2" Residue "X1 ARG 147": "NH1" <-> "NH2" Residue "X1 GLU 184": "OE1" <-> "OE2" Residue "X1 GLU 190": "OE1" <-> "OE2" Residue "X1 GLU 191": "OE1" <-> "OE2" Residue "X1 GLU 207": "OE1" <-> "OE2" Residue "X1 ARG 245": "NH1" <-> "NH2" Residue "Y1 ARG 85": "NH1" <-> "NH2" Residue "Y1 GLU 103": "OE1" <-> "OE2" Residue "Y1 GLU 123": "OE1" <-> "OE2" Residue "Y1 GLU 136": "OE1" <-> "OE2" Residue "Y1 GLU 166": "OE1" <-> "OE2" Residue "Y1 GLU 178": "OE1" <-> "OE2" Residue "Y1 GLU 200": "OE1" <-> "OE2" Residue "Z ARG 7": "NH1" <-> "NH2" Residue "Z TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 12": "NH1" <-> "NH2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z GLU 41": "OE1" <-> "OE2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z GLU 99": "OE1" <-> "OE2" Residue "Z ARG 123": "NH1" <-> "NH2" Residue "Z GLU 152": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 20.46, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.60 Conformation dependent library (CDL) restraints added in 7.3 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... running ksdssp... Secondary structure from input PDB file: 286 helices and 35 sheets defined 51.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.81 Creating SS restraints... Processing helix chain 'A1' and resid 10 through 27 Processing helix chain 'A1' and resid 44 through 46 No H-bonds generated for 'chain 'A1' and resid 44 through 46' Processing helix chain 'A1' and resid 70 through 78 removed outlier: 3.668A pdb=" N VALA1 76 " --> pdb=" O THRA1 72 " (cutoff:3.500A) Processing helix chain 'A1' and resid 87 through 89 No H-bonds generated for 'chain 'A1' and resid 87 through 89' Processing helix chain 'A1' and resid 101 through 105 Processing helix chain 'A1' and resid 109 through 125 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 145 through 158 Processing helix chain 'A1' and resid 181 through 195 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 213 Processing helix chain 'A1' and resid 222 through 241 removed outlier: 3.572A pdb=" N THRA1 237 " --> pdb=" O META1 233 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N CYSA1 239 " --> pdb=" O GLYA1 235 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEUA1 240 " --> pdb=" O ILEA1 236 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARGA1 241 " --> pdb=" O THRA1 237 " (cutoff:3.500A) Processing helix chain 'A1' and resid 250 through 257 Processing helix chain 'A1' and resid 279 through 281 No H-bonds generated for 'chain 'A1' and resid 279 through 281' Processing helix chain 'A1' and resid 286 through 293 removed outlier: 3.534A pdb=" N GLNA1 292 " --> pdb=" O GLUA1 288 " (cutoff:3.500A) Processing helix chain 'A1' and resid 296 through 298 No H-bonds generated for 'chain 'A1' and resid 296 through 298' Processing helix chain 'A1' and resid 305 through 307 No H-bonds generated for 'chain 'A1' and resid 305 through 307' Processing helix chain 'A1' and resid 323 through 336 Processing helix chain 'A1' and resid 373 through 389 removed outlier: 4.506A pdb=" N GLUA1 383 " --> pdb=" O ARGA1 380 " (cutoff:3.500A) Processing helix chain 'A1' and resid 395 through 401 removed outlier: 4.645A pdb=" N GLUA1 401 " --> pdb=" O TRPA1 397 " (cutoff:3.500A) Processing helix chain 'A1' and resid 405 through 425 Processing helix chain 'A2' and resid 10 through 27 removed outlier: 3.755A pdb=" N GLUA2 22 " --> pdb=" O ASNA2 18 " (cutoff:3.500A) Processing helix chain 'A2' and resid 48 through 51 removed outlier: 3.738A pdb=" N THRA2 51 " --> pdb=" O ALAA2 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A2' and resid 48 through 51' Processing helix chain 'A2' and resid 72 through 79 removed outlier: 4.369A pdb=" N VALA2 78 " --> pdb=" O VALA2 74 " (cutoff:3.500A) Processing helix chain 'A2' and resid 89 through 91 No H-bonds generated for 'chain 'A2' and resid 89 through 91' Processing helix chain 'A2' and resid 103 through 107 Processing helix chain 'A2' and resid 111 through 128 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 148 through 160 Processing helix chain 'A2' and resid 183 through 197 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) Processing helix chain 'A2' and resid 207 through 215 Processing helix chain 'A2' and resid 224 through 243 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 255 through 258 No H-bonds generated for 'chain 'A2' and resid 255 through 258' Processing helix chain 'A2' and resid 278 through 283 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) No H-bonds generated for 'chain 'A2' and resid 278 through 283' Processing helix chain 'A2' and resid 288 through 294 Processing helix chain 'A2' and resid 298 through 300 No H-bonds generated for 'chain 'A2' and resid 298 through 300' Processing helix chain 'A2' and resid 307 through 309 No H-bonds generated for 'chain 'A2' and resid 307 through 309' Processing helix chain 'A2' and resid 325 through 337 Processing helix chain 'A2' and resid 383 through 401 removed outlier: 3.593A pdb=" N PHEA2 388 " --> pdb=" O GLYA2 385 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HISA2 393 " --> pdb=" O ARGA2 390 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHEA2 395 " --> pdb=" O ASPA2 392 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEUA2 397 " --> pdb=" O LYSA2 394 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALAA2 400 " --> pdb=" O LEUA2 397 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSA2 401 " --> pdb=" O META2 398 " (cutoff:3.500A) Processing helix chain 'A2' and resid 405 through 411 Processing helix chain 'A2' and resid 415 through 436 Processing helix chain 'A3' and resid 10 through 28 Processing helix chain 'A3' and resid 41 through 44 No H-bonds generated for 'chain 'A3' and resid 41 through 44' Processing helix chain 'A3' and resid 70 through 78 Processing helix chain 'A3' and resid 87 through 89 No H-bonds generated for 'chain 'A3' and resid 87 through 89' Processing helix chain 'A3' and resid 101 through 105 Processing helix chain 'A3' and resid 109 through 125 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 145 through 158 Processing helix chain 'A3' and resid 181 through 195 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 213 Processing helix chain 'A3' and resid 222 through 241 removed outlier: 3.748A pdb=" N THRA3 237 " --> pdb=" O META3 233 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N CYSA3 239 " --> pdb=" O GLYA3 235 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEUA3 240 " --> pdb=" O ILEA3 236 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARGA3 241 " --> pdb=" O THRA3 237 " (cutoff:3.500A) Processing helix chain 'A3' and resid 250 through 257 Processing helix chain 'A3' and resid 286 through 293 removed outlier: 3.557A pdb=" N GLNA3 292 " --> pdb=" O GLUA3 288 " (cutoff:3.500A) Processing helix chain 'A3' and resid 305 through 307 No H-bonds generated for 'chain 'A3' and resid 305 through 307' Processing helix chain 'A3' and resid 323 through 336 Processing helix chain 'A3' and resid 373 through 391 removed outlier: 3.528A pdb=" N VALA3 381 " --> pdb=" O PHEA3 378 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLUA3 383 " --> pdb=" O ARGA3 380 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARGA3 390 " --> pdb=" O ALAA3 387 " (cutoff:3.500A) Processing helix chain 'A3' and resid 396 through 399 No H-bonds generated for 'chain 'A3' and resid 396 through 399' Processing helix chain 'A3' and resid 405 through 425 Processing helix chain 'A4' and resid 11 through 28 removed outlier: 3.507A pdb=" N GLUA4 22 " --> pdb=" O ASNA4 18 " (cutoff:3.500A) Processing helix chain 'A4' and resid 48 through 51 removed outlier: 4.006A pdb=" N THRA4 51 " --> pdb=" O ALAA4 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 48 through 51' Processing helix chain 'A4' and resid 72 through 80 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) removed outlier: 3.649A pdb=" N THRA4 80 " --> pdb=" O ASPA4 76 " (cutoff:3.500A) Processing helix chain 'A4' and resid 82 through 85 removed outlier: 4.543A pdb=" N GLNA4 85 " --> pdb=" O THRA4 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 82 through 85' Processing helix chain 'A4' and resid 89 through 91 No H-bonds generated for 'chain 'A4' and resid 89 through 91' Processing helix chain 'A4' and resid 103 through 107 Processing helix chain 'A4' and resid 111 through 128 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 145 through 160 removed outlier: 3.772A pdb=" N GLYA4 150 " --> pdb=" O GLYA4 146 " (cutoff:3.500A) Processing helix chain 'A4' and resid 183 through 197 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) Processing helix chain 'A4' and resid 207 through 215 Processing helix chain 'A4' and resid 224 through 243 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 252 through 258 removed outlier: 4.075A pdb=" N GLNA4 256 " --> pdb=" O ILEA4 252 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THRA4 257 " --> pdb=" O THRA4 253 " (cutoff:3.500A) Processing helix chain 'A4' and resid 280 through 283 No H-bonds generated for 'chain 'A4' and resid 280 through 283' Processing helix chain 'A4' and resid 288 through 294 Processing helix chain 'A4' and resid 298 through 300 No H-bonds generated for 'chain 'A4' and resid 298 through 300' Processing helix chain 'A4' and resid 325 through 337 removed outlier: 3.515A pdb=" N ASNA4 329 " --> pdb=" O PROA4 325 " (cutoff:3.500A) Processing helix chain 'A4' and resid 383 through 401 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) removed outlier: 5.031A pdb=" N LYSA4 401 " --> pdb=" O LEUA4 397 " (cutoff:3.500A) Processing helix chain 'A4' and resid 405 through 411 Processing helix chain 'A4' and resid 416 through 436 Processing helix chain 'A5' and resid 10 through 27 Processing helix chain 'A5' and resid 41 through 43 No H-bonds generated for 'chain 'A5' and resid 41 through 43' Processing helix chain 'A5' and resid 70 through 78 Processing helix chain 'A5' and resid 87 through 89 No H-bonds generated for 'chain 'A5' and resid 87 through 89' Processing helix chain 'A5' and resid 101 through 105 Processing helix chain 'A5' and resid 109 through 125 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 145 through 156 Processing helix chain 'A5' and resid 181 through 195 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 213 Processing helix chain 'A5' and resid 222 through 236 Processing helix chain 'A5' and resid 238 through 241 No H-bonds generated for 'chain 'A5' and resid 238 through 241' Processing helix chain 'A5' and resid 250 through 257 Processing helix chain 'A5' and resid 279 through 281 No H-bonds generated for 'chain 'A5' and resid 279 through 281' Processing helix chain 'A5' and resid 286 through 293 removed outlier: 3.507A pdb=" N GLNA5 292 " --> pdb=" O GLUA5 288 " (cutoff:3.500A) Processing helix chain 'A5' and resid 296 through 298 No H-bonds generated for 'chain 'A5' and resid 296 through 298' Processing helix chain 'A5' and resid 305 through 307 No H-bonds generated for 'chain 'A5' and resid 305 through 307' Processing helix chain 'A5' and resid 323 through 336 Processing helix chain 'A5' and resid 338 through 340 No H-bonds generated for 'chain 'A5' and resid 338 through 340' Processing helix chain 'A5' and resid 373 through 389 removed outlier: 3.655A pdb=" N LYSA5 379 " --> pdb=" O GLUA5 376 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLUA5 383 " --> pdb=" O ARGA5 380 " (cutoff:3.500A) Processing helix chain 'A5' and resid 395 through 401 removed outlier: 4.761A pdb=" N GLUA5 401 " --> pdb=" O TRPA5 397 " (cutoff:3.500A) Processing helix chain 'A5' and resid 405 through 425 Processing helix chain 'A6' and resid 10 through 25 removed outlier: 3.883A pdb=" N GLUA6 22 " --> pdb=" O ASNA6 18 " (cutoff:3.500A) Processing helix chain 'A6' and resid 48 through 51 removed outlier: 3.576A pdb=" N THRA6 51 " --> pdb=" O ALAA6 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A6' and resid 48 through 51' Processing helix chain 'A6' and resid 73 through 80 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 89 through 91 No H-bonds generated for 'chain 'A6' and resid 89 through 91' Processing helix chain 'A6' and resid 103 through 107 Processing helix chain 'A6' and resid 111 through 128 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 148 through 160 Processing helix chain 'A6' and resid 183 through 196 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 207 through 215 Processing helix chain 'A6' and resid 224 through 243 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 255 through 258 No H-bonds generated for 'chain 'A6' and resid 255 through 258' Processing helix chain 'A6' and resid 278 through 282 Processing helix chain 'A6' and resid 288 through 294 Processing helix chain 'A6' and resid 298 through 300 No H-bonds generated for 'chain 'A6' and resid 298 through 300' Processing helix chain 'A6' and resid 325 through 337 Processing helix chain 'A6' and resid 383 through 399 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 405 through 411 Processing helix chain 'A6' and resid 416 through 436 Processing helix chain 'A7' and resid 10 through 27 Processing helix chain 'A7' and resid 41 through 43 No H-bonds generated for 'chain 'A7' and resid 41 through 43' Processing helix chain 'A7' and resid 70 through 78 Processing helix chain 'A7' and resid 87 through 89 No H-bonds generated for 'chain 'A7' and resid 87 through 89' Processing helix chain 'A7' and resid 101 through 105 Processing helix chain 'A7' and resid 109 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 145 through 158 Processing helix chain 'A7' and resid 181 through 195 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 204 through 213 Processing helix chain 'A7' and resid 222 through 241 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 250 through 257 Processing helix chain 'A7' and resid 286 through 293 Processing helix chain 'A7' and resid 305 through 307 No H-bonds generated for 'chain 'A7' and resid 305 through 307' Processing helix chain 'A7' and resid 323 through 336 Processing helix chain 'A7' and resid 373 through 389 removed outlier: 3.546A pdb=" N LYSA7 379 " --> pdb=" O GLUA7 376 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLUA7 383 " --> pdb=" O ARGA7 380 " (cutoff:3.500A) Processing helix chain 'A7' and resid 396 through 401 removed outlier: 4.183A pdb=" N GLUA7 401 " --> pdb=" O TRPA7 397 " (cutoff:3.500A) Processing helix chain 'A7' and resid 405 through 425 Processing helix chain 'B1' and resid 10 through 27 Processing helix chain 'B1' and resid 42 through 45 No H-bonds generated for 'chain 'B1' and resid 42 through 45' Processing helix chain 'B1' and resid 70 through 78 Processing helix chain 'B1' and resid 87 through 89 No H-bonds generated for 'chain 'B1' and resid 87 through 89' Processing helix chain 'B1' and resid 101 through 105 Processing helix chain 'B1' and resid 109 through 125 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 145 through 158 Processing helix chain 'B1' and resid 181 through 195 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 213 Processing helix chain 'B1' and resid 222 through 236 Processing helix chain 'B1' and resid 238 through 241 No H-bonds generated for 'chain 'B1' and resid 238 through 241' Processing helix chain 'B1' and resid 250 through 257 Processing helix chain 'B1' and resid 286 through 293 Processing helix chain 'B1' and resid 296 through 298 No H-bonds generated for 'chain 'B1' and resid 296 through 298' Processing helix chain 'B1' and resid 305 through 307 No H-bonds generated for 'chain 'B1' and resid 305 through 307' Processing helix chain 'B1' and resid 323 through 336 Processing helix chain 'B1' and resid 373 through 390 removed outlier: 3.608A pdb=" N PHEB1 378 " --> pdb=" O GLNB1 375 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLUB1 383 " --> pdb=" O ARGB1 380 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHEB1 385 " --> pdb=" O SERB1 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHEB1 389 " --> pdb=" O THRB1 386 " (cutoff:3.500A) Processing helix chain 'B1' and resid 396 through 401 removed outlier: 5.037A pdb=" N GLUB1 401 " --> pdb=" O TRPB1 397 " (cutoff:3.500A) Processing helix chain 'B1' and resid 405 through 425 Processing helix chain 'B2' and resid 10 through 27 removed outlier: 3.754A pdb=" N GLUB2 22 " --> pdb=" O ASNB2 18 " (cutoff:3.500A) Processing helix chain 'B2' and resid 48 through 51 removed outlier: 3.861A pdb=" N THRB2 51 " --> pdb=" O ALAB2 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 48 through 51' Processing helix chain 'B2' and resid 72 through 79 removed outlier: 3.522A pdb=" N VALB2 78 " --> pdb=" O VALB2 74 " (cutoff:3.500A) Processing helix chain 'B2' and resid 89 through 91 No H-bonds generated for 'chain 'B2' and resid 89 through 91' Processing helix chain 'B2' and resid 103 through 108 Processing helix chain 'B2' and resid 111 through 128 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 148 through 160 Processing helix chain 'B2' and resid 182 through 197 removed outlier: 3.710A pdb=" N VALB2 188 " --> pdb=" O TYRB2 185 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HISB2 192 " --> pdb=" O LEUB2 189 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEUB2 195 " --> pdb=" O HISB2 192 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HISB2 197 " --> pdb=" O LEUB2 194 " (cutoff:3.500A) Processing helix chain 'B2' and resid 207 through 215 Processing helix chain 'B2' and resid 224 through 243 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 252 through 258 removed outlier: 3.908A pdb=" N GLNB2 256 " --> pdb=" O ILEB2 252 " (cutoff:3.500A) Processing helix chain 'B2' and resid 278 through 283 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) No H-bonds generated for 'chain 'B2' and resid 278 through 283' Processing helix chain 'B2' and resid 288 through 294 Processing helix chain 'B2' and resid 298 through 300 No H-bonds generated for 'chain 'B2' and resid 298 through 300' Processing helix chain 'B2' and resid 307 through 309 No H-bonds generated for 'chain 'B2' and resid 307 through 309' Processing helix chain 'B2' and resid 325 through 337 Processing helix chain 'B2' and resid 383 through 400 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) Processing helix chain 'B2' and resid 405 through 411 Processing helix chain 'B2' and resid 416 through 435 Processing helix chain 'B3' and resid 10 through 27 Processing helix chain 'B3' and resid 41 through 43 No H-bonds generated for 'chain 'B3' and resid 41 through 43' Processing helix chain 'B3' and resid 70 through 78 Processing helix chain 'B3' and resid 87 through 89 No H-bonds generated for 'chain 'B3' and resid 87 through 89' Processing helix chain 'B3' and resid 101 through 105 Processing helix chain 'B3' and resid 109 through 125 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 145 through 158 Processing helix chain 'B3' and resid 181 through 195 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) Processing helix chain 'B3' and resid 204 through 213 Processing helix chain 'B3' and resid 222 through 236 Processing helix chain 'B3' and resid 238 through 241 No H-bonds generated for 'chain 'B3' and resid 238 through 