Starting phenix.real_space_refine on Sat Mar 23 16:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u84_42008/03_2024/8u84_42008.pdb" } resolution = 3.88 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= 0.002 sd= 1.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 275 5.16 5 C 23635 2.51 5 N 6635 2.21 5 O 7340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 GLU 229": "OE1" <-> "OE2" Residue "K2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 GLU 127": "OE1" <-> "OE2" Residue "K2 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 GLU 219": "OE1" <-> "OE2" Residue "K2 GLU 229": "OE1" <-> "OE2" Residue "K3 ARG 64": "NH1" <-> "NH2" Residue "K3 ASP 65": "OD1" <-> "OD2" Residue "K3 ASP 116": "OD1" <-> "OD2" Residue "K3 GLU 125": "OE1" <-> "OE2" Residue "K3 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 GLU 124": "OE1" <-> "OE2" Residue "K4 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 GLU 119": "OE1" <-> "OE2" Residue "K5 GLU 127": "OE1" <-> "OE2" Residue "K5 GLU 166": "OE1" <-> "OE2" Residue "K5 PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 79": "OE1" <-> "OE2" Residue "C1 GLU 83": "OE1" <-> "OE2" Residue "C1 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ASP 159": "OD1" <-> "OD2" Residue "C1 GLU 257": "OE1" <-> "OE2" Residue "C1 GLU 280": "OE1" <-> "OE2" Residue "C1 PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 79": "OE1" <-> "OE2" Residue "C2 ASP 92": "OD1" <-> "OD2" Residue "C2 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ASP 159": "OD1" <-> "OD2" Residue "C2 TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 215": "OE1" <-> "OE2" Residue "C2 GLU 258": "OE1" <-> "OE2" Residue "C2 GLU 265": "OE1" <-> "OE2" Residue "C2 GLU 358": "OE1" <-> "OE2" Residue "C2 ASP 363": "OD1" <-> "OD2" Residue "C3 GLU 79": "OE1" <-> "OE2" Residue "C3 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 258": "OE1" <-> "OE2" Residue "C3 GLU 315": "OE1" <-> "OE2" Residue "C3 GLU 375": "OE1" <-> "OE2" Residue "C4 GLU 27": "OE1" <-> "OE2" Residue "C4 ASP 35": "OD1" <-> "OD2" Residue "C4 ASP 92": "OD1" <-> "OD2" Residue "C4 GLU 211": "OE1" <-> "OE2" Residue "C4 GLU 257": "OE1" <-> "OE2" Residue "C5 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 GLU 79": "OE1" <-> "OE2" Residue "C5 GLU 83": "OE1" <-> "OE2" Residue "C5 ASP 159": "OD1" <-> "OD2" Residue "C5 GLU 211": "OE1" <-> "OE2" Residue "C5 GLU 215": "OE1" <-> "OE2" Residue "C5 GLU 227": "OE1" <-> "OE2" Residue "C5 TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 215": "OE1" <-> "OE2" Residue "B1 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 267": "OD1" <-> "OD2" Residue "B2 ASP 38": "OD1" <-> "OD2" Residue "B2 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 172": "OE1" <-> "OE2" Residue "B2 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 303": "OD1" <-> "OD2" Residue "B3 GLU 3": "OE1" <-> "OE2" Residue "B3 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 172": "OE1" <-> "OE2" Residue "B3 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 260": "OE1" <-> "OE2" Residue "B3 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 ASP 267": "OD1" <-> "OD2" Residue "B5 GLU 12": "OE1" <-> "OE2" Residue "B5 ASP 153": "OD1" <-> "OD2" Residue "B5 ASP 163": "OD1" <-> "OD2" Residue "B5 ASP 186": "OD1" <-> "OD2" Residue "B5 GLU 215": "OE1" <-> "OE2" Residue "B5 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 226": "OE1" <-> "OE2" Residue "B5 PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G3 ASP 26": "OD1" <-> "OD2" Residue "G4 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G5 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37885 Number of models: 1 Model: "" Number of chains: 20 Chain: "K1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K3" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K4" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K5" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "C1" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C2" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C3" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C4" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C5" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "B1" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B2" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B3" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B4" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B5" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G1" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G2" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G3" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G5" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Time building chain proxies: 18.41, per 1000 atoms: 0.49 Number of scatterers: 37885 At special positions: 0 Unit cell: (238.96, 250.29, 138.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 275 16.00 O 7340 8.00 N 6635 7.00 C 23635 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=0, symmetry=0 Time building additional restraints: 14.45 Conformation dependent library (CDL) restraints added in 7.3 seconds 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8970 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 47 sheets defined 48.