241' Processing helix chain 'B3' and resid 250 through 257 Processing helix chain 'B3' and resid 276 through 278 No H-bonds generated for 'chain 'B3' and resid 276 through 278' Processing helix chain 'B3' and resid 286 through 293 removed outlier: 3.635A pdb=" N GLNB3 292 " --> pdb=" O GLUB3 288 " (cutoff:3.500A) Processing helix chain 'B3' and resid 296 through 298 No H-bonds generated for 'chain 'B3' and resid 296 through 298' Processing helix chain 'B3' and resid 305 through 307 No H-bonds generated for 'chain 'B3' and resid 305 through 307' Processing helix chain 'B3' and resid 323 through 336 Processing helix chain 'B3' and resid 373 through 391 removed outlier: 4.256A pdb=" N GLUB3 383 " --> pdb=" O ARGB3 380 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THRB3 386 " --> pdb=" O GLUB3 383 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHEB3 389 " --> pdb=" O THRB3 386 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARGB3 390 " --> pdb=" O ALAB3 387 " (cutoff:3.500A) Processing helix chain 'B3' and resid 396 through 401 removed outlier: 4.846A pdb=" N GLUB3 401 " --> pdb=" O TRPB3 397 " (cutoff:3.500A) Processing helix chain 'B3' and resid 405 through 425 Processing helix chain 'B4' and resid 10 through 27 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 48 through 51 removed outlier: 3.852A pdb=" N THRB4 51 " --> pdb=" O ALAB4 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B4' and resid 48 through 51' Processing helix chain 'B4' and resid 72 through 80 removed outlier: 3.582A pdb=" N VALB4 78 " --> pdb=" O VALB4 74 " (cutoff:3.500A) Processing helix chain 'B4' and resid 111 through 128 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 148 through 160 Processing helix chain 'B4' and resid 182 through 197 removed outlier: 3.789A pdb=" N VALB4 188 " --> pdb=" O TYRB4 185 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SERB4 190 " --> pdb=" O SERB4 187 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HISB4 192 " --> pdb=" O LEUB4 189 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEUB4 195 " --> pdb=" O HISB4 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLUB4 196 " --> pdb=" O SERB4 193 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HISB4 197 " --> pdb=" O LEUB4 194 " (cutoff:3.500A) Processing helix chain 'B4' and resid 207 through 215 Processing helix chain 'B4' and resid 224 through 243 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 252 through 258 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) Processing helix chain 'B4' and resid 278 through 283 removed outlier: 4.201A pdb=" N TYRB4 282 " --> pdb=" O ALAB4 278 " (cutoff:3.500A) Processing helix chain 'B4' and resid 288 through 294 Processing helix chain 'B4' and resid 298 through 300 No H-bonds generated for 'chain 'B4' and resid 298 through 300' Processing helix chain 'B4' and resid 325 through 337 Processing helix chain 'B4' and resid 383 through 400 removed outlier: 3.990A pdb=" N PHEB4 388 " --> pdb=" O GLYB4 385 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HISB4 393 " --> pdb=" O ARGB4 390 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEUB4 397 " --> pdb=" O LYSB4 394 " (cutoff:3.500A) Processing helix chain 'B4' and resid 405 through 411 Processing helix chain 'B4' and resid 415 through 436 Processing helix chain 'B5' and resid 10 through 27 Processing helix chain 'B5' and resid 41 through 43 No H-bonds generated for 'chain 'B5' and resid 41 through 43' Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 87 through 89 No H-bonds generated for 'chain 'B5' and resid 87 through 89' Processing helix chain 'B5' and resid 101 through 105 Processing helix chain 'B5' and resid 109 through 124 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 145 through 158 Processing helix chain 'B5' and resid 181 through 195 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 204 through 213 Processing helix chain 'B5' and resid 222 through 236 Processing helix chain 'B5' and resid 250 through 257 Processing helix chain 'B5' and resid 276 through 278 No H-bonds generated for 'chain 'B5' and resid 276 through 278' Processing helix chain 'B5' and resid 286 through 293 Processing helix chain 'B5' and resid 296 through 298 No H-bonds generated for 'chain 'B5' and resid 296 through 298' Processing helix chain 'B5' and resid 305 through 307 No H-bonds generated for 'chain 'B5' and resid 305 through 307' Processing helix chain 'B5' and resid 323 through 336 Processing helix chain 'B5' and resid 374 through 389 removed outlier: 4.480A pdb=" N GLUB5 383 " --> pdb=" O ARGB5 380 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THRB5 386 " --> pdb=" O GLUB5 383 " (cutoff:3.500A) Processing helix chain 'B5' and resid 395 through 401 removed outlier: 4.710A pdb=" N GLUB5 401 " --> pdb=" O TRPB5 397 " (cutoff:3.500A) Processing helix chain 'B5' and resid 405 through 425 Processing helix chain 'B6' and resid 10 through 28 Processing helix chain 'B6' and resid 48 through 51 removed outlier: 4.093A pdb=" N THRB6 51 " --> pdb=" O ALAB6 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B6' and resid 48 through 51' Processing helix chain 'B6' and resid 72 through 79 Processing helix chain 'B6' and resid 89 through 91 No H-bonds generated for 'chain 'B6' and resid 89 through 91' Processing helix chain 'B6' and resid 103 through 107 Processing helix chain 'B6' and resid 111 through 128 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 145 through 160 Processing helix chain 'B6' and resid 182 through 197 removed outlier: 3.755A pdb=" N VALB6 188 " --> pdb=" O TYRB6 185 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HISB6 192 " --> pdb=" O LEUB6 189 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEUB6 195 " --> pdb=" O HISB6 192 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HISB6 197 " --> pdb=" O LEUB6 194 " (cutoff:3.500A) Processing helix chain 'B6' and resid 206 through 215 Processing helix chain 'B6' and resid 224 through 243 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 259 removed outlier: 4.193A pdb=" N GLNB6 256 " --> pdb=" O ILEB6 252 " (cutoff:3.500A) Processing helix chain 'B6' and resid 278 through 283 removed outlier: 3.659A pdb=" N HISB6 283 " --> pdb=" O GLUB6 279 " (cutoff:3.500A) Processing helix chain 'B6' and resid 288 through 294 Processing helix chain 'B6' and resid 298 through 300 No H-bonds generated for 'chain 'B6' and resid 298 through 300' Processing helix chain 'B6' and resid 307 through 309 No H-bonds generated for 'chain 'B6' and resid 307 through 309' Processing helix chain 'B6' and resid 325 through 337 Processing helix chain 'B6' and resid 383 through 401 removed outlier: 4.139A pdb=" N PHEB6 388 " --> pdb=" O GLYB6 385 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HISB6 393 " --> pdb=" O ARGB6 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASPB6 396 " --> pdb=" O HISB6 393 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUB6 397 " --> pdb=" O LYSB6 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N METB6 398 " --> pdb=" O PHEB6 395 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALAB6 400 " --> pdb=" O LEUB6 397 " (cutoff:3.500A) Processing helix chain 'B6' and resid 405 through 411 Processing helix chain 'B6' and resid 415 through 435 Processing helix chain 'B7' and resid 10 through 28 Processing helix chain 'B7' and resid 41 through 46 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 70 through 78 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) Processing helix chain 'B7' and resid 87 through 89 No H-bonds generated for 'chain 'B7' and resid 87 through 89' Processing helix chain 'B7' and resid 108 through 125 removed outlier: 5.272A pdb=" N ILEB7 113 " --> pdb=" O ALAB7 110 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASPB7 114 " --> pdb=" O GLUB7 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUB7 117 " --> pdb=" O ASPB7 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALB7 120 " --> pdb=" O LEUB7 117 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUB7 125 " --> pdb=" O LYSB7 122 " (cutoff:3.500A) Processing helix chain 'B7' and resid 145 through 158 Processing helix chain 'B7' and resid 181 through 195 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 213 Processing helix chain 'B7' and resid 222 through 236 Processing helix chain 'B7' and resid 238 through 241 No H-bonds generated for 'chain 'B7' and resid 238 through 241' Processing helix chain 'B7' and resid 250 through 257 Processing helix chain 'B7' and resid 286 through 293 removed outlier: 3.629A pdb=" N GLNB7 292 " --> pdb=" O GLUB7 288 " (cutoff:3.500A) Processing helix chain 'B7' and resid 296 through 298 No H-bonds generated for 'chain 'B7' and resid 296 through 298' Processing helix chain 'B7' and resid 305 through 307 No H-bonds generated for 'chain 'B7' and resid 305 through 307' Processing helix chain 'B7' and resid 323 through 336 Processing helix chain 'B7' and resid 338 through 340 No H-bonds generated for 'chain 'B7' and resid 338 through 340' Processing helix chain 'B7' and resid 372 through 389 removed outlier: 3.505A pdb=" N LYSB7 379 " --> pdb=" O GLUB7 376 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLUB7 383 " --> pdb=" O ARGB7 380 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THRB7 386 " --> pdb=" O GLUB7 383 " (cutoff:3.500A) Processing helix chain 'B7' and resid 396 through 399 No H-bonds generated for 'chain 'B7' and resid 396 through 399' Processing helix chain 'B7' and resid 405 through 425 Processing helix chain 'C' and resid 273 through 308 removed outlier: 3.573A pdb=" N LEU C 300 " --> pdb=" O TYR C 296 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 314 through 330 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 339 through 361 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 414 through 439 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 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 455 through 468 removed outlier: 3.745A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 505 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 345 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) removed outlier: 6.536A pdb=" N VAL X 280 " --> pdb=" O GLU X 275 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG X 281 " --> pdb=" O ARG X 276 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU X 282 " --> pdb=" O ARG X 277 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU X 283 " --> pdb=" O ARG X 278 " (cutoff:3.500A) 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 381 Processing helix chain 'Y' and resid 176 through 246 Processing helix chain 'Y' and resid 268 through 280 Processing helix chain 'Y' and resid 284 through 313 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 166 removed outlier: 3.825A pdb=" N ARGX1 130 " --> pdb=" O LYSX1 126 " (cutoff:3.500A) Processing helix chain 'X1' and resid 172 through 259 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 114 removed outlier: 3.758A pdb=" N ILEY1 73 " --> pdb=" O GLNY1 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASPY1 78 " --> pdb=" O ARGY1 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUY1 79 " --> pdb=" O LEUY1 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THRY1 94 " --> pdb=" O METY1 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASPY1 98 " --> pdb=" O LYSY1 95 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEUY1 101 " --> pdb=" O ASPY1 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLUY1 103 " --> pdb=" O GLNY1 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N METY1 104 " --> pdb=" O LEUY1 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THRY1 110 " --> pdb=" O THRY1 107 " (cutoff:3.500A) Processing helix chain 'Y1' and resid 120 through 212 removed outlier: 3.814A pdb=" N METY1 169 " --> pdb=" O ARGY1 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 26 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 36 through 46 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 54 through 62 removed outlier: 3.786A pdb=" N VAL Z 62 " --> pdb=" O MET Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 83 Processing helix chain 'Z' and resid 93 through 102 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 121 removed outlier: 3.507A pdb=" N ILE Z 119 " --> pdb=" O ALA Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 132 removed outlier: 3.519A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 161 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) Processing sheet with id= A, 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: 7.153A pdb=" N CYSA1 129 " --> pdb=" O GLUA1 3 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N VALA1 5 " --> pdb=" O CYSA1 129 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLNA1 131 " --> pdb=" O VALA1 5 " (cutoff:3.500A) removed outlier: 13.012A pdb=" N ILEA1 7 " --> pdb=" O GLNA1 131 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N PHEA1 133 " --> pdb=" O ILEA1 7 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N GLYA1 9 " --> pdb=" O PHEA1 133 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N VALA1 135 " --> pdb=" O GLYA1 9 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N META1 163 " --> pdb=" O PHEA1 133 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VALA1 135 " --> pdb=" O META1 163 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEUA1 165 " --> pdb=" O VALA1 135 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HISA1 137 " --> pdb=" O LEUA1 165 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHEA1 167 " --> pdb=" O HISA1 137 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLUA1 198 " --> pdb=" O THRA1 166 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SERA1 168 " --> pdb=" O GLUA1 198 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N META1 200 " --> pdb=" O SERA1 168 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VALA1 170 " --> pdb=" O META1 200 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEUA1 202 " --> pdb=" O VALA1 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A1' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'A1' and resid 267 through 271 removed outlier: 3.537A pdb=" N THRA1 312 " --> pdb=" O ASNA1 370 " (cutoff:3.500A) Processing sheet with id= D, 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: 6.416A pdb=" N SERA2 165 " --> pdb=" O PHEA2 135 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VALA2 137 " --> pdb=" O SERA2 165 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEUA2 167 " --> pdb=" O VALA2 137 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASNA2 139 " --> pdb=" O LEUA2 167 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHEA2 169 " --> pdb=" O ASNA2 139 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VALA2 200 " --> pdb=" O GLYA2 168 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THRA2 170 " --> pdb=" O VALA2 200 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VALA2 202 " --> pdb=" O THRA2 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A2' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'A2' and resid 268 through 273 removed outlier: 3.900A pdb=" N ALAA2 314 " --> pdb=" O ASNA2 380 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A3' and resid 90 through 92 removed outlier: 7.834A pdb=" N VALA3 91 " --> pdb=" O ALAA3 63 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEUA3 65 " --> pdb=" O VALA3 91 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ILEA3 64 " --> pdb=" O ILEA3 4 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HISA3 6 " --> pdb=" O ILEA3 64 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N META3 66 " --> pdb=" O HISA3 6 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLNA3 8 " --> pdb=" O META3 66 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYSA3 129 " --> pdb=" O GLUA3 3 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N VALA3 5 " --> pdb=" O CYSA3 129 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N GLNA3 131 " --> pdb=" O VALA3 5 " (cutoff:3.500A) removed outlier: 12.971A pdb=" N ILEA3 7 " --> pdb=" O GLNA3 131 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N PHEA3 133 " --> pdb=" O ILEA3 7 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N GLYA3 9 " --> pdb=" O PHEA3 133 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VALA3 135 " --> pdb=" O GLYA3 9 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N META3 163 " --> pdb=" O PHEA3 133 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VALA3 135 " --> pdb=" O META3 163 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEUA3 165 " --> pdb=" O VALA3 135 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HISA3 137 " --> pdb=" O LEUA3 165 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHEA3 167 " --> pdb=" O HISA3 137 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLUA3 198 " --> pdb=" O THRA3 166 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SERA3 168 " --> pdb=" O GLUA3 198 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N META3 200 " --> pdb=" O SERA3 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VALA3 170 " --> pdb=" O META3 200 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEUA3 202 " --> pdb=" O VALA3 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A3' and resid 51 through 53 Processing sheet with id= I, first strand: chain 'A3' and resid 267 through 271 Processing sheet with id= J, 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: 7.995A pdb=" N ILEA4 5 " --> pdb=" O GLNA4 133 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHEA4 135 " --> pdb=" O ILEA4 5 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILEA4 7 " --> pdb=" O PHEA4 135 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VALA4 137 " --> pdb=" O ILEA4 7 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILEA4 9 " --> pdb=" O VALA4 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASNA4 139 " --> pdb=" O ILEA4 9 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N SERA4 165 " --> pdb=" O PHEA4 135 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VALA4 137 " --> pdb=" O SERA4 165 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEUA4 167 " --> pdb=" O VALA4 137 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASNA4 139 " --> pdb=" O LEUA4 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHEA4 169 " --> pdb=" O ASNA4 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VALA4 200 " --> pdb=" O GLYA4 168 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THRA4 170 " --> pdb=" O VALA4 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VALA4 202 " --> pdb=" O THRA4 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A4' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'A4' and resid 268 through 273 removed outlier: 4.023A pdb=" N ALAA4 314 " --> pdb=" O ASNA4 380 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A5' and resid 63 through 66 removed outlier: 8.586A pdb=" N ILEA5 64 " --> pdb=" O ILEA5 4 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HISA5 6 " --> pdb=" O ILEA5 64 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N META5 66 " --> pdb=" O HISA5 6 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLNA5 8 " --> pdb=" O META5 66 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N CYSA5 129 " --> pdb=" O GLUA5 3 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VALA5 5 " --> pdb=" O CYSA5 129 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLNA5 131 " --> pdb=" O VALA5 5 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N ILEA5 7 " --> pdb=" O GLNA5 131 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N PHEA5 133 " --> pdb=" O ILEA5 7 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N GLYA5 9 " --> pdb=" O PHEA5 133 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VALA5 135 " --> pdb=" O GLYA5 9 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N META5 163 " --> pdb=" O PHEA5 133 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N VALA5 135 " --> pdb=" O META5 163 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEUA5 165 " --> pdb=" O VALA5 135 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HISA5 137 " --> pdb=" O LEUA5 165 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHEA5 167 " --> pdb=" O HISA5 137 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLUA5 198 " --> pdb=" O THRA5 166 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SERA5 168 " --> pdb=" O GLUA5 198 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N META5 200 " --> pdb=" O SERA5 168 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VALA5 170 " --> pdb=" O META5 200 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEUA5 202 " --> pdb=" O VALA5 170 " (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= N, first strand: chain 'A5' and resid 51 through 53 Processing sheet with id= O, 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: 8.104A pdb=" N ILEA6 5 " --> pdb=" O GLNA6 133 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHEA6 135 " --> pdb=" O ILEA6 5 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILEA6 7 " --> pdb=" O PHEA6 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VALA6 137 " --> pdb=" O ILEA6 7 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILEA6 9 " --> pdb=" O VALA6 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASNA6 139 " --> pdb=" O ILEA6 9 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SERA6 165 " --> pdb=" O PHEA6 135 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VALA6 137 " --> pdb=" O SERA6 165 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEUA6 167 " --> pdb=" O VALA6 137 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASNA6 139 " --> pdb=" O LEUA6 167 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHEA6 169 " --> pdb=" O ASNA6 139 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VALA6 200 " --> pdb=" O GLYA6 168 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THRA6 170 " --> pdb=" O VALA6 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VALA6 202 " --> pdb=" O THRA6 170 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYRA6 172 " --> pdb=" O VALA6 202 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEUA6 204 " --> pdb=" O TYRA6 172 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A6' and resid 53 through 55 Processing sheet with id= Q, first strand: chain 'A6' and resid 268 through 273 removed outlier: 3.816A pdb=" N ALAA6 314 " --> pdb=" O ASNA6 380 " (cutoff:3.500A) Processing sheet with id= R, 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: 8.915A pdb=" N ILEA7 64 " --> pdb=" O ILEA7 4 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HISA7 6 " --> pdb=" O ILEA7 64 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N META7 66 " --> pdb=" O HISA7 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLNA7 8 " --> pdb=" O META7 66 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VALA7 5 " --> pdb=" O GLNA7 131 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHEA7 133 " --> pdb=" O VALA7 5 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILEA7 7 " --> pdb=" O PHEA7 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VALA7 135 " --> pdb=" O ILEA7 7 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLYA7 9 " --> pdb=" O VALA7 135 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HISA7 137 " --> pdb=" O GLYA7 9 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N META7 163 " --> pdb=" O PHEA7 133 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N VALA7 135 " --> pdb=" O META7 163 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEUA7 165 " --> pdb=" O VALA7 135 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HISA7 137 " --> pdb=" O LEUA7 165 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHEA7 167 " --> pdb=" O HISA7 137 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLUA7 198 " --> pdb=" O THRA7 166 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SERA7 168 " --> pdb=" O GLUA7 198 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N META7 200 " --> pdb=" O SERA7 168 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A7' and resid 51 through 53 Processing sheet with id= T, first strand: chain 'A7' and resid 267 through 271 Processing sheet with id= U, first strand: chain 'B1' and resid 63 through 66 removed outlier: 8.844A pdb=" N ILEB1 64 " --> pdb=" O ILEB1 4 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HISB1 6 " --> pdb=" O ILEB1 64 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N METB1 66 " --> pdb=" O HISB1 6 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLNB1 8 " --> pdb=" O METB1 66 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYSB1 129 " --> pdb=" O GLUB1 3 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VALB1 5 " --> pdb=" O CYSB1 129 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLNB1 131 " --> pdb=" O VALB1 5 " (cutoff:3.500A) removed outlier: 12.806A pdb=" N ILEB1 7 " --> pdb=" O GLNB1 131 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N PHEB1 133 " --> pdb=" O ILEB1 7 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N GLYB1 9 " --> pdb=" O PHEB1 133 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N VALB1 135 " --> pdb=" O GLYB1 9 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N METB1 163 " --> pdb=" O PHEB1 133 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VALB1 135 " --> pdb=" O METB1 163 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEUB1 165 " --> pdb=" O VALB1 135 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HISB1 137 " --> pdb=" O LEUB1 165 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHEB1 167 " --> pdb=" O HISB1 137 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLUB1 198 " --> pdb=" O THRB1 166 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SERB1 168 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N METB1 200 " --> pdb=" O SERB1 168 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VALB1 170 " --> pdb=" O METB1 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEUB1 202 " --> pdb=" O VALB1 170 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VALB1 268 " --> pdb=" O VALB1 201 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ASPB1 203 " --> pdb=" O VALB1 268 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N PHEB1 270 " --> pdb=" O ASPB1 203 " (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) Processing sheet with id= V, first strand: chain 'B2' and resid 65 through 68 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: 3.547A pdb=" N ILEB2 5 " --> pdb=" O GLYB2 134 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALAB2 140 " --> pdb=" O ILEB2 9 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SERB2 165 " --> pdb=" O PHEB2 135 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VALB2 137 " --> pdb=" O SERB2 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEUB2 167 " --> pdb=" O VALB2 137 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASNB2 139 " --> pdb=" O LEUB2 167 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHEB2 169 " --> pdb=" O ASNB2 139 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VALB2 200 " --> pdb=" O GLYB2 168 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THRB2 170 " --> pdb=" O VALB2 200 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VALB2 202 " --> pdb=" O THRB2 170 " (cutoff:3.500A) Processing sheet with id= W, 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= X, first strand: chain 'B3' and resid 90 through 92 removed outlier: 7.728A pdb=" N VALB3 91 " --> pdb=" O ALAB3 63 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEUB3 65 " --> pdb=" O VALB3 91 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ILEB3 64 " --> pdb=" O ILEB3 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HISB3 6 " --> pdb=" O ILEB3 64 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N METB3 66 " --> pdb=" O HISB3 6 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLNB3 8 " --> pdb=" O METB3 66 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N CYSB3 129 " --> pdb=" O GLUB3 3 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VALB3 5 " --> pdb=" O CYSB3 129 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLNB3 131 " --> pdb=" O VALB3 5 " (cutoff:3.500A) removed outlier: 13.024A pdb=" N ILEB3 7 " --> pdb=" O GLNB3 131 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N PHEB3 133 " --> pdb=" O ILEB3 7 " (cutoff:3.500A) removed outlier: 12.134A pdb=" N GLYB3 9 " --> pdb=" O PHEB3 133 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N VALB3 135 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N METB3 163 " --> pdb=" O PHEB3 133 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VALB3 135 " --> pdb=" O METB3 163 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEUB3 165 " --> pdb=" O VALB3 135 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HISB3 137 " --> pdb=" O LEUB3 165 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHEB3 167 " --> pdb=" O HISB3 137 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLUB3 198 " --> pdb=" O THRB3 166 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SERB3 168 " --> pdb=" O GLUB3 198 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N METB3 200 " --> pdb=" O SERB3 168 " (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) Processing sheet with id= Y, first strand: chain 'B4' and resid 65 through 68 removed outlier: 7.010A pdb=" N SERB4 6 " --> pdb=" O ILEB4 66 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEUB4 68 " --> pdb=" O SERB4 6 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HISB4 8 " --> pdb=" O LEUB4 68 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALAB4 140 " --> pdb=" O ILEB4 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SERB4 165 " --> pdb=" O PHEB4 135 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VALB4 137 " --> pdb=" O SERB4 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEUB4 167 " --> pdb=" O VALB4 137 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASNB4 139 " --> pdb=" O LEUB4 167 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHEB4 169 " --> pdb=" O ASNB4 139 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VALB4 200 " --> pdb=" O GLYB4 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THRB4 170 " --> pdb=" O VALB4 200 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VALB4 202 " --> pdb=" O THRB4 170 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B4' and resid 269 through 273 Processing sheet with id= AA, first strand: chain 'B5' and resid 90 through 92 removed outlier: 7.679A pdb=" N VALB5 91 " --> pdb=" O ALAB5 63 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEUB5 65 " --> pdb=" O VALB5 91 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILEB5 64 " --> pdb=" O ILEB5 4 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HISB5 6 " --> pdb=" O ILEB5 64 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N METB5 66 " --> pdb=" O HISB5 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLNB5 8 " --> pdb=" O METB5 66 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYSB5 129 " --> pdb=" O GLUB5 3 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VALB5 5 " --> pdb=" O CYSB5 129 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N GLNB5 131 " --> pdb=" O VALB5 5 " (cutoff:3.500A) removed outlier: 12.602A pdb=" N ILEB5 7 " --> pdb=" O GLNB5 131 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N PHEB5 133 " --> pdb=" O ILEB5 7 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N GLYB5 9 " --> pdb=" O PHEB5 133 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N VALB5 135 " --> pdb=" O GLYB5 9 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N METB5 163 " --> pdb=" O PHEB5 133 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VALB5 135 " --> pdb=" O METB5 163 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEUB5 165 " --> pdb=" O VALB5 135 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HISB5 137 " --> pdb=" O LEUB5 165 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHEB5 167 " --> pdb=" O HISB5 137 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLUB5 198 " --> pdb=" O THRB5 166 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N SERB5 168 " --> pdb=" O GLUB5 198 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N METB5 200 " --> pdb=" O SERB5 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'B5' and resid 51 through 53 Processing sheet with id= AC, first strand: chain 'B5' and resid 267 through 271 Processing sheet with id= AD, 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: 7.948A pdb=" N ILEB6 5 " --> pdb=" O GLNB6 133 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHEB6 135 " --> pdb=" O ILEB6 5 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILEB6 7 " --> pdb=" O PHEB6 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VALB6 137 " --> pdb=" O ILEB6 7 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILEB6 9 " --> pdb=" O VALB6 137 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASNB6 139 " --> pdb=" O ILEB6 9 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SERB6 165 " --> pdb=" O PHEB6 135 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VALB6 137 " --> pdb=" O SERB6 165 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEUB6 167 " --> pdb=" O VALB6 137 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASNB6 139 " --> pdb=" O LEUB6 167 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHEB6 169 " --> pdb=" O ASNB6 139 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VALB6 200 " --> pdb=" O GLYB6 168 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THRB6 170 " --> pdb=" O VALB6 200 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VALB6 202 " --> pdb=" O THRB6 170 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B6' and resid 53 through 55 Processing sheet with id= AF, 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= AG, 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: 7.293A pdb=" N CYSB7 129 " --> pdb=" O GLUB7 3 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VALB7 5 " --> pdb=" O CYSB7 129 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLNB7 131 " --> pdb=" O VALB7 5 " (cutoff:3.500A) removed outlier: 12.638A pdb=" N ILEB7 7 " --> pdb=" O GLNB7 131 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N PHEB7 133 " --> pdb=" O ILEB7 7 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N GLYB7 9 " --> pdb=" O PHEB7 133 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N VALB7 135 " --> pdb=" O GLYB7 9 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N METB7 163 " --> pdb=" O PHEB7 133 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VALB7 135 " --> pdb=" O METB7 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEUB7 165 " --> pdb=" O VALB7 135 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HISB7 137 " --> pdb=" O LEUB7 165 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHEB7 167 " --> pdb=" O HISB7 137 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLUB7 198 " --> pdb=" O THRB7 166 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SERB7 168 " --> pdb=" O GLUB7 198 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N METB7 200 " --> pdb=" O SERB7 168 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VALB7 170 " --> pdb=" O METB7 200 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEUB7 202 " --> pdb=" O VALB7 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'B7' and resid 51 through 53 Processing sheet with id= AI, first strand: chain 'B7' and resid 267 through 271 2541 hydrogen bonds defined for protein. 6954 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: 16.92 Time building geometry restraints manager: 17.10 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: 95.08 - 103.33: 701 103.33 - 111.58: 23885 111.58 - 119.82: 24033 119.82 - 128.07: 25736 128.07 - 136.32: 408 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: 40770 3.10 - 4.00: 141343 4.00 - 4.90: 259928 Warning: very small nonbonded interaction distances. Nonbonded interactions: 442094 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 442089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 0.920 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: 0.030 Extract box with map and model: 6.800 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 107.250 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.970 ------------------------------------------------------------------------------- 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= 0.306 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 fitting. rotamer outliers: 17 poor density : 1016 time to evaluate : 4.692 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: 0.5305 time to fit residues: 902.6985 Evaluate side-chains 794 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 791 time to evaluate : 4.590 ------------------------------------------------------------------------------- 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: 0.6980 chunk 513 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 530 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 394 optimal weight: 0.0570 chunk 614 optimal weight: 20.0000 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 99 ASN A1 134 GLN A1 227 HIS ** A1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 414 ASN ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 190 HIS ** A3 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 332 ASN ** A3 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 206 ASN A5 14 ASN ** A7 204 ASN ** 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 329 ASN B3 190 HIS B3 384 GLN ** B4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 88 HIS ** B4 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 100 ASN 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 ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN X 250 GLN Y 229 GLN X1 224 GLN Z 103 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1600 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= 0.217 Angle : 0.635 9.652 74763 Z= 0.324 Chirality : 0.044 0.203 8221 Planarity : 0.005 0.083 9726 Dihedral : 10.419 170.170 7618 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.93 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 9.49 % Favored : 89.11 % 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: -0.69 (0.10), residues: 6799 helix: 0.56 (0.09), residues: 3379 sheet: -0.60 (0.17), residues: 902 loop : -1.78 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPB7 397 HIS 0.008 0.001 HISB3 190 PHE 0.026 0.002 PHEB5 92 TYR 0.018 0.001 TYR Z 10 ARG 0.007 0.001 ARG X 257 *********************** 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 949 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 868 time to evaluate : 4.