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'K1' and resid 59 through 63 Processing helix chain 'K1' and resid 68 through 75 removed outlier: 3.683A pdb=" N GLNK1 75 " --> pdb=" O TYRK1 71 " (cutoff:3.500A) Processing helix chain 'K1' and resid 96 through 98 No H-bonds generated for 'chain 'K1' and resid 96 through 98' Processing helix chain 'K1' and resid 99 through 108 removed outlier: 3.537A pdb=" N LEUK1 106 " --> pdb=" O VALK1 102 " (cutoff:3.500A) Processing helix chain 'K1' and resid 118 through 129 Processing helix chain 'K1' and resid 131 through 150 Processing helix chain 'K1' and resid 164 through 174 removed outlier: 3.842A pdb=" N THRK1 169 " --> pdb=" O GLUK1 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLNK1 170 " --> pdb=" O GLUK1 166 " (cutoff:3.500A) Processing helix chain 'K1' and resid 221 through 233 removed outlier: 4.087A pdb=" N ARGK1 233 " --> pdb=" O GLUK1 229 " (cutoff:3.500A) Processing helix chain 'K2' and resid 59 through 63 Processing helix chain 'K2' and resid 69 through 75 Processing helix chain 'K2' and resid 95 through 109 Proline residue: K2 101 - end of helix removed outlier: 3.543A pdb=" N HISK2 108 " --> pdb=" O ASNK2 104 " (cutoff:3.500A) Processing helix chain 'K2' and resid 118 through 130 Processing helix chain 'K2' and resid 131 through 149 Processing helix chain 'K2' and resid 164 through 174 removed outlier: 4.390A pdb=" N THRK2 169 " --> pdb=" O GLUK2 165 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLNK2 170 " --> pdb=" O GLUK2 166 " (cutoff:3.500A) Processing helix chain 'K2' and resid 190 through 195 removed outlier: 4.209A pdb=" N TYRK2 193 " --> pdb=" O SERK2 190 " (cutoff:3.500A) Processing helix chain 'K2' and resid 221 through 233 Processing helix chain 'K3' and resid 59 through 63 Processing helix chain 'K3' and resid 70 through 76 removed outlier: 3.612A pdb=" N GLNK3 75 " --> pdb=" O TYRK3 71 " (cutoff:3.500A) Processing helix chain 'K3' and resid 98 through 109 removed outlier: 4.146A pdb=" N VALK3 102 " --> pdb=" O TYRK3 98 " (cutoff:3.500A) Processing helix chain 'K3' and resid 118 through 129 Processing helix chain 'K3' and resid 131 through 152 removed outlier: 4.563A pdb=" N VALK3 152 " --> pdb=" O LYSK3 148 " (cutoff:3.500A) Processing helix chain 'K3' and resid 167 through 174 removed outlier: 4.006A pdb=" N METK3 171 " --> pdb=" O GLUK3 167 " (cutoff:3.500A) Processing helix chain 'K3' and resid 191 through 195 removed outlier: 3.502A pdb=" N ASNK3 195 " --> pdb=" O ASNK3 192 " (cutoff:3.500A) Processing helix chain 'K3' and resid 221 through 233 Processing helix chain 'K4' and resid 59 through 63 Processing helix chain 'K4' and resid 68 through 75 removed outlier: 3.524A pdb=" N ARGK4 72 " --> pdb=" O SERK4 68 " (cutoff:3.500A) Processing helix chain 'K4' and resid 98 through 109 Processing helix chain 'K4' and resid 118 through 130 removed outlier: 3.679A pdb=" N VALK4 122 " --> pdb=" O ALAK4 118 " (cutoff:3.500A) Processing helix chain 'K4' and resid 131 through 149 Processing helix chain 'K4' and resid 167 through 174 Processing helix chain 'K4' and resid 221 through 233 Processing helix chain 'K5' and resid 59 through 63 Processing helix chain 'K5' and resid 68 through 74 removed outlier: 3.606A pdb=" N ARGK5 72 " --> pdb=" O SERK5 68 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUK5 73 " --> pdb=" O PHEK5 69 " (cutoff:3.500A) Processing helix chain 'K5' and resid 98 through 109 removed outlier: 3.760A pdb=" N VALK5 102 " --> pdb=" O TYRK5 98 " (cutoff:3.500A) Processing helix chain 'K5' and resid 118 through 129 removed outlier: 3.801A pdb=" N PHEK5 128 " --> pdb=" O GLUK5 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYRK5 129 " --> pdb=" O GLUK5 125 " (cutoff:3.500A) Processing helix chain 'K5' and resid 131 through 150 Processing helix chain 'K5' and resid 164 through 174 removed outlier: 4.717A pdb=" N THRK5 169 " --> pdb=" O GLUK5 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLNK5 170 " --> pdb=" O GLUK5 166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N METK5 171 " --> pdb=" O GLUK5 167 " (cutoff:3.500A) Processing helix chain 'K5' and resid 197 through 199 No H-bonds generated for 'chain 'K5' and resid 197 through 199' Processing helix chain 'K5' and resid 221 through 233 removed outlier: 3.612A pdb=" N LYSK5 225 " --> pdb=" O SERK5 221 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARGK5 233 " --> pdb=" O GLUK5 229 " (cutoff:3.500A) Processing helix chain 'C1' and resid 27 through 46 Processing helix chain 'C1' and resid 53 through 67 removed outlier: 3.595A pdb=" N LEUC1 57 " --> pdb=" O SERC1 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALC1 65 " --> pdb=" O ALAC1 61 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUC1 66 " --> pdb=" O TYRC1 62 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HISC1 67 " --> pdb=" O THRC1 63 " (cutoff:3.500A) Processing helix chain 'C1' and resid 69 through 88 Processing helix chain 'C1' and resid 88 through 95 Processing helix chain 'C1' and resid 100 through 123 Processing helix chain 'C1' and resid 123 through 134 removed outlier: 3.603A pdb=" N ASPC1 127 " --> pdb=" O LEUC1 123 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALC1 131 " --> pdb=" O ASPC1 127 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLNC1 132 " --> pdb=" O ARGC1 128 " (cutoff:3.500A) Processing helix chain 'C1' and resid 138 through 152 removed outlier: 3.864A pdb=" N PHEC1 147 " --> pdb=" O GLYC1 143 " (cutoff:3.500A) Processing helix chain 'C1' and resid 154 through 175 Processing helix chain 'C1' and resid 179 through 194 Processing helix chain 'C1' and resid 198 through 205 removed outlier: 3.539A pdb=" N PHEC1 205 " --> pdb=" O TYRC1 201 " (cutoff:3.500A) Processing helix chain 'C1' and resid 205 through 228 Processing helix chain 'C1' and resid 229 through 252 Processing helix chain 'C1' and resid 253 through 255 No H-bonds generated for 'chain 'C1' and resid 253 through 255' Processing helix chain 'C1' and resid 256 through 269 removed outlier: 3.901A pdb=" N ILEC1 260 " --> pdb=" O THRC1 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEC1 269 " --> pdb=" O GLUC1 