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 3 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7121 (tm-30) REVERT: A1 294 TRP cc_start: 0.5838 (m100) cc_final: 0.4490 (t60) REVERT: A1 361 LEU cc_start: 0.6581 (tp) cc_final: 0.5887 (mp) REVERT: A1 363 MET cc_start: 0.6142 (ttm) cc_final: 0.5929 (ttt) REVERT: A1 401 GLU cc_start: 0.6097 (tm-30) cc_final: 0.5735 (tm-30) REVERT: A2 120 ASP cc_start: 0.8072 (t0) cc_final: 0.7860 (t0) REVERT: A2 371 VAL cc_start: 0.6628 (t) cc_final: 0.6416 (p) REVERT: A3 3 GLU cc_start: 0.7177 (mp0) cc_final: 0.6935 (mp0) REVERT: A3 26 ASP cc_start: 0.6373 (m-30) cc_final: 0.6078 (m-30) REVERT: A3 282 ARG cc_start: 0.5851 (ptt180) cc_final: 0.5405 (tpp-160) REVERT: A3 293 MET cc_start: 0.6511 (ttt) cc_final: 0.6183 (ttm) REVERT: A3 299 MET cc_start: 0.6296 (mmm) cc_final: 0.5933 (mmm) REVERT: A3 391 ARG cc_start: 0.7441 (tpt90) cc_final: 0.7221 (tpt90) REVERT: A4 62 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8571 (p) REVERT: A4 122 ILE cc_start: 0.8856 (tt) cc_final: 0.8590 (mt) REVERT: A4 370 LYS cc_start: 0.7630 (tptt) cc_final: 0.6724 (pttt) REVERT: A4 377 MET cc_start: 0.7745 (tmm) cc_final: 0.6087 (tmm) REVERT: A5 271 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7822 (m) REVERT: A6 5 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8058 (pt) REVERT: A6 154 LEU cc_start: 0.8526 (mm) cc_final: 0.8326 (mm) REVERT: A6 370 LYS cc_start: 0.7667 (tptt) cc_final: 0.6919 (pttt) REVERT: A6 398 MET cc_start: 0.6407 (mtm) cc_final: 0.6201 (mtt) REVERT: A6 401 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7603 (tptt) REVERT: A7 251 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7266 (ttm170) REVERT: A7 294 TRP cc_start: 0.6195 (m100) cc_final: 0.3869 (t60) REVERT: A7 299 MET cc_start: 0.7626 (mmt) cc_final: 0.7380 (mmp) REVERT: A7 359 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7825 (mtmt) REVERT: B1 200 MET cc_start: 0.8134 (mpp) cc_final: 0.7925 (mpp) REVERT: B1 289 LEU cc_start: 0.8583 (mt) cc_final: 0.8310 (mt) REVERT: B1 294 TRP cc_start: 0.8594 (m100) cc_final: 0.8280 (m100) REVERT: B2 301 MET cc_start: 0.7482 (mtt) cc_final: 0.7241 (mtt) REVERT: B4 24 TYR cc_start: 0.8198 (m-10) cc_final: 0.7744 (m-10) REVERT: B4 71 GLU cc_start: 0.5695 (pt0) cc_final: 0.5244 (pm20) REVERT: B4 78 VAL cc_start: 0.8955 (t) cc_final: 0.8682 (t) REVERT: B5 276 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6893 (ttm170) REVERT: B6 275 ILE cc_start: 0.8761 (mm) cc_final: 0.8467 (tp) REVERT: B7 3 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6521 (mp0) REVERT: B7 73 MET cc_start: 0.8544 (mmp) cc_final: 0.8278 (mmt) REVERT: B7 150 LEU cc_start: 0.7551 (pp) cc_final: 0.6574 (tp) REVERT: C 320 PRO cc_start: 0.3768 (Cg_endo) cc_final: 0.3551 (Cg_exo) REVERT: X 248 LYS cc_start: 0.7400 (ptmm) cc_final: 0.7051 (tmtt) REVERT: X 264 GLU cc_start: 0.5513 (pp20) cc_final: 0.5110 (pp20) REVERT: X 274 ARG cc_start: 0.4865 (mtt180) cc_final: 0.4313 (mmt-90) REVERT: Y 210 ASN cc_start: 0.7160 (m110) cc_final: 0.6766 (m110) REVERT: Y 213 LYS cc_start: 0.6081 (ttpp) cc_final: 0.5651 (tttt) REVERT: Y 221 GLN cc_start: 0.8609 (tt0) cc_final: 0.7243 (tm-30) REVERT: Y 271 LYS cc_start: 0.1303 (mtpt) cc_final: 0.0792 (tppp) REVERT: X1 124 ASP cc_start: 0.7481 (m-30) cc_final: 0.7214 (m-30) REVERT: X1 132 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7469 (mp) REVERT: X1 250 GLN cc_start: 0.6098 (tm-30) cc_final: 0.5763 (tt0) REVERT: Y1 152 HIS cc_start: 0.7796 (t70) cc_final: 0.7249 (t-90) REVERT: Y1 185 LYS cc_start: 0.7426 (ptmt) cc_final: 0.6931 (pttp) REVERT: Z 7 ARG cc_start: 0.7636 (ptp-170) cc_final: 0.7276 (ptp-170) REVERT: Z 29 LYS cc_start: 0.6420 (ptpp) cc_final: 0.5885 (pttt) REVERT: Z 45 ARG cc_start: 0.7105 (mmm-85) cc_final: 0.6586 (tpt170) REVERT: Z 120 MET cc_start: 0.7554 (ttm) cc_final: 0.6902 (tpp) outliers start: 81 outliers final: 46 residues processed: 911 average time/residue: 0.5452 time to fit residues: 824.3407 Evaluate side-chains 827 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 777 time to evaluate : 4.609 ------------------------------------------------------------------------------- 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 428 LEU Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL 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 95 THR 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 A6 residue 239 THR Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain A7 residue 388 MET Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B3 residue 126 SER Chi-restraints excluded: chain B3 residue 249 ASP Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B4 residue 397 LEU 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 404 ASP Chi-restraints excluded: chain B6 residue 177 VAL 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 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 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 511 optimal weight: 8.9990 chunk 418 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 615 optimal weight: 30.0000 chunk 665 optimal weight: 6.9990 chunk 548 optimal weight: 9.9990 chunk 610 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 494 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 6 HIS A1 134 GLN ** A1 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 227 HIS ** A1 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 28 HIS A2 226 ASN A2 293 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 15 GLN A3 195 ASN A3 280 GLN ** A3 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 334 GLN ** A4 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 50 ASN ** A4 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 28 HIS ** A6 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 43 GLN ** B1 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 15 GLN B3 89 ASN B3 348 ASN ** B4 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 15 GLN B5 99 ASN 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 28 HIS B6 101 ASN B6 266 HIS ** B6 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B7 89 ASN B7 280 GLN B7 329 GLN ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN X 224 GLN X 250 GLN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1 240 HIS ** Z 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.099 55199 Z= 0.780 Angle : 0.982 12.252 74763 Z= 0.508 Chirality : 0.059 0.297 8221 Planarity : 0.007 0.073 9726 Dihedral : 11.380 177.400 7618 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 3.66 % Allowed : 15.31 % Favored : 81.03 % 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: -1.21 (0.10), residues: 6799 helix: -0.02 (0.08), residues: 3386 sheet: -0.60 (0.17), residues: 860 loop : -1.86 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRPB4 346 HIS 0.018 0.003 HISB2 266 PHE 0.046 0.004 PHEB2 395 TYR 0.042 0.004 TYRB2 172 ARG 0.015 0.001 ARG Y 228 *********************** 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 1010 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 799 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 100 ASN cc_start: 0.7957 (m-40) cc_final: 0.7705 (m-40) REVERT: A1 163 MET cc_start: 0.6908 (mmm) cc_final: 0.6516 (tpp) REVERT: A1 294 TRP cc_start: 0.6006 (m100) cc_final: 0.4950 (t60) REVERT: A1 361 LEU cc_start: 0.5963 (tp) cc_final: 0.5211 (mp) REVERT: A3 3 GLU cc_start: 0.7383 (mp0) cc_final: 0.7045 (mp0) REVERT: A3 125 GLU cc_start: 0.7397 (pp20) cc_final: 0.7036 (pp20) REVERT: A3 293 MET cc_start: 0.6803 (ttt) cc_final: 0.6525 (ttm) REVERT: A3 299 MET cc_start: 0.6457 (mmm) cc_final: 0.6197 (mmm) REVERT: A4 203 MET cc_start: 0.7368 (mpp) cc_final: 0.7116 (mpp) REVERT: A4 346 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.6639 (p-90) REVERT: A4 386 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6581 (pt0) REVERT: A5 282 ARG cc_start: 0.5608 (ttm-80) cc_final: 0.4613 (ttp-170) REVERT: A5 293 MET cc_start: 0.6662 (ttp) cc_final: 0.6216 (ttm) REVERT: A5 294 TRP cc_start: 0.6541 (m100) cc_final: 0.6171 (m100) REVERT: A6 11 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7384 (tp-100) REVERT: A6 68 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8076 (tp) REVERT: A6 370 LYS cc_start: 0.7800 (tptt) cc_final: 0.6915 (pttt) REVERT: A6 398 MET cc_start: 0.6609 (mtm) cc_final: 0.6335 (mtm) REVERT: A6 401 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7868 (tptp) REVERT: A7 163 MET cc_start: 0.8008 (mmm) cc_final: 0.7525 (mmt) REVERT: A7 247 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7955 (p0) REVERT: A7 251 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7337 (ttm170) REVERT: A7 294 TRP cc_start: 0.7361 (m100) cc_final: 0.4500 (t60) REVERT: A7 299 MET cc_start: 0.8034 (mmp) cc_final: 0.7775 (mmp) REVERT: A7 359 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7895 (mtmt) REVERT: A7 391 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6494 (tmt170) REVERT: B1 200 MET cc_start: 0.8442 (mpp) cc_final: 0.8130 (mpp) REVERT: B1 300 MET cc_start: 0.8296 (mtt) cc_final: 0.8093 (mtt) REVERT: B2 5 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (pt) REVERT: B2 11 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8878 (tt0) REVERT: B2 121 ARG cc_start: 0.7184 (tpp80) cc_final: 0.6534 (tpp-160) REVERT: B2 123 ARG cc_start: 0.7597 (tpt90) cc_final: 0.7174 (tpt170) REVERT: B3 189 VAL cc_start: 0.8874 (p) cc_final: 0.8659 (t) REVERT: B4 203 MET cc_start: 0.7918 (mmm) cc_final: 0.7418 (mmm) REVERT: B5 125 GLU cc_start: 0.5951 (pt0) cc_final: 0.5605 (pt0) REVERT: B5 276 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7018 (ttm-80) REVERT: B6 423 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: B7 149 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7657 (m) REVERT: B7 150 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.6995 (tp) REVERT: C 323 MET cc_start: 0.6953 (mtt) cc_final: 0.6721 (mtm) REVERT: X 248 LYS cc_start: 0.7393 (ptmm) cc_final: 0.7094 (tmtt) REVERT: X 264 GLU cc_start: 0.6064 (pp20) cc_final: 0.5645 (pp20) REVERT: X 274 ARG cc_start: 0.4950 (mtt180) cc_final: 0.4375 (mmp80) REVERT: Y 179 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7759 (mtt-85) REVERT: Y 209 MET cc_start: 0.6802 (mmm) cc_final: 0.6160 (tmm) REVERT: Y 213 LYS cc_start: 0.5993 (ttpp) cc_final: 0.5487 (tttt) REVERT: Y 221 GLN cc_start: 0.8740 (tt0) cc_final: 0.7375 (tm-30) REVERT: Y 271 LYS cc_start: 0.1417 (mtpt) cc_final: 0.0732 (tppp) REVERT: X1 132 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7740 (mp) REVERT: X1 229 ASP cc_start: 0.6861 (p0) cc_final: 0.6358 (p0) REVERT: X1 240 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.5883 (t-90) REVERT: X1 250 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6162 (tt0) REVERT: Y1 152 HIS cc_start: 0.8125 (t70) cc_final: 0.7577 (t-90) REVERT: Y1 178 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: Y1 191 MET cc_start: 0.6130 (tmm) cc_final: 0.5425 (tmm) REVERT: Z 51 LYS cc_start: 0.6568 (mtpp) cc_final: 0.6159 (mmtm) REVERT: Z 70 ILE cc_start: 0.7844 (mp) cc_final: 0.7005 (tt) REVERT: Z 90 GLU cc_start: 0.6273 (mm-30) cc_final: 0.6000 (mm-30) outliers start: 211 outliers final: 145 residues processed: 930 average time/residue: 0.5212 time to fit residues: 810.7793 Evaluate side-chains 898 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 740 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 39 ASP Chi-restraints excluded: chain A1 residue 48 ASN Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 128 ASP Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 240 LEU Chi-restraints excluded: chain A1 residue 249 ASP Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 263 LEU 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 A1 residue 355 ASP 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 251 ASP Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 289 LEU 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 11 GLN Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 26 LEU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 62 VAL Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 223 THR Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 292 THR Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 346 TRP Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A4 residue 368 LEU Chi-restraints excluded: chain A4 residue 386 GLU Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 95 THR 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 312 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 68 LEU Chi-restraints excluded: chain A6 residue 77 GLU Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 182 VAL Chi-restraints excluded: chain A6 residue 190 SER Chi-restraints excluded: chain A6 residue 334 THR Chi-restraints excluded: chain A6 residue 384 ILE 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 166 THR Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 247 ASN Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 78 SER Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 267 MET Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B1 residue 271 THR Chi-restraints excluded: chain B1 residue 312 THR Chi-restraints excluded: chain B1 residue 377 MET Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 11 GLN Chi-restraints excluded: chain B2 residue 119 LEU Chi-restraints excluded: chain B2 residue 149 LEU Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 205 ASP Chi-restraints excluded: chain B2 residue 288 VAL Chi-restraints excluded: chain B2 residue 301 MET Chi-restraints excluded: chain B2 residue 305 CYS Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B3 residue 95 THR 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 205 GLU Chi-restraints excluded: chain B3 residue 232 VAL Chi-restraints excluded: chain B3 residue 249 ASP Chi-restraints excluded: chain B4 residue 114 ILE Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 269 LEU 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 396 ASP Chi-restraints excluded: chain B4 residue 397 LEU Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 66 MET 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 200 MET Chi-restraints excluded: chain B5 residue 249 ASP Chi-restraints excluded: chain B5 residue 268 VAL Chi-restraints excluded: chain B5 residue 337 ASN 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 177 VAL Chi-restraints excluded: chain B6 residue 182 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B6 residue 423 GLU Chi-restraints excluded: chain B7 residue 47 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 170 VAL Chi-restraints excluded: chain B7 residue 249 ASP Chi-restraints excluded: chain B7 residue 267 MET Chi-restraints excluded: chain C residue 420 PHE 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 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 87 ILE Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 109 THR Chi-restraints excluded: chain Y1 residue 168 ILE Chi-restraints excluded: chain Y1 residue 178 GLU 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 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: 5.9990 chunk 463 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 413 optimal weight: 0.9990 chunk 618 optimal weight: 8.9990 chunk 654 optimal weight: 0.9980 chunk 322 optimal weight: 5.9990 chunk 585 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 99 ASN ** A1 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 227 HIS ** A2 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 256 GLN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 15 GLN ** A3 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 61 HIS A7 204 ASN ** A7 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 329 ASN B3 347 ASN B4 206 ASN ** 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** ** B6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 256 ASN ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 GLN X 250 GLN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 55199 Z= 0.231 Angle : 0.632 12.943 74763 Z= 0.318 Chirality : 0.043 0.193 8221 Planarity : 0.004 0.057 9726 Dihedral : 10.746 178.341 7618 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.10 % Allowed : 17.74 % Favored : 79.16 % 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: 0.61 (0.09), residues: 3391 sheet: -0.39 (0.17), residues: 899 loop : -1.55 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPB2 21 HIS 0.006 0.001 HISB5 6 PHE 0.033 0.002 PHEA5 92 TYR 0.012 0.001 TYRA2 210 ARG 0.005 0.000 ARG X 245 *********************** 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 976 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 797 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 3 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A1 101 TRP cc_start: 0.7247 (t60) cc_final: 0.7030 (t60) REVERT: A1 163 MET cc_start: 0.6873 (mmm) cc_final: 0.6581 (tpp) REVERT: A1 164 MET cc_start: 0.7364 (ttm) cc_final: 0.7050 (ttm) REVERT: A1 174 LYS cc_start: 0.7425 (tmtt) cc_final: 0.7222 (tmtt) REVERT: A1 294 TRP cc_start: 0.5906 (m100) cc_final: 0.4624 (t60) REVERT: A1 361 LEU cc_start: 0.6321 (tp) cc_final: 0.5648 (mp) REVERT: A1 401 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5817 (tm-30) REVERT: A2 77 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: A2 339 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.4507 (tpm170) REVERT: A3 121 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7744 (ttm110) REVERT: A3 125 GLU cc_start: 0.7262 (pp20) cc_final: 0.6844 (pp20) REVERT: A3 293 MET cc_start: 0.6640 (ttt) cc_final: 0.6283 (ttm) REVERT: A3 294 TRP cc_start: 0.6445 (m100) cc_final: 0.4761 (t60) REVERT: A3 299 MET cc_start: 0.6449 (mmm) cc_final: 0.6156 (mmm) REVERT: A3 407 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: A4 11 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A4 203 MET cc_start: 0.6974 (mpp) cc_final: 0.6612 (mtp) REVERT: A4 370 LYS cc_start: 0.7822 (tptt) cc_final: 0.6950 (pttt) REVERT: A5 92 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6595 (t80) REVERT: A5 293 MET cc_start: 0.6703 (ttp) cc_final: 0.6405 (ttm) REVERT: A5 330 MET cc_start: 0.6055 (mmt) cc_final: 0.5827 (mmp) REVERT: A5 388 MET cc_start: 0.6676 (mtt) cc_final: 0.6410 (mtm) REVERT: A6 11 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: A6 370 LYS cc_start: 0.7694 (tptt) cc_final: 0.6872 (pttt) REVERT: A6 401 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7853 (tptt) REVERT: A7 163 MET cc_start: 0.8013 (mmm) cc_final: 0.7633 (mmt) REVERT: A7 251 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7149 (ttm170) REVERT: A7 294 TRP cc_start: 0.6991 (m100) cc_final: 0.5254 (t60) REVERT: A7 299 MET cc_start: 0.8114 (mmp) cc_final: 0.7545 (mmp) REVERT: A7 359 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7873 (mtmt) REVERT: A7 391 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6413 (tmt170) REVERT: B1 200 MET cc_start: 0.8357 (mpp) cc_final: 0.7957 (mpp) REVERT: B1 377 MET cc_start: 0.7603 (tmm) cc_final: 0.6946 (ptt) REVERT: B2 50 ASN cc_start: 0.8516 (t0) cc_final: 0.8304 (t0) REVERT: B2 301 MET cc_start: 0.7423 (mtt) cc_final: 0.7021 (mtt) REVERT: B2 302 MET cc_start: 0.7884 (mmm) cc_final: 0.7531 (mtt) REVERT: B3 177 ASP cc_start: 0.6572 (m-30) cc_final: 0.6259 (m-30) REVERT: B4 24 TYR cc_start: 0.8251 (m-10) cc_final: 0.7764 (m-10) REVERT: B4 203 MET cc_start: 0.7707 (mmm) cc_final: 0.7459 (mmm) REVERT: B4 302 MET cc_start: 0.8638 (mmm) cc_final: 0.8421 (mtp) REVERT: B5 125 GLU cc_start: 0.5766 (pt0) cc_final: 0.5352 (pt0) REVERT: B5 200 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6941 (mtm) REVERT: B5 276 ARG cc_start: 0.7661 (ttt180) cc_final: 0.6943 (ttm-80) REVERT: B5 348 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6697 (m-40) REVERT: B5 388 MET cc_start: 0.7455 (mmt) cc_final: 0.7101 (mmt) REVERT: B5 418 LEU cc_start: 0.7576 (tp) cc_final: 0.7362 (tt) REVERT: B6 163 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6989 (mmmt) REVERT: B6 268 MET cc_start: 0.8655 (mmm) cc_final: 0.8247 (mmt) REVERT: B7 100 ASN cc_start: 0.7951 (t0) cc_final: 0.7745 (t0) REVERT: B7 150 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7267 (tt) REVERT: X 252 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: X 258 MET cc_start: 0.7259 (mmm) cc_final: 0.6977 (mmp) REVERT: X 264 GLU cc_start: 0.5963 (pp20) cc_final: 0.5547 (pp20) REVERT: X 274 ARG cc_start: 0.4970 (mtt180) cc_final: 0.4304 (mmt-90) REVERT: Y 209 MET cc_start: 0.6629 (mmm) cc_final: 0.6057 (tmm) REVERT: Y 210 ASN cc_start: 0.7632 (m110) cc_final: 0.6314 (m110) REVERT: Y 213 LYS cc_start: 0.5867 (ttpp) cc_final: 0.5321 (tttt) REVERT: Y 221 GLN cc_start: 0.8704 (tt0) cc_final: 0.7328 (tm-30) REVERT: Y 271 LYS cc_start: 0.1388 (mtpt) cc_final: 0.0840 (tppp) REVERT: X1 126 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7758 (tmtt) REVERT: X1 132 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7603 (mp) REVERT: X1 183 ASP cc_start: 0.7553 (t0) cc_final: 0.7339 (m-30) REVERT: X1 204 LEU cc_start: 0.7971 (pp) cc_final: 0.7588 (mt) REVERT: X1 229 ASP cc_start: 0.6647 (p0) cc_final: 0.6211 (p0) REVERT: X1 250 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6326 (tt0) REVERT: Y1 152 HIS cc_start: 0.7906 (t70) cc_final: 0.7361 (t-90) REVERT: Y1 178 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: Y1 191 MET cc_start: 0.6209 (tmm) cc_final: 0.5541 (tmm) REVERT: Z 33 LYS cc_start: 0.5946 (mmmt) cc_final: 0.5665 (mmmt) REVERT: Z 51 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6553 (mmtm) REVERT: Z 70 ILE cc_start: 0.8137 (mp) cc_final: 0.7665 (tt) REVERT: Z 90 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6266 (mm-30) outliers start: 179 outliers final: 115 residues processed: 916 average time/residue: 0.5332 time to fit residues: 819.9983 Evaluate side-chains 881 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 753 time to evaluate : 4.636 ------------------------------------------------------------------------------- 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 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 77 GLU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 223 THR Chi-restraints excluded: chain A2 residue 305 CYS Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 195 ASN Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 363 MET Chi-restraints excluded: chain A3 residue 407 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 11 GLN Chi-restraints excluded: chain A4 residue 26 LEU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 68 LEU Chi-restraints excluded: chain A4 residue 147 SER Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 251 ASP Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 327 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 92 PHE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU Chi-restraints excluded: chain A5 residue 164 MET 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 225 LEU 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 56 THR Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 182 VAL Chi-restraints excluded: chain A6 residue 190 SER Chi-restraints excluded: chain A6 residue 269 LEU Chi-restraints excluded: chain A6 residue 384 ILE Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 78 SER Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 159 VAL 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 B2 residue 341 ILE 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 B3 residue 205 GLU Chi-restraints excluded: chain B3 residue 249 ASP Chi-restraints excluded: chain B4 residue 191 THR Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 313 MET Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 72 THR 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 200 MET Chi-restraints excluded: chain B5 residue 348 ASN Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B6 residue 76 ASP Chi-restraints excluded: chain B6 residue 119 LEU Chi-restraints excluded: chain B6 residue 182 VAL Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 24 VAL Chi-restraints excluded: chain B7 residue 47 ILE Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 250 LEU Chi-restraints excluded: chain B7 residue 267 MET Chi-restraints excluded: chain B7 residue 293 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 252 GLU Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 132 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 76 GLN Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 HIS 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: 0.9990 chunk 9 optimal weight: 10.0000 chunk 487 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 558 optimal weight: 2.9990 chunk 452 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 chunk 587 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 184 ASN A1 227 HIS ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 332 ASN ** A4 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 347 ASN A7 190 HIS ** A7 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 105 HIS ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 15 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 ** B6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 206 ASN B7 14 ASN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 GLN X 250 GLN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1 240 HIS ** Z 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 55199 Z= 0.208 Angle : 0.597 11.122 74763 Z= 0.299 Chirality : 0.042 0.186 8221 Planarity : 0.004 0.053 9726 Dihedral : 10.423 174.069 7617 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.31 % Allowed : 18.92 % Favored : 77.77 % 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: -0.12 (0.10), residues: 6799 helix: 0.94 (0.09), residues: 3368 sheet: -0.24 (0.17), residues: 906 loop : -1.38 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPB2 21 HIS 0.014 0.001 HISA1 227 PHE 0.034 0.001 PHEA5 92 TYR 0.014 0.001 TYRA5 422 ARG 0.008 0.000 ARG X 245 *********************** 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 1002 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 811 time to evaluate : 4.618 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: 0.7599 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A1 101 TRP cc_start: 0.7109 (t60) cc_final: 0.6884 (t60) REVERT: A1 129 CYS cc_start: 0.7280 (m) cc_final: 0.7022 (t) REVERT: A1 163 MET cc_start: 0.6888 (mmm) cc_final: 0.6626 (tpp) REVERT: A1 164 MET cc_start: 0.7421 (ttm) cc_final: 0.7131 (ttm) REVERT: A1 174 LYS cc_start: 0.7452 (tmtt) cc_final: 0.7249 (tmtt) REVERT: A1 294 TRP cc_start: 0.5938 (m100) cc_final: 0.4700 (t60) REVERT: A1 361 LEU cc_start: 0.6293 (tp) cc_final: 0.5623 (mp) REVERT: A1 401 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5923 (tp30) REVERT: A2 339 ARG cc_start: 0.4861 (OUTLIER) cc_final: 0.4468 (tpm170) REVERT: A3 121 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7737 (ttm110) REVERT: A3 293 MET cc_start: 0.6663 (ttt) cc_final: 0.6314 (ttm) REVERT: A3 294 TRP cc_start: 0.6421 (m100) cc_final: 0.4847 (t60) REVERT: A3 299 MET cc_start: 0.6500 (mmm) cc_final: 0.6123 (mmm) REVERT: A3 407 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: A4 203 MET cc_start: 0.6930 (mpp) cc_final: 0.6524 (mtp) REVERT: A4 370 LYS cc_start: 0.7859 (tptt) cc_final: 0.6939 (pttt) REVERT: A5 293 MET cc_start: 0.6783 (ttp) cc_final: 0.6536 (ttm) REVERT: A5 388 MET cc_start: 0.6683 (mtt) cc_final: 0.6478 (mtm) REVERT: A6 5 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8134 (pt) REVERT: A6 7 ILE cc_start: 0.8353 (pt) cc_final: 0.8110 (mt) REVERT: A6 370 LYS cc_start: 0.7713 (tptt) cc_final: 0.6916 (pttt) REVERT: A6 401 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7848 (tptt) REVERT: A7 163 MET cc_start: 0.8118 (mmm) cc_final: 0.7708 (mmt) REVERT: A7 251 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7261 (ttm170) REVERT: A7 294 TRP cc_start: 0.6941 (m100) cc_final: 0.5366 (t60) REVERT: A7 359 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7874 (mtmt) REVERT: A7 391 ARG cc_start: 0.6883 (ttm170) cc_final: 0.6327 (tmt170) REVERT: B1 101 TRP cc_start: 0.8743 (t60) cc_final: 0.8344 (t60) REVERT: B1 200 MET cc_start: 0.8312 (mpp) cc_final: 0.7889 (mpp) REVERT: B1 377 MET cc_start: 0.7738 (tmm) cc_final: 0.7006 (ptt) REVERT: B2 5 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7484 (pt) REVERT: B2 50 ASN cc_start: 0.8469 (t0) cc_final: 0.8195 (t0) REVERT: B2 301 MET cc_start: 0.7533 (mtt) cc_final: 0.7128 (mtt) REVERT: B2 302 MET cc_start: 0.7861 (mmm) cc_final: 0.7584 (mtt) REVERT: B2 379 SER cc_start: 0.7709 (p) cc_final: 0.7398 (t) REVERT: B3 177 ASP cc_start: 0.6639 (m-30) cc_final: 0.6361 (m-30) REVERT: B4 24 TYR cc_start: 0.8260 (m-10) cc_final: 0.7705 (m-10) REVERT: B4 121 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6409 (tmm-80) REVERT: B4 136 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7593 (pp) REVERT: B4 203 MET cc_start: 0.7741 (mmm) cc_final: 0.7512 (mmm) REVERT: B4 302 MET cc_start: 0.8644 (mmm) cc_final: 0.8420 (mtp) REVERT: B5 125 GLU cc_start: 0.5877 (pt0) cc_final: 0.5388 (pt0) REVERT: B5 200 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7056 (mtm) REVERT: B5 276 ARG cc_start: 0.7613 (ttt180) cc_final: 0.6922 (ttm-80) REVERT: B5 418 LEU cc_start: 0.7554 (tp) cc_final: 0.7349 (tt) REVERT: B6 163 LYS cc_start: 0.7217 (mmmt) cc_final: 0.7005 (mmmt) REVERT: B6 268 MET cc_start: 0.8671 (mmm) cc_final: 0.8235 (mmt) REVERT: B6 290 GLU cc_start: 0.7726 (pm20) cc_final: 0.7422 (pt0) REVERT: B7 100 ASN cc_start: 0.7998 (t0) cc_final: 0.7770 (t0) REVERT: B7 150 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7230 (tt) REVERT: C 329 MET cc_start: 0.5573 (mmm) cc_final: 0.5120 (mmm) REVERT: C 362 MET cc_start: 0.7021 (mtp) cc_final: 0.5691 (mmm) REVERT: X 228 LYS cc_start: 0.7428 (pptt) cc_final: 0.7129 (pptt) REVERT: X 252 GLU cc_start: 0.7943 (pm20) cc_final: 0.7681 (pm20) REVERT: X 264 GLU cc_start: 0.5997 (pp20) cc_final: 0.5599 (pp20) REVERT: X 274 ARG cc_start: 0.4916 (mtt180) cc_final: 0.4207 (mmt-90) REVERT: Y 209 MET cc_start: 0.6631 (mmm) cc_final: 0.6030 (tmm) REVERT: Y 210 ASN cc_start: 0.7660 (m110) cc_final: 0.6318 (m110) REVERT: Y 213 LYS cc_start: 0.6129 (ttpp) cc_final: 0.5515 (tttt) REVERT: Y 221 GLN cc_start: 0.8719 (tt0) cc_final: 0.7340 (tm-30) REVERT: Y 271 LYS cc_start: 0.1390 (mtpt) cc_final: 0.0784 (tppp) REVERT: X1 126 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7645 (tmtt) REVERT: X1 132 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7529 (mp) REVERT: X1 183 ASP cc_start: 0.7547 (t0) cc_final: 0.7311 (m-30) REVERT: X1 204 LEU cc_start: 0.7905 (pp) cc_final: 0.7655 (mt) REVERT: X1 229 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6343 (p0) REVERT: X1 233 ASP cc_start: 0.6838 (m-30) cc_final: 0.6512 (m-30) REVERT: X1 250 GLN cc_start: 0.6793 (tm-30) cc_final: 0.6191 (tt0) REVERT: Y1 104 MET cc_start: 0.7267 (tpp) cc_final: 0.6944 (tpp) REVERT: Y1 152 HIS cc_start: 0.7914 (t70) cc_final: 0.7335 (t-90) REVERT: Y1 174 GLN cc_start: 0.6718 (mm110) cc_final: 0.6033 (mm110) REVERT: Y1 178 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: Y1 185 LYS cc_start: 0.7369 (ptmt) cc_final: 0.6899 (pttp) REVERT: Y1 191 MET cc_start: 0.6395 (tmm) cc_final: 0.5722 (tmm) REVERT: Z 51 LYS cc_start: 0.6868 (mtpp) cc_final: 0.6464 (mmtm) REVERT: Z 70 ILE cc_start: 0.8016 (mp) cc_final: 0.7579 (tt) REVERT: Z 90 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6336 (mm-30) outliers start: 191 outliers final: 126 residues processed: 949 average time/residue: 0.5186 time to fit residues: 823.6203 Evaluate side-chains 911 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 773 time to evaluate : 4.611 ------------------------------------------------------------------------------- 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 60 VAL 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 221 THR Chi-restraints excluded: chain A1 residue 227 HIS 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 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 223 THR Chi-restraints excluded: chain A2 residue 305 CYS Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 384 ILE Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 290 THR 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 363 MET Chi-restraints excluded: chain A3 residue 407 GLU 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 147 SER Chi-restraints excluded: chain A4 residue 149 LEU Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 251 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU Chi-restraints excluded: chain A5 residue 164 MET 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 225 LEU 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 56 THR 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 A6 residue 384 ILE Chi-restraints excluded: chain A6 residue 398 MET 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 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 78 SER Chi-restraints excluded: chain B1 residue 95 THR Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 178 THR Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 344 VAL Chi-restraints excluded: chain B2 residue 387 ILE Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 126 SER Chi-restraints excluded: chain B3 residue 143 THR Chi-restraints excluded: chain B3 residue 166 THR Chi-restraints excluded: chain B3 residue 249 ASP Chi-restraints excluded: chain B4 residue 121 ARG 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 305 CYS Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 41 ASP Chi-restraints excluded: chain B5 residue 72 THR 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 200 MET Chi-restraints excluded: chain B5 residue 404 ASP Chi-restraints excluded: chain B6 residue 223 THR Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 24 VAL Chi-restraints excluded: chain B7 residue 47 ILE Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 250 LEU Chi-restraints excluded: chain B7 residue 267 MET Chi-restraints excluded: chain B7 residue 293 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 254 GLU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 218 MET Chi-restraints excluded: chain X1 residue 229 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 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 76 GLN Chi-restraints excluded: chain Z residue 92 ARG Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 HIS Chi-restraints excluded: chain Z residue 165 LEU Chi-restraints excluded: chain Z residue 170 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 7.9990 chunk 589 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 384 optimal weight: 0.0000 chunk 161 optimal weight: 0.6980 chunk 655 optimal weight: 4.9990 chunk 543 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 99 ASN A1 227 HIS ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 48 ASN A3 195 ASN A3 332 ASN A4 15 GLN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 347 ASN ** A7 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 206 ASN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 108 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 55199 Z= 0.232 Angle : 0.608 11.558 74763 Z= 0.303 Chirality : 0.043 0.185 8221 Planarity : 0.004 0.054 9726 Dihedral : 10.303 170.971 7617 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.73 % Allowed : 19.63 % Favored : 76.64 % 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: -0.03 (0.10), residues: 6799 helix: 1.01 (0.09), residues: 3370 sheet: -0.24 (0.17), residues: 915 loop : -1.30 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPB2 21 HIS 0.008 0.001 HISA1 227 PHE 0.026 0.001 PHEB5 92 TYR 0.013 0.001 TYRA5 422 ARG 0.007 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 1015 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 800 time to evaluate : 4.683 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: 0.7616 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A1 129 CYS cc_start: 0.7285 (m) cc_final: 0.7056 (t) REVERT: A1 163 MET cc_start: 0.6868 (mmm) cc_final: 0.6576 (tpp) REVERT: A1 164 MET cc_start: 0.7459 (ttm) cc_final: 0.7246 (ttm) REVERT: A1 294 TRP cc_start: 0.5586 (m100) cc_final: 0.4664 (t60) REVERT: A1 361 LEU cc_start: 0.6275 (tp) cc_final: 0.5685 (mp) REVERT: A1 404 ASP cc_start: 0.6782 (m-30) cc_final: 0.6546 (p0) REVERT: A2 77 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6486 (pm20) REVERT: A2 110 ILE cc_start: 0.7640 (mt) cc_final: 0.7328 (mt) REVERT: A2 123 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7495 (tpm170) REVERT: A2 339 ARG cc_start: 0.5009 (OUTLIER) cc_final: 0.4734 (tpm170) REVERT: A3 121 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7759 (ttm110) REVERT: A3 293 MET cc_start: 0.6684 (ttt) cc_final: 0.6325 (ttm) REVERT: A3 294 TRP cc_start: 0.6434 (m100) cc_final: 0.4863 (t60) REVERT: A3 299 MET cc_start: 0.6498 (mmm) cc_final: 0.6017 (mmm) REVERT: A3 407 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: A4 203 MET cc_start: 0.6939 (mpp) cc_final: 0.6555 (mtp) REVERT: A4 370 LYS cc_start: 0.7825 (tptt) cc_final: 0.6880 (pttt) REVERT: A5 94 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7294 (tp40) REVERT: A5 293 MET cc_start: 0.6886 (ttp) cc_final: 0.6609 (ttm) REVERT: A5 337 ASN cc_start: 0.5851 (p0) cc_final: 0.5284 (p0) REVERT: A5 388 MET cc_start: 0.6660 (mtt) cc_final: 0.6451 (mtm) REVERT: A6 370 LYS cc_start: 0.7705 (tptt) cc_final: 0.6896 (pttt) REVERT: A6 401 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7870 (tptt) REVERT: A7 163 MET cc_start: 0.8113 (mmm) cc_final: 0.7697 (mmt) REVERT: A7 294 TRP cc_start: 0.6939 (m100) cc_final: 0.4980 (t60) REVERT: A7 359 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7891 (mtmt) REVERT: A7 391 ARG cc_start: 0.6885 (ttm170) cc_final: 0.6325 (tmt170) REVERT: B1 101 TRP cc_start: 0.8716 (t60) cc_final: 0.8338 (t60) REVERT: B1 200 MET cc_start: 0.8335 (mpp) cc_final: 0.7886 (mpp) REVERT: B1 363 MET cc_start: 0.8052 (ttp) cc_final: 0.7749 (mtp) REVERT: B2 5 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7478 (pt) REVERT: B2 