265 " (cutoff:3.500A) Processing helix chain 'C1' and resid 272 through 277 removed outlier: 3.710A pdb=" N ILEC1 276 " --> pdb=" O HISC1 272 " (cutoff:3.500A) Processing helix chain 'C1' and resid 284 through 289 Processing helix chain 'C1' and resid 292 through 304 removed outlier: 3.986A pdb=" N LEUC1 296 " --> pdb=" O LYSC1 292 " (cutoff:3.500A) Processing helix chain 'C1' and resid 308 through 330 Processing helix chain 'C1' and resid 337 through 342 removed outlier: 3.545A pdb=" N ILEC1 342 " --> pdb=" O PROC1 338 " (cutoff:3.500A) Processing helix chain 'C1' and resid 343 through 359 Processing helix chain 'C1' and resid 363 through 379 removed outlier: 3.567A pdb=" N ASNC1 379 " --> pdb=" O GLUC1 375 " (cutoff:3.500A) Processing helix chain 'C2' and resid 26 through 46 removed outlier: 4.215A pdb=" N SERC2 32 " --> pdb=" O LYSC2 28 " (cutoff:3.500A) Processing helix chain 'C2' and resid 53 through 66 removed outlier: 3.805A pdb=" N LEUC2 66 " --> pdb=" O TYRC2 62 " (cutoff:3.500A) Processing helix chain 'C2' and resid 69 through 88 Processing helix chain 'C2' and resid 88 through 96 removed outlier: 3.781A pdb=" N SERC2 96 " --> pdb=" O ASPC2 92 " (cutoff:3.500A) Processing helix chain 'C2' and resid 100 through 123 removed outlier: 4.155A pdb=" N METC2 118 " --> pdb=" O THRC2 114 " (cutoff:3.500A) Processing helix chain 'C2' and resid 129 through 134 Processing helix chain 'C2' and resid 138 through 151 removed outlier: 4.007A pdb=" N PHEC2 147 " --> pdb=" O GLYC2 143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALC2 151 " --> pdb=" O PHEC2 147 " (cutoff:3.500A) Processing helix chain 'C2' and resid 154 through 174 removed outlier: 4.113A pdb=" N HISC2 160 " --> pdb=" O CYSC2 156 " (cutoff:3.500A) Processing helix chain 'C2' and resid 179 through 194 removed outlier: 4.191A pdb=" N ILEC2 183 " --> pdb=" O ASPC2 179 " (cutoff:3.500A) Processing helix chain 'C2' and resid 198 through 205 Processing helix chain 'C2' and resid 205 through 228 Processing helix chain 'C2' and resid 229 through 252 Processing helix chain 'C2' and resid 253 through 255 No H-bonds generated for 'chain 'C2' and resid 253 through 255' Processing helix chain 'C2' and resid 256 through 268 removed outlier: 3.701A pdb=" N ILEC2 260 " --> pdb=" O THRC2 256 " (cutoff:3.500A) Processing helix chain 'C2' and resid 284 through 291 removed outlier: 3.704A pdb=" N LEUC2 288 " --> pdb=" O LEUC2 284 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYSC2 289 " --> pdb=" O VALC2 285 " (cutoff:3.500A) Processing helix chain 'C2' and resid 292 through 304 removed outlier: 3.783A pdb=" N LEUC2 296 " --> pdb=" O LYSC2 292 " (cutoff:3.500A) Processing helix chain 'C2' and resid 310 through 330 Processing helix chain 'C2' and resid 343 through 359 Processing helix chain 'C2' and resid 363 through 380 Processing helix chain 'C3' and resid 26 through 46 Processing helix chain 'C3' and resid 53 through 67 Processing helix chain 'C3' and resid 69 through 88 Processing helix chain 'C3' and resid 88 through 96 Processing helix chain 'C3' and resid 100 through 123 removed outlier: 3.694A pdb=" N THRC3 104 " --> pdb=" O ASNC3 100 " (cutoff:3.500A) Processing helix chain 'C3' and resid 123 through 135 removed outlier: 4.058A pdb=" N VALC3 131 " --> pdb=" O ASPC3 127 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLNC3 132 " --> pdb=" O ARGC3 128 " (cutoff:3.500A) Processing helix chain 'C3' and resid 138 through 151 Processing helix chain 'C3' and resid 154 through 175 Processing helix chain 'C3' and resid 179 through 194 removed outlier: 4.106A pdb=" N GLYC3 194 " --> pdb=" O LEUC3 190 " (cutoff:3.500A) Processing helix chain 'C3' and resid 198 through 205 removed outlier: 3.595A pdb=" N PHEC3 205 " --> pdb=" O TYRC3 201 " (cutoff:3.500A) Processing helix chain 'C3' and resid 205 through 228 Processing helix chain 'C3' and resid 229 through 252 Processing helix chain 'C3' and resid 253 through 255 No H-bonds generated for 'chain 'C3' and resid 253 through 255' Processing helix chain 'C3' and resid 256 through 269 removed outlier: 3.966A pdb=" N ILEC3 260 " --> pdb=" O THRC3 256 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYSC3 262 " --> pdb=" O GLUC3 258 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEUC3 268 " --> pdb=" O VALC3 264 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILEC3 269 " --> pdb=" O GLUC3 265 " (cutoff:3.500A) Processing helix chain 'C3' and resid 274 through 278 Processing helix chain 'C3' and resid 283 through 290 removed outlier: 3.750A pdb=" N LYSC3 289 " --> pdb=" O VALC3 285 " (cutoff:3.500A) Processing helix chain 'C3' and resid 292 through 306 removed outlier: 3.943A pdb=" N LEUC3 296 " --> pdb=" O LYSC3 292 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARGC3 305 " --> pdb=" O LYSC3 301 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALC3 306 " --> pdb=" O LEUC3 302 " (cutoff:3.500A) Processing helix chain 'C3' and resid 308 through 330 removed outlier: 3.565A pdb=" N THRC3 312 " --> pdb=" O ASNC3 308 " (cutoff:3.500A) Processing helix chain 'C3' and resid 343 through 359 Processing helix chain 'C3' and resid 363 through 379 Processing helix chain 'C4' and resid 25 through 47 Processing helix chain 'C4' and resid 53 through 67 removed outlier: 3.625A pdb=" N LEUC4 57 " --> pdb=" O SERC4 53 " (cutoff:3.500A) Processing helix chain 'C4' and resid 69 through 99 removed outlier: 3.980A pdb=" N ARGC4 90 " --> pdb=" O ILEC4 86 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLUC4 91 " --> pdb=" O ASNC4 87 " (cutoff:3.500A) Processing helix chain 'C4' and resid 100 through 123 removed outlier: 3.601A pdb=" N LEUC4 123 " --> pdb=" O ILEC4 119 " (cutoff:3.500A) Processing helix