11 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: B2 301 MET cc_start: 0.7543 (mtt) cc_final: 0.7176 (mtt) REVERT: B2 302 MET cc_start: 0.7882 (mmm) cc_final: 0.7631 (mtt) REVERT: B2 379 SER cc_start: 0.7729 (p) cc_final: 0.7497 (t) REVERT: B3 69 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6790 (mt-10) REVERT: B3 177 ASP cc_start: 0.6698 (m-30) cc_final: 0.6426 (m-30) REVERT: B3 388 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6030 (mmt) REVERT: B4 121 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6445 (tmm-80) REVERT: B4 136 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7423 (pp) REVERT: B4 203 MET cc_start: 0.7779 (mmm) cc_final: 0.7536 (mmm) REVERT: B4 256 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: B4 302 MET cc_start: 0.8661 (mmm) cc_final: 0.8453 (mtp) REVERT: B5 200 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6870 (mtm) REVERT: B5 276 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6930 (ttm-80) REVERT: B5 348 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6634 (m-40) REVERT: B5 418 LEU cc_start: 0.7592 (tp) cc_final: 0.7374 (tt) REVERT: B6 268 MET cc_start: 0.8709 (mmm) cc_final: 0.8224 (mmt) REVERT: B6 286 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7103 (mm) REVERT: B7 5 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8342 (t) REVERT: B7 73 MET cc_start: 0.8574 (mmm) cc_final: 0.8175 (mmp) REVERT: B7 150 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7342 (tt) REVERT: C 328 MET cc_start: 0.3345 (ptt) cc_final: 0.2544 (ptt) REVERT: C 329 MET cc_start: 0.5894 (mmm) cc_final: 0.5104 (mtt) REVERT: C 362 MET cc_start: 0.7006 (mtp) cc_final: 0.5715 (mmm) REVERT: X 264 GLU cc_start: 0.6029 (pp20) cc_final: 0.5585 (pp20) REVERT: X 274 ARG cc_start: 0.5262 (mtt180) cc_final: 0.4388 (mmp80) REVERT: Y 183 LYS cc_start: 0.6181 (ptpp) cc_final: 0.5902 (ptpt) REVERT: Y 209 MET cc_start: 0.6556 (mmm) cc_final: 0.5900 (tmm) REVERT: Y 210 ASN cc_start: 0.7716 (m110) cc_final: 0.6412 (m110) REVERT: Y 213 LYS cc_start: 0.6152 (ttpp) cc_final: 0.5542 (tttt) REVERT: Y 221 GLN cc_start: 0.8719 (tt0) cc_final: 0.7342 (tm-30) REVERT: Y 238 LYS cc_start: 0.5977 (mmtt) cc_final: 0.5775 (mmtt) REVERT: Y 271 LYS cc_start: 0.1384 (mtpt) cc_final: 0.0792 (tppp) REVERT: X1 126 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7641 (tmtt) REVERT: X1 132 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7518 (mp) REVERT: X1 204 LEU cc_start: 0.8126 (pp) cc_final: 0.7803 (mt) REVERT: X1 216 MET cc_start: 0.7787 (tmm) cc_final: 0.7006 (tmm) REVERT: X1 229 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6503 (p0) REVERT: Y1 104 MET cc_start: 0.7384 (tpp) cc_final: 0.7024 (tpp) REVERT: Y1 152 HIS cc_start: 0.7923 (t70) cc_final: 0.7352 (t-90) REVERT: Y1 174 GLN cc_start: 0.6713 (mm110) cc_final: 0.6126 (mm110) REVERT: Y1 178 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: Y1 185 LYS cc_start: 0.7410 (ptmt) cc_final: 0.6984 (pttp) REVERT: Y1 191 MET cc_start: 0.6796 (tmm) cc_final: 0.6234 (tmm) REVERT: Z 51 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6690 (mmtm) REVERT: Z 70 ILE cc_start: 0.8105 (mp) cc_final: 0.7833 (tt) REVERT: Z 92 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4571 (ttm-80) outliers start: 215 outliers final: 161 residues processed: 945 average time/residue: 0.5168 time to fit residues: 819.7733 Evaluate side-chains 944 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 764 time to evaluate : 4.569 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 128 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 221 THR Chi-restraints excluded: chain A1 residue 225 LEU Chi-restraints excluded: chain A1 residue 227 HIS Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 314 SER Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE Chi-restraints excluded: chain A2 residue 26 LEU Chi-restraints excluded: chain A2 residue 77 GLU 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 223 THR Chi-restraints excluded: chain A2 residue 303 VAL Chi-restraints excluded: chain A2 residue 305 CYS Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 384 ILE Chi-restraints excluded: chain A2 residue 387 ILE Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 118 ASP Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 200 MET Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 290 THR Chi-restraints excluded: chain A3 residue 333 VAL Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 363 MET Chi-restraints excluded: chain A3 residue 404 ASP Chi-restraints excluded: chain A3 residue 407 GLU Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 2 ARG 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 147 SER Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 251 ASP Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 327 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU Chi-restraints excluded: chain A5 residue 164 MET 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 225 LEU 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 A5 residue 415 MET Chi-restraints excluded: chain A6 residue 5 ILE Chi-restraints excluded: chain A6 residue 56 THR Chi-restraints excluded: chain A6 residue 68 LEU Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 154 LEU 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 384 ILE Chi-restraints excluded: chain A6 residue 398 MET Chi-restraints excluded: chain A6 residue 413 MET Chi-restraints excluded: chain A6 residue 425 LEU Chi-restraints excluded: chain A7 residue 44 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 236 ILE Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain B1 residue 39 ASP 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 178 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 5 ILE Chi-restraints excluded: chain B2 residue 11 GLN Chi-restraints excluded: chain B2 residue 159 VAL 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 B2 residue 341 ILE Chi-restraints excluded: chain B2 residue 344 VAL Chi-restraints excluded: chain B2 residue 387 ILE Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 112 LEU 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 249 ASP Chi-restraints excluded: chain B3 residue 388 MET Chi-restraints excluded: chain B4 residue 5 ILE Chi-restraints excluded: chain B4 residue 121 ARG Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 256 GLN Chi-restraints excluded: chain B4 residue 305 CYS Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 24 VAL Chi-restraints excluded: chain B5 residue 41 ASP Chi-restraints excluded: chain B5 residue 72 THR Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 108 GLU 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 B5 residue 348 ASN Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 76 ASP 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 223 THR Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 313 MET Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 5 VAL Chi-restraints excluded: chain B7 residue 24 VAL Chi-restraints excluded: chain B7 residue 47 ILE Chi-restraints excluded: chain B7 residue 150 LEU Chi-restraints excluded: chain B7 residue 151 LEU Chi-restraints excluded: chain B7 residue 250 LEU Chi-restraints excluded: chain B7 residue 267 MET Chi-restraints excluded: chain B7 residue 293 MET Chi-restraints excluded: chain B7 residue 339 SER 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 254 GLU Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 218 MET Chi-restraints excluded: chain X1 residue 229 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 ILE Chi-restraints excluded: chain Y1 residue 151 THR 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 76 GLN Chi-restraints excluded: chain Z residue 92 ARG Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 HIS Chi-restraints excluded: chain Z residue 165 LEU Chi-restraints excluded: chain Z residue 170 THR 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: 3.9990 chunk 373 optimal weight: 4.9990 chunk 478 optimal weight: 2.9990 chunk 370 optimal weight: 0.1980 chunk 551 optimal weight: 0.8980 chunk 365 optimal weight: 0.9980 chunk 652 optimal weight: 2.9990 chunk 408 optimal weight: 0.5980 chunk 397 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 99 ASN A1 184 ASN A1 227 HIS ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 195 ASN A3 332 ASN A4 31 GLN ** A4 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 190 HIS A5 347 ASN ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 191 GLN ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 292 GLN ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 341 HIS ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN ** Z 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 55199 Z= 0.195 Angle : 0.584 11.914 74763 Z= 0.291 Chirality : 0.042 0.181 8221 Planarity : 0.004 0.053 9726 Dihedral : 10.082 165.144 7617 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.83 % Allowed : 19.68 % Favored : 76.49 % 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: 0.12 (0.10), residues: 6799 helix: 1.12 (0.09), residues: 3379 sheet: -0.18 (0.17), residues: 915 loop : -1.23 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPB7 397 HIS 0.018 0.001 HISA1 227 PHE 0.024 0.001 PHEB5 92 TYR 0.013 0.001 TYR C 476 ARG 0.007 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 1019 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 798 time to evaluate : 4.670 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: 0.7629 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A1 163 MET cc_start: 0.6847 (mmm) cc_final: 0.6619 (tpp) REVERT: A1 164 MET cc_start: 0.7398 (ttm) cc_final: 0.7174 (ttm) REVERT: A1 237 THR cc_start: 0.7769 (m) cc_final: 0.7478 (t) REVERT: A1 294 TRP cc_start: 0.5549 (m100) cc_final: 0.5015 (t60) REVERT: A1 361 LEU cc_start: 0.6335 (tp) cc_final: 0.5764 (mp) REVERT: A1 383 GLU cc_start: 0.7683 (pm20) cc_final: 0.7294 (pm20) REVERT: A1 404 ASP cc_start: 0.6796 (m-30) cc_final: 0.6556 (p0) REVERT: A2 77 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6494 (pm20) REVERT: A2 110 ILE cc_start: 0.7411 (mt) cc_final: 0.7149 (mt) REVERT: A2 123 ARG cc_start: 0.7814 (tpp-160) cc_final: 0.7475 (tpm170) REVERT: A2 339 ARG cc_start: 0.5135 (OUTLIER) cc_final: 0.3881 (ttm110) REVERT: A3 293 MET cc_start: 0.6669 (ttt) cc_final: 0.6311 (ttm) REVERT: A3 294 TRP cc_start: 0.6389 (m100) cc_final: 0.4896 (t60) REVERT: A3 299 MET cc_start: 0.6595 (mmm) cc_final: 0.6213 (mmm) REVERT: A3 407 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: A4 203 MET cc_start: 0.6902 (mpp) cc_final: 0.6523 (mtp) REVERT: A4 370 LYS cc_start: 0.7820 (tptt) cc_final: 0.6874 (pttt) REVERT: A5 94 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7512 (tp-100) REVERT: A5 337 ASN cc_start: 0.5816 (p0) cc_final: 0.5275 (p0) REVERT: A5 388 MET cc_start: 0.6557 (mtt) cc_final: 0.6345 (mtm) REVERT: A6 5 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7962 (pt) REVERT: A6 98 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6280 (m-30) REVERT: A6 101 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: A6 123 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7158 (mmm160) REVERT: A6 154 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A6 370 LYS cc_start: 0.7692 (tptt) cc_final: 0.6891 (pttt) REVERT: A6 401 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7804 (tptt) REVERT: A7 163 MET cc_start: 0.8053 (mmm) cc_final: 0.7707 (mmt) REVERT: A7 294 TRP cc_start: 0.6832 (m100) cc_final: 0.5020 (t60) REVERT: A7 359 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7912 (mtmt) REVERT: A7 391 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6237 (tmt170) REVERT: B1 101 TRP cc_start: 0.8677 (t60) cc_final: 0.8337 (t60) REVERT: B1 164 MET cc_start: 0.7917 (tpp) cc_final: 0.7636 (ttm) REVERT: B1 200 MET cc_start: 0.8304 (mpp) cc_final: 0.7847 (mpp) REVERT: B1 418 LEU cc_start: 0.7867 (tp) cc_final: 0.7656 (tt) REVERT: B2 5 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7377 (pt) REVERT: B2 11 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: B2 248 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8689 (mt) REVERT: B2 268 MET cc_start: 0.8311 (mmm) cc_final: 0.7906 (mmm) REVERT: B2 302 MET cc_start: 0.7821 (mmm) cc_final: 0.7600 (mtt) REVERT: B2 379 SER cc_start: 0.7807 (p) cc_final: 0.7434 (t) REVERT: B3 69 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6812 (mt-10) REVERT: B3 177 ASP cc_start: 0.6615 (m-30) cc_final: 0.6339 (m-30) REVERT: B3 388 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6181 (mmt) REVERT: B4 24 TYR cc_start: 0.8238 (m-10) cc_final: 0.7680 (m-10) REVERT: B4 121 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6342 (tmm-80) REVERT: B4 256 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7035 (mm-40) REVERT: B5 200 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6946 (mtm) REVERT: B5 276 ARG cc_start: 0.7593 (ttt180) cc_final: 0.6893 (ttm-80) REVERT: B5 348 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6521 (m-40) REVERT: B5 388 MET cc_start: 0.7373 (mmt) cc_final: 0.7147 (mmt) REVERT: B5 418 LEU cc_start: 0.7555 (tp) cc_final: 0.7352 (tt) REVERT: B6 268 MET cc_start: 0.8694 (mmm) cc_final: 0.8185 (mmt) REVERT: B6 286 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7210 (mm) REVERT: B7 5 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8407 (t) REVERT: B7 150 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7209 (tt) REVERT: B7 375 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: C 295 LYS cc_start: 0.6338 (mmtt) cc_final: 0.6064 (tttt) REVERT: C 328 MET cc_start: 0.3008 (ptt) cc_final: 0.2151 (ptt) REVERT: C 329 MET cc_start: 0.5966 (mmm) cc_final: 0.5201 (mtt) REVERT: C 362 MET cc_start: 0.6908 (mtp) cc_final: 0.5664 (mmm) REVERT: X 228 LYS cc_start: 0.7396 (pptt) cc_final: 0.6719 (ptmt) REVERT: X 264 GLU cc_start: 0.6124 (pp20) cc_final: 0.5718 (pp20) REVERT: X 274 ARG cc_start: 0.5238 (mtt180) cc_final: 0.4386 (mmp80) REVERT: Y 183 LYS cc_start: 0.6145 (ptpp) cc_final: 0.5891 (ptpt) REVERT: Y 209 MET cc_start: 0.6538 (mmm) cc_final: 0.5859 (tmm) REVERT: Y 210 ASN cc_start: 0.7747 (m110) cc_final: 0.6430 (m110) REVERT: Y 213 LYS cc_start: 0.6160 (ttpp) cc_final: 0.5534 (tttt) REVERT: Y 221 GLN cc_start: 0.8724 (tt0) cc_final: 0.7346 (tm-30) REVERT: Y 271 LYS cc_start: 0.1397 (mtpt) cc_final: 0.0857 (tppp) REVERT: X1 126 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7555 (tmtt) REVERT: X1 183 ASP cc_start: 0.6813 (m-30) cc_final: 0.6484 (m-30) REVERT: X1 204 LEU cc_start: 0.8208 (pp) cc_final: 0.7806 (mt) REVERT: X1 216 MET cc_start: 0.7843 (tmm) cc_final: 0.6872 (tmm) REVERT: X1 229 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6406 (p0) REVERT: X1 250 GLN cc_start: 0.6543 (tm-30) cc_final: 0.5951 (tt0) REVERT: Y1 104 MET cc_start: 0.7467 (tpp) cc_final: 0.7112 (tpp) REVERT: Y1 152 HIS cc_start: 0.7919 (t70) cc_final: 0.7358 (t-90) REVERT: Y1 174 GLN cc_start: 0.6676 (mm110) cc_final: 0.5925 (mm-40) REVERT: Y1 178 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: Y1 185 LYS cc_start: 0.7331 (ptmt) cc_final: 0.6916 (pttp) REVERT: Y1 191 MET cc_start: 0.6963 (tmm) cc_final: 0.6474 (tmm) REVERT: Z 51 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6682 (mmtm) REVERT: Z 70 ILE cc_start: 0.8075 (mp) cc_final: 0.7804 (tt) REVERT: Z 86 LYS cc_start: 0.6813 (mtpt) cc_final: 0.6568 (mtpt) REVERT: Z 92 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.4470 (ttm-80) outliers start: 221 outliers final: 152 residues processed: 951 average time/residue: 0.5261 time to fit residues: 840.7907 Evaluate side-chains 940 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 765 time to evaluate : 4.683 ------------------------------------------------------------------------------- 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 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 221 THR Chi-restraints excluded: chain A1 residue 225 LEU Chi-restraints excluded: chain A1 residue 240 LEU Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 314 SER Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE 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 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 223 THR Chi-restraints excluded: chain A2 residue 303 VAL Chi-restraints excluded: chain A2 residue 305 CYS Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 118 ASP Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 195 ASN Chi-restraints excluded: chain A3 residue 200 MET Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER 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 363 MET Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 404 ASP Chi-restraints excluded: chain A3 residue 407 GLU Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 2 ARG 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 147 SER Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 251 ASP Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 327 ASP Chi-restraints excluded: chain A4 residue 328 VAL Chi-restraints excluded: chain A4 residue 347 CYS Chi-restraints excluded: chain A5 residue 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU 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 A5 residue 414 ASN Chi-restraints excluded: chain A5 residue 415 MET Chi-restraints excluded: chain A6 residue 5 ILE Chi-restraints excluded: chain A6 residue 56 THR Chi-restraints excluded: chain A6 residue 68 LEU Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 98 ASP Chi-restraints excluded: chain A6 residue 101 ASN Chi-restraints excluded: chain A6 residue 154 LEU 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 345 ASP Chi-restraints excluded: chain A6 residue 413 MET Chi-restraints excluded: chain A6 residue 425 LEU Chi-restraints excluded: chain A7 residue 44 LEU Chi-restraints excluded: chain A7 residue 147 MET Chi-restraints excluded: chain A7 residue 169 VAL Chi-restraints excluded: chain A7 residue 170 VAL Chi-restraints excluded: chain A7 residue 219 THR Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain A7 residue 386 THR Chi-restraints excluded: chain B1 residue 1 MET Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 95 THR Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 178 THR Chi-restraints excluded: chain B1 residue 190 HIS Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 11 GLN Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 159 VAL Chi-restraints excluded: chain B2 residue 195 LEU Chi-restraints excluded: chain B2 residue 248 LEU Chi-restraints excluded: chain B2 residue 270 SER Chi-restraints excluded: chain B2 residue 323 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 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 249 ASP Chi-restraints excluded: chain B3 residue 388 MET Chi-restraints excluded: chain B4 residue 5 ILE Chi-restraints excluded: chain B4 residue 121 ARG Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 256 GLN Chi-restraints excluded: chain B4 residue 305 CYS Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 41 ASP Chi-restraints excluded: chain B5 residue 66 MET Chi-restraints excluded: chain B5 residue 72 THR Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 108 GLU Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 127 CYS Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 200 MET Chi-restraints excluded: chain B5 residue 246 LEU Chi-restraints excluded: chain B5 residue 348 ASN Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 74 VAL Chi-restraints excluded: chain B6 residue 76 ASP Chi-restraints excluded: chain B6 residue 182 VAL Chi-restraints excluded: chain B6 residue 223 THR Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 290 GLU Chi-restraints excluded: chain B6 residue 313 MET Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B7 residue 5 VAL Chi-restraints excluded: chain B7 residue 24 VAL 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 250 LEU Chi-restraints excluded: chain B7 residue 293 MET Chi-restraints excluded: chain B7 residue 375 GLN 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 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 229 ASP Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 ILE Chi-restraints excluded: chain Y1 residue 134 LEU 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 76 GLN Chi-restraints excluded: chain Z residue 92 ARG Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 HIS 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: 3.9990 chunk 260 optimal weight: 1.9990 chunk 389 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 128 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 444 optimal weight: 0.6980 chunk 322 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 512 optimal weight: 3.