chain 'C4' and resid 124 through 129 removed outlier: 3.591A pdb=" N VALC4 129 " --> pdb=" O TYRC4 125 " (cutoff:3.500A) Processing helix chain 'C4' and resid 129 through 134 Processing helix chain 'C4' and resid 138 through 151 Processing helix chain 'C4' and resid 154 through 175 Processing helix chain 'C4' and resid 179 through 195 removed outlier: 3.523A pdb=" N ILEC4 183 " --> pdb=" O ASPC4 179 " (cutoff:3.500A) Processing helix chain 'C4' and resid 197 through 205 removed outlier: 4.080A pdb=" N TYRC4 201 " --> pdb=" O GLYC4 197 " (cutoff:3.500A) Processing helix chain 'C4' and resid 205 through 228 Processing helix chain 'C4' and resid 229 through 252 Processing helix chain 'C4' and resid 253 through 269 removed outlier: 3.973A pdb=" N GLUC4 258 " --> pdb=" O LYSC4 254 " (cutoff:3.500A) Proline residue: C4 259 - end of helix Processing helix chain 'C4' and resid 272 through 278 removed outlier: 3.891A pdb=" N VALC4 277 " --> pdb=" O METC4 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLUC4 278 " --> pdb=" O LYSC4 274 " (cutoff:3.500A) Processing helix chain 'C4' and resid 283 through 291 removed outlier: 3.574A pdb=" N GLYC4 291 " --> pdb=" O METC4 287 " (cutoff:3.500A) Processing helix chain 'C4' and resid 292 through 306 removed outlier: 3.906A pdb=" N VALC4 306 " --> pdb=" O LEUC4 302 " (cutoff:3.500A) Processing helix chain 'C4' and resid 308 through 330 removed outlier: 3.579A pdb=" N THRC4 312 " --> pdb=" O ASNC4 308 " (cutoff:3.500A) Processing helix chain 'C4' and resid 337 through 361 removed outlier: 3.674A pdb=" N GLUC4 358 " --> pdb=" O ARGC4 354 " (cutoff:3.500A) Processing helix chain 'C4' and resid 363 through 381 removed outlier: 3.636A pdb=" N LYSC4 367 " --> pdb=" O ASPC4 363 " (cutoff:3.500A) Processing helix chain 'C5' and resid 26 through 46 Processing helix chain 'C5' and resid 53 through 67 Processing helix chain 'C5' and resid 69 through 88 Processing helix chain 'C5' and resid 88 through 96 removed outlier: 4.152A pdb=" N SERC5 96 " --> pdb=" O ASPC5 92 " (cutoff:3.500A) Processing helix chain 'C5' and resid 100 through 123 removed outlier: 4.121A pdb=" N METC5 118 " --> pdb=" O THRC5 114 " (cutoff:3.500A) Processing helix chain 'C5' and resid 123 through 134 removed outlier: 3.973A pdb=" N ASPC5 127 " --> pdb=" O LEUC5 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARGC5 128 " --> pdb=" O METC5 124 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VALC5 131 " --> pdb=" O ASPC5 127 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLNC5 132 " --> pdb=" O ARGC5 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLNC5 133 " --> pdb=" O VALC5 129 " (cutoff:3.500A) Processing helix chain 'C5' and resid 138 through 151 Processing helix chain 'C5' and resid 154 through 174 Processing helix chain 'C5' and resid 179 through 193 removed outlier: 3.770A pdb=" N ILEC5 183 " --> pdb=" O ASPC5 179 " (cutoff:3.500A) Processing helix chain 'C5' and resid 198 through 205 Processing helix chain 'C5' and resid 205 through 227 Processing helix chain 'C5' and resid 229 through 251 Processing helix chain 'C5' and resid 253 through 255 No H-bonds generated for 'chain 'C5' and resid 253 through 255' Processing helix chain 'C5' and resid 256 through 269 removed outlier: 3.714A pdb=" N ILEC5 260 " --> pdb=" O THRC5 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEC5 269 " --> pdb=" O GLUC5 265 " (cutoff:3.500A) Processing helix chain 'C5' and resid 272 through 278 Processing helix chain 'C5' and resid 283 through 291 removed outlier: 3.569A pdb=" N ASNC5 290 " --> pdb=" O HISC5 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLYC5 291 " --> pdb=" O METC5 287 " (cutoff:3.500A) Processing helix chain 'C5' and resid 292 through 305 removed outlier: 3.717A pdb=" N LEUC5 296 " --> pdb=" O LYSC5 292 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGC5 305 " --> pdb=" O LYSC5 301 " (cutoff:3.500A) Processing helix chain 'C5' and resid 308 through 330 Processing helix chain 'C5' and resid 337 through 342 Processing helix chain 'C5' and resid 342 through 359 removed outlier: 3.908A pdb=" N LEUC5 346 " --> pdb=" O ILEC5 342 " (cutoff:3.500A) Processing helix chain 'C5' and resid 363 through 380 removed outlier: 4.094A pdb=" N ASPC5 373 " --> pdb=" O THRC5 369 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUC5 380 " --> pdb=" O TYRC5 376 " (cutoff:3.500A) Processing helix chain 'B1' and resid 3 through 26 Processing helix chain 'B1' and resid 29 through 34 Processing helix chain 'B2' and resid 3 through 26 Processing helix chain 'B2' and resid 29 through 34 removed outlier: 3.572A pdb=" N ILEB2 33 " --> pdb=" O THRB2 29 " (cutoff:3.500A) Processing helix chain 'B3' and resid 3 through 25 Processing helix chain 'B3' and resid 29 through 34 Processing helix chain 'B4' and resid 3 through 25 Processing helix chain 'B4' and resid 29 through 34 removed outlier: 3.744A pdb=" N ILEB4 33 " --> pdb=" O THRB4 29 " (cutoff:3.500A) Processing helix chain 'B5' and resid 3 through 26 removed outlier: 3.527A pdb=" N GLNB5 9 " --> pdb=" O ASPB5 5 " (cutoff:3.500A) Processing helix chain 'B5' and resid 29 through 34 removed outlier: 3.527A pdb=" N ILEB5 33 " --> pdb=" O THRB5 29 " (cutoff:3.500A) Processing helix chain 'G1' and resid 8 through 25 removed outlier: 3.547A pdb=" N ILEG1 25 " --> pdb=" O METG1 21 " (cutoff:3.500A) Processing helix chain 'G1' and resid 29 through 44 Processing helix chain 'G2' and resid 8 through 24 removed outlier: 3.718A pdb=" N ALAG2 12 " --> pdb=" O SERG2 8 " (cutoff:3.500A) Processing helix chain 'G2' and resid 29 through 46 removed outlier: 4.064A pdb=" N LYSG2 46 " --> pdb=" O GLUG2 42 " (cutoff:3.500A) Processing helix chain 'G3' and resid 8 through 24 