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 227 HIS ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 293 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 134 GLN A3 195 ASN A3 332 ASN ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 329 GLN ** B3 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 11 GLN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 55199 Z= 0.169 Angle : 0.584 12.981 74763 Z= 0.288 Chirality : 0.042 0.211 8221 Planarity : 0.004 0.051 9726 Dihedral : 9.798 160.522 7617 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 20.18 % Favored : 76.38 % 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: 0.27 (0.10), residues: 6799 helix: 1.24 (0.09), residues: 3376 sheet: -0.06 (0.17), residues: 913 loop : -1.16 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPB7 397 HIS 0.009 0.001 HISA1 227 PHE 0.025 0.001 PHE Y 199 TYR 0.018 0.001 TYRA5 422 ARG 0.008 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 8 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 1006 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 808 time to evaluate : 4.622 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: 0.7628 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A1 21 TRP cc_start: 0.7115 (m100) cc_final: 0.6875 (m100) REVERT: A1 164 MET cc_start: 0.7294 (ttm) cc_final: 0.7078 (ttm) REVERT: A1 294 TRP cc_start: 0.5481 (m100) cc_final: 0.5002 (t60) REVERT: A1 361 LEU cc_start: 0.6159 (tp) cc_final: 0.5560 (mp) REVERT: A2 77 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: A2 123 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7493 (tpm170) REVERT: A2 301 MET cc_start: 0.6386 (mmp) cc_final: 0.6071 (mmp) REVERT: A2 339 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.4847 (tpm170) REVERT: A3 293 MET cc_start: 0.6663 (ttt) cc_final: 0.6298 (ttm) REVERT: A3 294 TRP cc_start: 0.6351 (m100) cc_final: 0.4899 (t60) REVERT: A3 299 MET cc_start: 0.6615 (mmm) cc_final: 0.6153 (mmm) REVERT: A4 370 LYS cc_start: 0.7812 (tptt) cc_final: 0.6872 (pttt) REVERT: A5 337 ASN cc_start: 0.5679 (p0) cc_final: 0.5263 (p0) REVERT: A5 388 MET cc_start: 0.6452 (mtt) cc_final: 0.6217 (mtm) REVERT: A6 98 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6155 (m-30) REVERT: A6 123 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7257 (mmm160) REVERT: A6 154 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A6 370 LYS cc_start: 0.7632 (tptt) cc_final: 0.6851 (pttt) REVERT: A6 401 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7799 (tptt) REVERT: A7 163 MET cc_start: 0.8044 (mmm) cc_final: 0.7723 (mmt) REVERT: A7 294 TRP cc_start: 0.6750 (m100) cc_final: 0.4997 (t60) REVERT: A7 359 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7922 (mtmt) REVERT: A7 391 ARG cc_start: 0.6781 (ttm170) cc_final: 0.6299 (tmt170) REVERT: B1 101 TRP cc_start: 0.8680 (t60) cc_final: 0.8347 (t60) REVERT: B1 164 MET cc_start: 0.7910 (tpp) cc_final: 0.7595 (ttm) REVERT: B1 200 MET cc_start: 0.8260 (mpp) cc_final: 0.7859 (mpp) REVERT: B1 363 MET cc_start: 0.8068 (ttp) cc_final: 0.7778 (mtp) REVERT: B2 268 MET cc_start: 0.8232 (mmm) cc_final: 0.7814 (mmm) REVERT: B2 379 SER cc_start: 0.7829 (p) cc_final: 0.7424 (t) REVERT: B3 69 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6817 (mt-10) REVERT: B3 177 ASP cc_start: 0.6663 (m-30) cc_final: 0.6389 (m-30) REVERT: B3 388 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6234 (mmt) REVERT: B4 24 TYR cc_start: 0.8176 (m-10) cc_final: 0.7645 (m-10) REVERT: B4 256 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6963 (mm-40) REVERT: B5 276 ARG cc_start: 0.7537 (ttt180) cc_final: 0.6826 (ttm-80) REVERT: B5 297 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7942 (mmmm) REVERT: B5 348 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6467 (m-40) REVERT: B5 418 LEU cc_start: 0.7504 (tp) cc_final: 0.7296 (tt) REVERT: B6 163 LYS cc_start: 0.7140 (mmmt) cc_final: 0.6886 (mmmt) REVERT: B6 268 MET cc_start: 0.8662 (mmm) cc_final: 0.8135 (mmt) REVERT: B6 286 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7070 (mm) REVERT: B6 415 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6483 (mm-30) REVERT: B7 5 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8349 (t) REVERT: B7 150 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 295 LYS cc_start: 0.6320 (mmtt) cc_final: 0.6049 (tttt) REVERT: C 328 MET cc_start: 0.2998 (ptt) cc_final: 0.2129 (ptt) REVERT: C 329 MET cc_start: 0.6048 (mmm) cc_final: 0.5235 (mtt) REVERT: C 362 MET cc_start: 0.7072 (mtp) cc_final: 0.5878 (mmm) REVERT: C 432 ASP cc_start: 0.5842 (m-30) cc_final: 0.5102 (t0) REVERT: X 228 LYS cc_start: 0.7284 (pptt) cc_final: 0.6705 (ptmt) REVERT: X 248 LYS cc_start: 0.7578 (tmtt) cc_final: 0.7332 (ptpt) REVERT: X 264 GLU cc_start: 0.6116 (pp20) cc_final: 0.5726 (pp20) REVERT: X 274 ARG cc_start: 0.5218 (mtt180) cc_final: 0.4372 (mmp80) REVERT: Y 209 MET cc_start: 0.6528 (mmm) cc_final: 0.5865 (tmm) REVERT: Y 210 ASN cc_start: 0.7757 (m110) cc_final: 0.6435 (m110) REVERT: Y 213 LYS cc_start: 0.6161 (ttpp) cc_final: 0.5526 (tttt) REVERT: Y 221 GLN cc_start: 0.8716 (tt0) cc_final: 0.7344 (tm-30) REVERT: Y 238 LYS cc_start: 0.6031 (mmtt) cc_final: 0.5744 (mmtt) REVERT: Y 271 LYS cc_start: 0.1478 (mtpt) cc_final: 0.0948 (tppp) REVERT: X1 126 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7488 (tmtt) REVERT: X1 183 ASP cc_start: 0.6789 (m-30) cc_final: 0.6423 (m-30) REVERT: X1 204 LEU cc_start: 0.8162 (pp) cc_final: 0.7840 (mt) REVERT: X1 216 MET cc_start: 0.7822 (tmm) cc_final: 0.6898 (tmm) REVERT: X1 229 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6750 (p0) REVERT: Y1 94 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6543 (t) REVERT: Y1 152 HIS cc_start: 0.7875 (t70) cc_final: 0.7294 (t-90) REVERT: Y1 174 GLN cc_start: 0.6552 (mm110) cc_final: 0.6228 (mm-40) REVERT: Y1 181 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7088 (mt) REVERT: Y1 185 LYS cc_start: 0.7393 (ptmt) cc_final: 0.6979 (pttp) REVERT: Y1 191 MET cc_start: 0.7049 (tmm) cc_final: 0.6502 (tmm) REVERT: Z 51 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6664 (mmtm) REVERT: Z 70 ILE cc_start: 0.8067 (mp) cc_final: 0.7795 (tt) REVERT: Z 81 ARG cc_start: 0.7476 (ptp-110) cc_final: 0.6906 (mtp85) outliers start: 198 outliers final: 145 residues processed: 944 average time/residue: 0.5140 time to fit residues: 821.7125 Evaluate side-chains 944 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 784 time to evaluate : 4.598 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 94 GLN Chi-restraints excluded: chain A1 residue 128 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 178 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 221 THR Chi-restraints excluded: chain A1 residue 240 LEU Chi-restraints excluded: chain A1 residue 250 LEU Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 314 SER Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE 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 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 339 ARG Chi-restraints excluded: chain A2 residue 384 ILE Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 118 ASP Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 195 ASN Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 332 ASN Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 363 MET Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 404 ASP Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 2 ARG Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 147 SER Chi-restraints excluded: chain A4 residue 251 ASP Chi-restraints excluded: chain A4 residue 327 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU 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 A5 residue 414 ASN Chi-restraints excluded: chain A5 residue 415 MET Chi-restraints excluded: chain A6 residue 68 LEU Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 98 ASP Chi-restraints excluded: chain A6 residue 154 LEU Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 345 ASP Chi-restraints excluded: chain A6 residue 413 MET Chi-restraints excluded: chain A7 residue 44 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 236 ILE Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain A7 residue 386 THR Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 190 HIS Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 159 VAL 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 B2 residue 387 ILE Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 112 LEU 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 249 ASP Chi-restraints excluded: chain B3 residue 388 MET Chi-restraints excluded: chain B4 residue 5 ILE Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 256 GLN Chi-restraints excluded: chain B4 residue 305 CYS Chi-restraints excluded: chain B4 residue 340 THR Chi-restraints excluded: chain B4 residue 384 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 24 VAL Chi-restraints excluded: chain B5 residue 41 ASP Chi-restraints excluded: chain B5 residue 66 MET Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 127 CYS Chi-restraints excluded: chain B5 residue 246 LEU Chi-restraints excluded: chain B5 residue 348 ASN Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 74 VAL Chi-restraints excluded: chain B6 residue 76 ASP Chi-restraints excluded: chain B6 residue 136 LEU Chi-restraints excluded: chain B6 residue 223 THR Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 290 GLU Chi-restraints excluded: chain B6 residue 313 MET Chi-restraints excluded: chain B6 residue 322 ASP Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B6 residue 415 GLU Chi-restraints excluded: chain B7 residue 5 VAL Chi-restraints excluded: chain B7 residue 24 VAL 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 250 LEU Chi-restraints excluded: chain B7 residue 293 MET Chi-restraints excluded: chain B7 residue 339 SER 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 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 229 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 94 THR Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 ILE Chi-restraints excluded: chain Y1 residue 181 LEU 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 92 ARG Chi-restraints excluded: chain Z residue 155 HIS Chi-restraints excluded: chain Z residue 165 LEU Chi-restraints excluded: chain Z residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 7.9990 chunk 625 optimal weight: 9.9990 chunk 570 optimal weight: 0.1980 chunk 608 optimal weight: 3.9990 chunk 624 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 477 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 549 optimal weight: 8.9990 chunk 575 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 184 ASN ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 293 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 99 ASN A5 347 ASN ** A5 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 233 GLN A7 52 ASN ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 15 GLN ** B4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 206 ASN ** 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** B6 226 ASN ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 55199 Z= 0.327 Angle : 0.678 12.935 74763 Z= 0.339 Chirality : 0.045 0.215 8221 Planarity : 0.004 0.052 9726 Dihedral : 10.101 165.949 7617 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.61 % Allowed : 20.37 % Favored : 76.02 % 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: 0.02 (0.10), residues: 6799 helix: 1.02 (0.09), residues: 3396 sheet: -0.18 (0.17), residues: 911 loop : -1.27 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPB7 397 HIS 0.007 0.001 HISA4 406 PHE 0.028 0.002 PHEB1 92 TYR 0.017 0.002 TYRB2 172 ARG 0.009 0.000 ARG Z 12 *********************** REFINEMENT MACRO_CYCLE 9 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 983 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 775 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 294 TRP cc_start: 0.5590 (m100) cc_final: 0.4642 (t60) REVERT: A1 361 LEU cc_start: 0.6830 (tp) cc_final: 0.6459 (mp) REVERT: A1 415 MET cc_start: 0.8027 (tpp) cc_final: 0.7532 (tpp) REVERT: A2 77 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6595 (pm20) REVERT: A2 110 ILE cc_start: 0.7500 (mt) cc_final: 0.7242 (mt) REVERT: A2 123 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7513 (tpm170) REVERT: A2 339 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4890 (tpm170) REVERT: A3 125 GLU cc_start: 0.7264 (pp20) cc_final: 0.6845 (pp20) REVERT: A3 293 MET cc_start: 0.6730 (ttt) cc_final: 0.6401 (ttm) REVERT: A3 294 TRP cc_start: 0.6481 (m100) cc_final: 0.4849 (t60) REVERT: A3 299 MET cc_start: 0.6575 (mmm) cc_final: 0.6181 (mmm) REVERT: A4 368 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4560 (pp) REVERT: A4 370 LYS cc_start: 0.7658 (tptt) cc_final: 0.6840 (pttt) REVERT: A5 94 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7661 (tp40) REVERT: A5 294 TRP cc_start: 0.6742 (m100) cc_final: 0.6155 (m100) REVERT: A5 337 ASN cc_start: 0.6222 (p0) cc_final: 0.5819 (p0) REVERT: A5 388 MET cc_start: 0.6441 (mtt) cc_final: 0.6148 (mtm) REVERT: A6 98 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: A6 123 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.7112 (mmm160) REVERT: A6 268 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7634 (mmt) REVERT: A6 370 LYS cc_start: 0.7673 (tptt) cc_final: 0.6834 (pttt) REVERT: A6 391 LEU cc_start: 0.8217 (pp) cc_final: 0.7338 (mt) REVERT: A6 401 LYS cc_start: 0.8410 (ttmt) cc_final: 0.7808 (tptp) REVERT: A7 163 MET cc_start: 0.8084 (mmm) cc_final: 0.7697 (mmt) REVERT: A7 294 TRP cc_start: 0.6840 (m100) cc_final: 0.4962 (t60) REVERT: A7 359 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7924 (mtmt) REVERT: A7 391 ARG cc_start: 0.6814 (ttm170) cc_final: 0.6241 (tmt170) REVERT: B1 164 MET cc_start: 0.7931 (tpp) cc_final: 0.7620 (ttm) REVERT: B1 200 MET cc_start: 0.8336 (mpp) cc_final: 0.8000 (mpp) REVERT: B2 5 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7506 (pt) REVERT: B2 268 MET cc_start: 0.8346 (mmm) cc_final: 0.7960 (mmm) REVERT: B2 379 SER cc_start: 0.7947 (p) cc_final: 0.7529 (t) REVERT: B3 388 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6108 (mmt) REVERT: B4 256 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7500 (mm-40) REVERT: B5 276 ARG cc_start: 0.7675 (ttt180) cc_final: 0.6936 (ttm-80) REVERT: B5 297 LYS cc_start: 0.8193 (mmmm) cc_final: 0.7895 (mmmm) REVERT: B5 348 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.6751 (m-40) REVERT: B5 418 LEU cc_start: 0.7607 (tp) cc_final: 0.7386 (tt) REVERT: B6 4 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8902 (p) REVERT: B6 286 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7459 (mm) REVERT: B6 415 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: B7 5 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8438 (t) REVERT: B7 73 MET cc_start: 0.8565 (mmm) cc_final: 0.8204 (mmp) REVERT: B7 150 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7321 (tt) REVERT: C 295 LYS cc_start: 0.6246 (mmtt) cc_final: 0.5958 (tttm) REVERT: C 328 MET cc_start: 0.3144 (ptt) cc_final: 0.2332 (ptt) REVERT: C 329 MET cc_start: 0.6110 (mmm) cc_final: 0.5354 (mtt) REVERT: C 362 MET cc_start: 0.7056 (mtp) cc_final: 0.5864 (mmm) REVERT: X 264 GLU cc_start: 0.6113 (pp20) cc_final: 0.5546 (pp20) REVERT: X 265 THR cc_start: 0.5077 (p) cc_final: 0.4838 (p) REVERT: X 274 ARG cc_start: 0.5250 (mtt180) cc_final: 0.4481 (mmt-90) REVERT: Y 209 MET cc_start: 0.6648 (mmm) cc_final: 0.5901 (tmm) REVERT: Y 210 ASN cc_start: 0.7757 (m110) cc_final: 0.6260 (m110) REVERT: Y 213 LYS cc_start: 0.6142 (ttpp) cc_final: 0.5403 (tttt) REVERT: Y 221 GLN cc_start: 0.8710 (tt0) cc_final: 0.7305 (tm-30) REVERT: Y 238 LYS cc_start: 0.5924 (mmtt) cc_final: 0.5618 (mmtt) REVERT: Y 271 LYS cc_start: 0.1489 (mtpt) cc_final: 0.0961 (tppp) REVERT: X1 183 ASP cc_start: 0.6869 (m-30) cc_final: 0.6479 (m-30) REVERT: X1 204 LEU cc_start: 0.8174 (pp) cc_final: 0.7865 (mt) REVERT: X1 216 MET cc_start: 0.7899 (tmm) cc_final: 0.6902 (tmm) REVERT: X1 229 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6712 (p0) REVERT: X1 250 GLN cc_start: 0.6468 (tm-30) cc_final: 0.5769 (tt0) REVERT: Y1 82 MET cc_start: 0.7525 (tmm) cc_final: 0.7260 (tmm) REVERT: Y1 94 THR cc_start: 0.6683 (OUTLIER) cc_final: 0.6382 (t) REVERT: Y1 152 HIS cc_start: 0.8023 (t70) cc_final: 0.7447 (t-90) REVERT: Y1 181 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7324 (mt) REVERT: Y1 185 LYS cc_start: 0.7348 (ptmt) cc_final: 0.6955 (pttp) REVERT: Y1 191 MET cc_start: 0.7015 (tmm) cc_final: 0.6496 (tmm) REVERT: Y1 202 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6419 (tmm-80) REVERT: Z 7 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7572 (ptp-170) REVERT: Z 51 LYS cc_start: 0.7113 (mtpp) cc_final: 0.6683 (mmtm) REVERT: Z 81 ARG cc_start: 0.7561 (ptp-110) cc_final: 0.6976 (mtp85) REVERT: Z 92 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4115 (ttm-80) outliers start: 208 outliers final: 171 residues processed: 920 average time/residue: 0.5213 time to fit residues: 804.5303 Evaluate side-chains 940 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 750 time to evaluate : 4.570 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain A1 residue 67 ASP Chi-restraints excluded: chain A1 residue 94 GLN Chi-restraints excluded: chain A1 residue 128 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 178 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 221 THR Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 314 SER Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE Chi-restraints