Processing helix chain 'G3' and resid 29 through 46 removed outlier: 3.682A pdb=" N ALAG3 33 " --> pdb=" O LYSG3 29 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYSG3 46 " --> pdb=" O GLUG3 42 " (cutoff:3.500A) Processing helix chain 'G4' and resid 8 through 25 removed outlier: 3.868A pdb=" N ALAG4 12 " --> pdb=" O SERG4 8 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N METG4 21 " --> pdb=" O GLUG4 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLUG4 22 " --> pdb=" O GLNG4 18 " (cutoff:3.500A) Processing helix chain 'G4' and resid 29 through 44 Processing helix chain 'G5' and resid 7 through 25 removed outlier: 4.478A pdb=" N GLNG5 11 " --> pdb=" O ALAG5 7 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N METG5 21 " --> pdb=" O GLUG5 17 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLUG5 22 " --> pdb=" O GLNG5 18 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALAG5 23 " --> pdb=" O LEUG5 19 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASNG5 24 " --> pdb=" O LYSG5 20 " (cutoff:3.500A) Processing helix chain 'G5' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'K1' and resid 53 through 58 removed outlier: 3.522A pdb=" N TYRK1 90 " --> pdb=" O ARGK1 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K1' and resid 157 through 163 removed outlier: 6.555A pdb=" N LEUK1 202 " --> pdb=" O LEUK1 184 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEUK1 184 " --> pdb=" O LEUK1 202 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VALK1 204 " --> pdb=" O GLUK1 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K2' and resid 53 through 58 removed outlier: 3.813A pdb=" N TYRK2 90 " --> pdb=" O ARGK2 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K2' and resid 155 through 163 removed outlier: 6.694A pdb=" N LEUK2 202 " --> pdb=" O LEUK2 184 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEUK2 184 " --> pdb=" O LEUK2 202 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VALK2 204 " --> pdb=" O GLUK2 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K3' and resid 53 through 58 Processing sheet with id=AA6, first strand: chain 'K3' and resid 155 through 163 removed outlier: 3.942A pdb=" N LYSK3 155 " --> pdb=" O LEUK3 209 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEUK3 202 " --> pdb=" O LEUK3 184 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEUK3 184 " --> pdb=" O LEUK3 202 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VALK3 204 " --> pdb=" O GLUK3 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K4' and resid 53 through 58 removed outlier: 7.454A pdb=" N ILEK4 92 " --> pdb=" O ARGK4 47 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASNK4 49 " --> pdb=" O ILEK4 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K4' and resid 157 through 162 removed outlier: 6.437A pdb=" N LEUK4 202 " --> pdb=" O LEUK4 184 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEUK4 184 " --> pdb=" O LEUK4 202 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALK4 204 " --> pdb=" O GLUK4 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K5' and resid 53 through 58 removed outlier: 4.071A pdb=" N TYRK5 90 " --> pdb=" O ARGK5 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILEK5 92 " --> pdb=" O ASNK5 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K5' and resid 156 through 163 removed outlier: 3.503A pdb=" N GLNK5 183 " --> pdb=" O VALK5 204 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SERK5 206 " --> pdb=" O PHEK5 181 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHEK5 181 " --> pdb=" O SERK5 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C1' and resid 278 through 279 Processing sheet with id=AB3, first strand: chain 'C2' and resid 278 through 279 removed outlier: 3.549A pdb=" N METC2 279 " --> pdb=" O SERC2 282 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SERC2 282 " --> pdb=" O METC2 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B1' and resid 47 through 52 removed outlier: 3.757A pdb=" N ARGB1 49 " --> pdb=" O ILEB1 338 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEUB1 336 " --> pdb=" O LEUB1 51 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHEB1 335 " --> pdb=" O SERB1 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERB1 331 " --> pdb=" O PHEB1 335 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYSB1 337 " --> pdb=" O THRB1 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYSB1 317 " --> pdb=" O GLYB1 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B1' and resid 58 through 63 removed outlier: 3.938A pdb=" N ALAB1 60 " --> pdb=" O ALAB1 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYSB1 78 " --> pdb=" O SERB1 74 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HISB1 91 " --> pdb=" O ILEB1 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B1' and resid 100 through 105 removed outlier: 3.680A pdb=" N GLYB1 115 " --> pdb=" O THRB1 102 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASNB1 125 " --> pdb=" O VALB1 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VALB1 135 " --> pdb=" O ASNB1 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B1' and resid 146 through 151 removed outlier: 7.068A pdb=" N SERB1 160 " --> pdb=" O SERB1 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYSB1 149 " --> pdb=" O VALB1 158 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VALB1 158 " --> pdb=" O CYSB1 149 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHEB1 151 " --> pdb=" O GLNB1 156 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLNB1 156 " --> pdb=" O PHEB1 151 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEUB1 168 " --> pdb=" O THRB1 177 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNB1 175 " --> pdb=" O ASPB1 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B1' and resid 191 through 192 removed outlier: 6.591A pdb=" N ASPB1 212 " --> pdb=" O CYSB1 218 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYSB1 218 " --> pdb=" O ASPB1 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B1' and resid 229 through 234 removed outlier: 7.116A pdb=" N GLYB1 244 " --> pdb=" O ASNB1 230 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILEB1 232 " --> pdb=" O ALAB1 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALAB1 242 " --> pdb=" O ILEB1 232 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHEB1 234 " --> pdb=" O ALAB1 240 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALAB1 240 " --> pdb=" O PHEB1 234 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SERB1 245 " --> pdb=" O THRB1 249 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THRB1 249 " --> pdb=" O SERB1 245 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYSB1 250 " --> pdb=" O THRB1 263 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THRB1 263 " --> pdb=" O CYSB1 250 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEUB1 252 " --> pdb=" O LEUB1 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B1' and resid 273 through 278 removed outlier: 3.629A pdb=" N SERB1 275 " --> pdb=" O GLYB1 288 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYSB1 294 " --> pdb=" O LEUB1 308 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASPB1 298 " --> pdb=" O ARGB1 304 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARGB1 304 " --> pdb=" O ASPB1 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 46 through 52 removed outlier: 5.178A pdb=" N THRB2 47 " --> pdb=" O ASNB2 340 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASNB2 340 " --> pdb=" O THRB2 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUB2 336 " --> pdb=" O LEUB2 51 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHEB2 335 " --> pdb=" O SERB2 331 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SERB2 331 " --> pdb=" O PHEB2 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSB2 337 " --> pdb=" O THRB2 329 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALAB2 328 " --> pdb=" O LEUB2 318 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEUB2 318 " --> pdb=" O ALAB2 328 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLYB2 330 " --> pdb=" O SERB2 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 58 through 63 removed outlier: 6.990A pdb=" N ALAB2 73 " --> pdb=" O TYRB2 59 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N METB2 61 " --> pdb=" O VALB2 71 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VALB2 71 " --> pdb=" O METB2 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRPB2 63 " --> pdb=" O LEUB2 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEUB2 69 " --> pdb=" O TRPB2 63 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYSB2 78 " --> pdb=" O SERB2 74 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEUB2 79 " --> pdb=" O ALAB2 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALAB2 92 " --> pdb=" O LEUB2 79 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILEB2 81 " --> pdb=" O VALB2 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B2' and resid 100 through 105 removed outlier: 5.558A pdb=" N ASNB2 125 " --> pdb=" O VALB2 135 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VALB2 135 " --> pdb=" O ASNB2 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B2' and resid 146 through 153 removed outlier: 6.585A pdb=" N SERB2 160 " --> pdb=" O SERB2 147 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYSB2 149 " --> pdb=" O VALB2 158 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VALB2 158 " --> pdb=" O CYSB2 149 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHEB2 151 " --> pdb=" O GLNB2 156 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLNB2 156 " --> pdb=" O PHEB2 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B2' and resid 198 through 202 removed outlier: 4.146A pdb=" N PHEB2 199 " --> pdb=" O TRPB2 211 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALAB2 208 " --> pdb=" O THRB2 221 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THRB2 221 " --> pdb=" O ALAB2 208 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUB2 210 " --> pdb=" O ARGB2 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N METB2 217 " --> pdb=" O ASPB2 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B2' and resid 229 through 234 removed outlier: 6.480A pdb=" N ASPB2 254 " --> pdb=" O GLUB2 260 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLUB2 260 " --> pdb=" O ASPB2 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B2' and resid 273 through 278 removed outlier: 3.868A pdb=" N SERB2 275 " --> pdb=" O GLYB2 288 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASPB2 298 " --> pdb=" O ARGB2 304 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARGB2 304 " --> pdb=" O ASPB2 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 47 through 52 removed outlier: 6.303A pdb=" N ILEB3 338 " --> pdb=" O ARGB3 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THRB3 50 " --> pdb=" O LEUB3 336 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEUB3 336 " --> pdb=" O THRB3 50 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHEB3 335 " --> pdb=" O SERB3 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYSB3 337 " --> pdb=" O THRB3 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALAB3 328 " --> pdb=" O GLYB3 319 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLYB3 319 " --> pdb=" O ALAB3 328 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 58 through 62 removed outlier: 4.109A pdb=" N ALAB3 60 " --> pdb=" O ALAB3 