excluded: chain A2 residue 7 ILE 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 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 223 THR Chi-restraints excluded: chain A2 residue 230 LEU Chi-restraints excluded: chain A2 residue 305 CYS Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 387 ILE Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 118 ASP Chi-restraints excluded: chain A3 residue 149 THR Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 163 MET Chi-restraints excluded: chain A3 residue 218 THR Chi-restraints excluded: chain A3 residue 247 ASN Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 256 ASN Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 289 LEU 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 363 MET Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 407 GLU Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 2 ARG Chi-restraints excluded: chain A4 residue 22 GLU Chi-restraints excluded: chain A4 residue 51 THR Chi-restraints excluded: chain A4 residue 147 SER Chi-restraints excluded: chain A4 residue 182 VAL Chi-restraints excluded: chain A4 residue 251 ASP Chi-restraints excluded: chain A4 residue 288 VAL Chi-restraints excluded: chain A4 residue 327 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU Chi-restraints excluded: chain A5 residue 164 MET 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 225 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 A5 residue 406 MET Chi-restraints excluded: chain A5 residue 414 ASN Chi-restraints excluded: chain A5 residue 415 MET Chi-restraints excluded: chain A6 residue 56 THR Chi-restraints excluded: chain A6 residue 68 LEU Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 98 ASP Chi-restraints excluded: chain A6 residue 154 LEU Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 268 MET Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 345 ASP Chi-restraints excluded: chain A6 residue 413 MET Chi-restraints excluded: chain A6 residue 425 LEU Chi-restraints excluded: chain A7 residue 44 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 236 ILE Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain A7 residue 386 THR Chi-restraints excluded: chain B1 residue 39 ASP Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 166 THR Chi-restraints excluded: chain B1 residue 178 THR Chi-restraints excluded: chain B1 residue 224 ASP Chi-restraints excluded: chain B1 residue 232 VAL Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 26 LEU Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 159 VAL 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 B2 residue 387 ILE Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 95 THR Chi-restraints excluded: chain B3 residue 112 LEU Chi-restraints excluded: chain B3 residue 115 SER 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 230 SER Chi-restraints excluded: chain B3 residue 249 ASP Chi-restraints excluded: chain B3 residue 388 MET Chi-restraints excluded: chain B4 residue 5 ILE Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 256 GLN Chi-restraints excluded: chain B4 residue 305 CYS Chi-restraints excluded: chain B4 residue 340 THR Chi-restraints excluded: chain B4 residue 341 ILE Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 24 VAL Chi-restraints excluded: chain B5 residue 41 ASP Chi-restraints excluded: chain B5 residue 66 MET Chi-restraints excluded: chain B5 residue 95 THR Chi-restraints excluded: chain B5 residue 108 GLU Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 127 CYS Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 246 LEU Chi-restraints excluded: chain B5 residue 348 ASN Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 4 VAL Chi-restraints excluded: chain B6 residue 74 VAL Chi-restraints excluded: chain B6 residue 136 LEU Chi-restraints excluded: chain B6 residue 182 VAL Chi-restraints excluded: chain B6 residue 223 THR Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 290 GLU Chi-restraints excluded: chain B6 residue 305 CYS Chi-restraints excluded: chain B6 residue 313 MET Chi-restraints excluded: chain B6 residue 322 ASP Chi-restraints excluded: chain B6 residue 332 VAL Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B6 residue 415 GLU Chi-restraints excluded: chain B7 residue 5 VAL Chi-restraints excluded: chain B7 residue 24 VAL 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 250 LEU Chi-restraints excluded: chain B7 residue 293 MET Chi-restraints excluded: chain B7 residue 339 SER Chi-restraints excluded: chain B7 residue 418 LEU 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 232 THR Chi-restraints excluded: chain X1 residue 126 LYS 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 229 ASP Chi-restraints excluded: chain X1 residue 232 ASP Chi-restraints excluded: chain Y1 residue 94 THR Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 ILE Chi-restraints excluded: chain Y1 residue 134 LEU Chi-restraints excluded: chain Y1 residue 151 THR Chi-restraints excluded: chain Y1 residue 168 ILE Chi-restraints excluded: chain Y1 residue 181 LEU Chi-restraints excluded: chain Y1 residue 187 ASP Chi-restraints excluded: chain Y1 residue 196 ASN Chi-restraints excluded: chain Y1 residue 202 ARG 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 92 ARG Chi-restraints excluded: chain Z residue 155 HIS Chi-restraints excluded: chain Z residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 3.9990 chunk 399 optimal weight: 0.0570 chunk 642 optimal weight: 0.9990 chunk 392 optimal weight: 0.9990 chunk 305 optimal weight: 0.0270 chunk 446 optimal weight: 2.9990 chunk 674 optimal weight: 10.0000 chunk 620 optimal weight: 0.9990 chunk 537 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 414 optimal weight: 1.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 184 ASN ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 293 ASN ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 61 HIS A4 102 ASN A5 347 ASN A5 375 GLN A5 423 GLN A6 233 GLN A7 332 ASN ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 15 GLN B4 206 ASN ** B5 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3613 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= 0.164 Angle : 0.602 12.292 74763 Z= 0.295 Chirality : 0.042 0.201 8221 Planarity : 0.004 0.055 9726 Dihedral : 9.713 169.868 7617 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 21.28 % Favored : 75.98 % 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: 0.25 (0.10), residues: 6799 helix: 1.19 (0.09), residues: 3412 sheet: -0.03 (0.17), residues: 911 loop : -1.17 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPB7 397 HIS 0.005 0.001 HISB7 396 PHE 0.030 0.001 PHE Y 199 TYR 0.014 0.001 TYRA5 422 ARG 0.011 0.000 ARG Z 12 ********************** REFINEMENT MACRO_CYCLE 10 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 941 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 783 time to evaluate : 4.713 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: 0.7665 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A1 21 TRP cc_start: 0.7075 (m100) cc_final: 0.6841 (m100) REVERT: A1 294 TRP cc_start: 0.5593 (m100) cc_final: 0.5027 (t60) REVERT: A1 321 MET cc_start: 0.3873 (ttt) cc_final: 0.3666 (ttt) REVERT: A1 361 LEU cc_start: 0.6807 (tp) cc_final: 0.6430 (mp) REVERT: A1 363 MET cc_start: 0.6363 (ttm) cc_final: 0.5911 (tpt) REVERT: A1 415 MET cc_start: 0.7938 (tpp) cc_final: 0.7547 (tpp) REVERT: A2 77 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6442 (pm20) REVERT: A2 123 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7477 (tpm170) REVERT: A2 301 MET cc_start: 0.6583 (mmp) cc_final: 0.6213 (mmp) REVERT: A2 339 ARG cc_start: 0.5206 (OUTLIER) cc_final: 0.4930 (tpm170) REVERT: A3 282 ARG cc_start: 0.5830 (ptt180) cc_final: 0.5500 (tpm170) REVERT: A3 293 MET cc_start: 0.6676 (ttt) cc_final: 0.6311 (ttm) REVERT: A3 294 TRP cc_start: 0.6311 (m100) cc_final: 0.4819 (t60) REVERT: A3 299 MET cc_start: 0.6301 (mmm) cc_final: 0.5829 (mmm) REVERT: A3 363 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5845 (ttp) REVERT: A3 403 MET cc_start: 0.7060 (ptp) cc_final: 0.6692 (ptp) REVERT: A3 407 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: A4 370 LYS cc_start: 0.7748 (tptt) cc_final: 0.6838 (pttt) REVERT: A5 94 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7578 (tp40) REVERT: A5 294 TRP cc_start: 0.6599 (m100) cc_final: 0.6081 (m100) REVERT: A5 337 ASN cc_start: 0.6031 (p0) cc_final: 0.5669 (p0) REVERT: A5 388 MET cc_start: 0.6465 (mtt) cc_final: 0.6228 (mtm) REVERT: A6 98 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6328 (m-30) REVERT: A6 123 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7172 (mmm160) REVERT: A6 154 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A6 370 LYS cc_start: 0.7608 (tptt) cc_final: 0.6837 (pttt) REVERT: A6 391 LEU cc_start: 0.8147 (pp) cc_final: 0.7288 (mt) REVERT: A6 401 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7754 (tptp) REVERT: A7 163 MET cc_start: 0.8012 (mmm) cc_final: 0.7588 (mmt) REVERT: A7 294 TRP cc_start: 0.6730 (m100) cc_final: 0.4972 (t60) REVERT: A7 359 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7928 (mtmt) REVERT: A7 391 ARG cc_start: 0.6797 (ttm170) cc_final: 0.6258 (tmt170) REVERT: B1 164 MET cc_start: 0.7954 (tpp) cc_final: 0.7562 (ttm) REVERT: B1 200 MET cc_start: 0.8291 (mpp) cc_final: 0.7833 (mpp) REVERT: B2 5 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7205 (pt) REVERT: B2 117 LEU cc_start: 0.8828 (tt) cc_final: 0.8623 (tp) REVERT: B2 268 MET cc_start: 0.8241 (mmm) cc_final: 0.7842 (mmm) REVERT: B2 302 MET cc_start: 0.7938 (mtm) cc_final: 0.7694 (mtt) REVERT: B2 379 SER cc_start: 0.7813 (p) cc_final: 0.7404 (t) REVERT: B3 164 MET cc_start: 0.7759 (tpp) cc_final: 0.7404 (tpp) REVERT: B3 388 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6215 (mmt) REVERT: B4 203 MET cc_start: 0.7076 (mmm) cc_final: 0.6743 (mmm) REVERT: B4 302 MET cc_start: 0.8672 (mtp) cc_final: 0.8320 (mtp) REVERT: B5 276 ARG cc_start: 0.7518 (ttt180) cc_final: 0.6804 (ttm-80) REVERT: B5 297 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7859 (mmmm) REVERT: B6 4 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8904 (p) REVERT: B6 163 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6788 (mmmt) REVERT: B6 268 MET cc_start: 0.8654 (mmm) cc_final: 0.8117 (mmt) REVERT: B6 286 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7017 (mm) REVERT: B6 415 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6486 (mm-30) REVERT: B7 5 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8290 (t) REVERT: B7 150 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7274 (tt) REVERT: C 295 LYS cc_start: 0.6247 (mmtt) cc_final: 0.5944 (tttm) REVERT: C 328 MET cc_start: 0.3073 (ptt) cc_final: 0.2247 (ptt) REVERT: C 329 MET cc_start: 0.6118 (mmm) cc_final: 0.5359 (mtt) REVERT: C 362 MET cc_start: 0.7104 (mtp) cc_final: 0.5934 (mmm) REVERT: C 432 ASP cc_start: 0.5771 (m-30) cc_final: 0.5092 (t0) REVERT: X 228 LYS cc_start: 0.7338 (pptt) cc_final: 0.6679 (ptmt) REVERT: X 264 GLU cc_start: 0.6014 (pp20) cc_final: 0.5609 (pp20) REVERT: X 274 ARG cc_start: 0.5340 (mtt180) cc_final: 0.4427 (mmp80) REVERT: Y 188 MET cc_start: 0.5622 (mpp) cc_final: 0.5355 (mpp) REVERT: Y 209 MET cc_start: 0.6594 (mmm) cc_final: 0.5930 (tmm) REVERT: Y 210 ASN cc_start: 0.7777 (m110) cc_final: 0.6443 (m110) REVERT: Y 213 LYS cc_start: 0.6240 (ttpp) cc_final: 0.5543 (tttt) REVERT: Y 221 GLN cc_start: 0.8686 (tt0) cc_final: 0.7290 (tm-30) REVERT: Y 238 LYS cc_start: 0.5515 (mmtt) cc_final: 0.5148 (mmtt) REVERT: Y 271 LYS cc_start: 0.1751 (mtpt) cc_final: 0.1270 (tppp) REVERT: X1 183 ASP cc_start: 0.6746 (m-30) cc_final: 0.6390 (m-30) REVERT: X1 216 MET cc_start: 0.7831 (tmm) cc_final: 0.6913 (tmm) REVERT: X1 218 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (mmt) REVERT: Y1 94 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6291 (t) REVERT: Y1 152 HIS cc_start: 0.7873 (t70) cc_final: 0.7304 (t-90) REVERT: Y1 181 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7109 (mt) REVERT: Y1 185 LYS cc_start: 0.7417 (ptmt) cc_final: 0.7054 (pttp) REVERT: Y1 191 MET cc_start: 0.7067 (tmm) cc_final: 0.6702 (tmm) REVERT: Z 81 ARG cc_start: 0.7546 (ptp-110) cc_final: 0.7003 (mtp85) outliers start: 158 outliers final: 127 residues processed: 887 average time/residue: 0.5154 time to fit residues: 765.2548 Evaluate side-chains 906 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 763 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 39 ASP 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 101 TRP Chi-restraints excluded: chain A1 residue 128 ASP Chi-restraints excluded: chain A1 residue 166 THR Chi-restraints excluded: chain A1 residue 178 THR Chi-restraints excluded: chain A1 residue 201 VAL Chi-restraints excluded: chain A1 residue 221 THR Chi-restraints excluded: chain A1 residue 274 THR Chi-restraints excluded: chain A1 residue 314 SER Chi-restraints excluded: chain A1 residue 354 CYS Chi-restraints excluded: chain A1 residue 368 ILE 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 149 LEU Chi-restraints excluded: chain A2 residue 195 LEU Chi-restraints excluded: chain A2 residue 219 ILE Chi-restraints excluded: chain A2 residue 230 LEU Chi-restraints excluded: chain A2 residue 339 ARG Chi-restraints excluded: chain A2 residue 428 LEU Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 118 ASP Chi-restraints excluded: chain A3 residue 150 LEU Chi-restraints excluded: chain A3 residue 247 ASN Chi-restraints excluded: chain A3 residue 249 ASP Chi-restraints excluded: chain A3 residue 274 THR Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 289 LEU Chi-restraints excluded: chain A3 residue 349 VAL Chi-restraints excluded: chain A3 residue 363 MET Chi-restraints excluded: chain A3 residue 382 SER Chi-restraints excluded: chain A3 residue 407 GLU Chi-restraints excluded: chain A3 residue 412 GLU Chi-restraints excluded: chain A3 residue 418 LEU Chi-restraints excluded: chain A4 residue 2 ARG 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 147 SER Chi-restraints excluded: chain A4 residue 327 ASP 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 47 ILE Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 139 LEU 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 A5 residue 406 MET Chi-restraints excluded: chain A5 residue 415 MET Chi-restraints excluded: chain A6 residue 68 LEU Chi-restraints excluded: chain A6 residue 82 THR Chi-restraints excluded: chain A6 residue 98 ASP Chi-restraints excluded: chain A6 residue 154 LEU Chi-restraints excluded: chain A6 residue 170 THR Chi-restraints excluded: chain A6 residue 303 VAL Chi-restraints excluded: chain A6 residue 413 MET Chi-restraints excluded: chain A7 residue 44 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 236 ILE Chi-restraints excluded: chain A7 residue 249 ASP Chi-restraints excluded: chain A7 residue 332 ASN Chi-restraints excluded: chain A7 residue 347 ASN Chi-restraints excluded: chain A7 residue 386 THR Chi-restraints excluded: chain B1 residue 151 LEU Chi-restraints excluded: chain B1 residue 178 THR Chi-restraints excluded: chain B1 residue 190 HIS Chi-restraints excluded: chain B1 residue 232 VAL Chi-restraints excluded: chain B1 residue 239 CYS Chi-restraints excluded: chain B1 residue 268 VAL Chi-restraints excluded: chain B2 residue 5 ILE Chi-restraints excluded: chain B2 residue 26 LEU Chi-restraints excluded: chain B2 residue 130 THR Chi-restraints excluded: chain B2 residue 159 VAL 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 B2 residue 387 ILE Chi-restraints excluded: chain B3 residue 5 VAL Chi-restraints excluded: chain B3 residue 112 LEU 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 249 ASP Chi-restraints excluded: chain B3 residue 388 MET Chi-restraints excluded: chain B4 residue 5 ILE Chi-restraints excluded: chain B4 residue 136 LEU Chi-restraints excluded: chain B4 residue 305 CYS Chi-restraints excluded: chain B4 residue 340 THR Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 24 VAL Chi-restraints excluded: chain B5 residue 126 SER Chi-restraints excluded: chain B5 residue 127 CYS Chi-restraints excluded: chain B5 residue 149 THR Chi-restraints excluded: chain B5 residue 246 LEU Chi-restraints excluded: chain B5 residue 424 GLN Chi-restraints excluded: chain B6 residue 4 VAL Chi-restraints excluded: chain B6 residue 136 LEU Chi-restraints excluded: chain B6 residue 223 THR Chi-restraints excluded: chain B6 residue 286 LEU Chi-restraints excluded: chain B6 residue 290 GLU Chi-restraints excluded: chain B6 residue 305 CYS Chi-restraints excluded: chain B6 residue 322 ASP Chi-restraints excluded: chain B6 residue 341 ILE Chi-restraints excluded: chain B6 residue 415 GLU Chi-restraints excluded: chain B7 residue 5 VAL Chi-restraints excluded: chain B7 residue 24 VAL 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 293 MET Chi-restraints excluded: chain B7 residue 339 SER Chi-restraints excluded: chain B7 residue 418 LEU 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 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 Y1 residue 94 THR Chi-restraints excluded: chain Y1 residue 96 MET Chi-restraints excluded: chain Y1 residue 132 ILE Chi-restraints excluded: chain Y1 residue 134 LEU Chi-restraints excluded: chain Y1 residue 181 LEU 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 155 HIS Chi-restraints excluded: chain Z residue 165 LEU Chi-restraints excluded: chain Z residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 6.9990 chunk 426 optimal weight: 5.9990 chunk 572 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 495 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 537 optimal weight: 0.2980 chunk 225 optimal weight: 0.9990 chunk 552 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 18 ASN ** A2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 48 ASN ** A3 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 195 ASN ** A3 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 102 ASN A6 233 GLN A7 332 ASN ** B1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 307 HIS ** B1 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 206 ASN ** 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** ** B7 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.103344 restraints weight = 102786.897| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.11 r_work: 0.3771 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55199 Z= 0.166 Angle : 0.603 17.861 74763 Z= 0.293 Chirality : 0.042 0.191 8221 Planarity : 0.004 0.055 9726 Dihedral : 9.501 177.128 7617 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.81 % Allowed : 21.28 % Favored : 75.91 % Cbeta Deviations : 0.00 % 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: 0.34 (0.10), residues: 6799 helix: 1.25 (0.09), residues: 3409 sheet: 0.08 (0.18), residues: 911 loop : -1.12 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPB7 397 HIS 0.005 0.001 HISB2 197 PHE 0.030 0.001 PHE Y 199 TYR 0.017 0.001 TYRA5 422 ARG 0.007 0.000 ARGA3 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13587.70 seconds wall clock time: 238 minutes 50.92 seconds (14330.92 seconds total)