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEUB3 79 " --> pdb=" O ALAB3 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALAB3 92 " --> pdb=" O LEUB3 79 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILEB3 81 " --> pdb=" O VALB3 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 100 through 105 removed outlier: 3.503A pdb=" N THRB3 102 " --> pdb=" O GLYB3 115 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLYB3 116 " --> pdb=" O ILEB3 120 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILEB3 120 " --> pdb=" O GLYB3 116 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYSB3 121 " --> pdb=" O GLUB3 138 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLUB3 138 " --> pdb=" O CYSB3 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEB3 123 " --> pdb=" O SERB3 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGB3 134 " --> pdb=" O ASNB3 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 149 through 151 Processing sheet with id=AD4, first strand: chain 'B3' and resid 198 through 202 Processing sheet with id=AD5, first strand: chain 'B3' and resid 229 through 234 removed outlier: 7.135A pdb=" N GLYB3 244 " --> pdb=" O ASNB3 230 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILEB3 232 " --> pdb=" O ALAB3 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALAB3 242 " --> pdb=" O ILEB3 232 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHEB3 234 " --> pdb=" O ALAB3 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALAB3 240 " --> pdb=" O PHEB3 234 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYSB3 250 " --> pdb=" O THRB3 263 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THRB3 263 " --> pdb=" O CYSB3 250 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEUB3 252 " --> pdb=" O LEUB3 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B3' and resid 273 through 278 removed outlier: 3.642A pdb=" N SERB3 275 " --> pdb=" O GLYB3 288 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASPB3 298 " --> pdb=" O ARGB3 304 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARGB3 304 " --> pdb=" O ASPB3 298 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B4' and resid 46 through 50 removed outlier: 6.048A pdb=" N THRB4 47 " --> pdb=" O ASNB4 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASNB4 340 " --> pdb=" O THRB4 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARGB4 49 " --> pdb=" O ILEB4 338 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYSB4 337 " --> pdb=" O THRB4 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B4' and resid 58 through 62 removed outlier: 3.567A pdb=" N ALAB4 60 " --> pdb=" O ALAB4 73 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEUB4 79 " --> pdb=" O ALAB4 92 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALAB4 92 " --> pdb=" O LEUB4 79 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILEB4 81 " --> pdb=" O VALB4 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B4' and resid 102 through 105 removed outlier: 3.618A pdb=" N THRB4 102 " --> pdb=" O GLYB4 115 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N CYSB4 121 " --> pdb=" O GLUB4 138 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLUB4 138 " --> pdb=" O CYSB4 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEB4 123 " --> pdb=" O SERB4 136 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGB4 134 " --> pdb=" O ASNB4 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 146 through 151 removed outlier: 6.835A pdb=" N SERB4 160 " --> pdb=" O SERB4 147 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYSB4 149 " --> pdb=" O VALB4 158 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VALB4 158 " --> pdb=" O CYSB4 149 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHEB4 151 " --> pdb=" O GLNB4 156 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLNB4 156 " --> pdb=" O PHEB4 151 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEUB4 168 " --> pdb=" O THRB4 177 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B4' and resid 191 through 192 Processing sheet with id=AE3, first strand: chain 'B4' and resid 229 through 234 removed outlier: 3.835A pdb=" N ALAB4 231 " --> pdb=" O GLYB4 244 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SERB4 245 " --> pdb=" O THRB4 249 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THRB4 249 " --> pdb=" O SERB4 245 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYSB4 250 " --> pdb=" O THRB4 263 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THRB4 263 " --> pdb=" O CYSB4 250 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEUB4 252 " --> pdb=" O LEUB4 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B4' and resid 273 through 278 removed outlier: 3.544A pdb=" N SERB4 277 " --> pdb=" O LEUB4 286 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASPB4 298 " --> pdb=" O ARGB4 304 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARGB4 304 " --> pdb=" O ASPB4 298 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B5' and resid 46 through 51 removed outlier: 6.540A pdb=" N ILEB5 338 " --> pdb=" O ARGB5 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THRB5 50 " --> pdb=" O LEUB5 336 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEUB5 336 " --> pdb=" O THRB5 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSB5 337 " --> pdb=" O THRB5 329 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 58 through 63 removed outlier: 6.899A pdb=" N ALAB5 73 " --> pdb=" O TYRB5 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N METB5 61 " --> pdb=" O VALB5 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VALB5 71 " --> pdb=" O METB5 61 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRPB5 63 " --> pdb=" O LEUB5 69 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEUB5 69 " --> pdb=" O TRPB5 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYSB5 78 " --> pdb=" O SERB5 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HISB5 91 " --> pdb=" O ILEB5 81 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASPB5 83 " --> pdb=" O LYSB5 89 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYSB5 89 " --> pdb=" O ASPB5 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B5' and resid 100 through 105 removed outlier: 6.822A pdb=" N GLYB5 115 " --> pdb=" O METB5 101 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYSB5 103 " --> pdb=" O ALAB5 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALAB5 113 " --> pdb=" O CYSB5 103 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYRB5 105 " --> pdb=" O TYRB5 111 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYRB5 111 " --> pdb=" O TYRB5 105 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASNB5 125 " --> pdb=" O VALB5 135 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VALB5 135 " --> pdb=" O ASNB5 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 148 through 151 removed outlier: 3.533A pdb=" N CYSB5 148 " --> pdb=" O SERB5 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEUB5 168 " --> pdb=" O THRB5 177 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 187 through 192 removed outlier: 6.090A pdb=" N ASPB5 212 " --> pdb=" O CYSB5 218 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYSB5 218 " --> pdb=" O ASPB5 212 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B5' and resid 229 through 234 removed outlier: 3.587A pdb=" N ALAB5 231 " --> pdb=" O GLYB5 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N METB5 262 " --> pdb=" O LEUB5 252 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASPB5 254 " --> pdb=" O GLUB5 260 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLUB5 260 " --> pdb=" O ASPB5 254 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B5' and resid 273 through 278 removed outlier: 3.606A pdb=" N SERB5 275 " --> pdb=" O GLYB5 288 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASPB5 298 " --> pdb=" O ARGB5 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARGB5 304 " --> pdb=" O ASPB5 298 " (cutoff:3.500A) 1954 hydrogen bonds defined for protein. 5703 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: 13.57 Time building geometry restraints manager: 15.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10391 1.33 - 1.46: 8202 1.46 - 1.58: 19497 1.58 - 1.71: 0 1.71 - 1.83: 425 Bond restraints: 38515 Sorted by residual: bond pdb=" N VALK1 154 " pdb=" CA VALK1 154 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.84e+00 bond pdb=" N VALK2 154 " pdb=" CA VALK2 154 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.54e+00 bond pdb=" N VALK2 152 " pdb=" CA VALK2 152 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.03e+00 bond pdb=" N ILEC2 260 " pdb=" CA ILEC2 260 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N ILEC1 192 " pdb=" CA ILEC1 192 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.11e+00 ... (remaining 38510 not shown) Histogram of bond angle deviations from ideal: 94.49 - 102.42: 151 102.42 - 110.36: 7890 110.36 - 118.29: 21621 118.29 - 126.22: 21881 126.22 - 134.16: 442 Bond angle restraints: 51985 Sorted by residual: angle pdb=" N PROK1 213 " pdb=" CA PROK1 213 " pdb=" C PROK1 213 " ideal model delta sigma weight residual 113.75 106.17 7.58 1.49e+00 4.50e-01 2.59e+01 angle pdb=" N LEUC1 193 " pdb=" CA LEUC1 193 " pdb=" C LEUC1 193 " ideal model delta sigma weight residual 111.71 105.90 5.81 1.15e+00 7.56e-01 2.55e+01 angle pdb=" N ASPB5 323 " pdb=" CA ASPB5 323 " pdb=" C ASPB5 323 " ideal model delta sigma weight residual 114.39 107.45 6.94 1.45e+00 4.76e-01 2.29e+01 angle pdb=" CA METK2 171 " pdb=" CB METK2 171 " pdb=" CG METK2 171 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" N GLUC4 196 " pdb=" CA GLUC4 196 " pdb=" C GLUC4 196 " ideal model delta sigma weight residual 114.16 107.25 6.91 1.48e+00 4.57e-01 2.18e+01 ... (remaining 51980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20730 17.99 - 35.98: 1959 35.98 - 53.97: 392 53.97 - 71.95: 200 71.95 - 89.94: 99 Dihedral angle restraints: 23380 sinusoidal: 9495 harmonic: 13885 Sorted by residual: dihedral pdb=" CD ARGK3 64 " pdb=" NE ARGK3 64 " pdb=" CZ ARGK3 64 " pdb=" NH1 ARGK3 64 " ideal model delta sinusoidal sigma weight residual 0.00 76.96 -76.96 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CA SERB4 74 " pdb=" C SERB4 74 " pdb=" N GLNB4 75 " pdb=" CA GLNB4 75 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASPK3 197 " pdb=" C ASPK3 197 " pdb=" N GLNK3 198 " pdb=" CA GLNK3 198 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 23377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5001 0.066 - 0.131: 717 0.131 - 0.197: 54 0.197 - 0.263: 6 0.263 - 0.329: 2 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CG LEUC3 348 " pdb=" CB LEUC3 348 " pdb=" CD1 LEUC3 348 " pdb=" CD2 LEUC3 348 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILEK4 131 " pdb=" CA ILEK4 131 " pdb=" CG1 ILEK4 131 " pdb=" CG2 ILEK4 131 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEUC3 36 " pdb=" CB LEUC3 36 " pdb=" CD1 LEUC3 36 " pdb=" CD2 LEUC3 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5777 not shown) Planarity restraints: 6775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGK3 64 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARGK3 64 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARGK3 64 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARGK3 64 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARGK3 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC5 184 " -0.405 9.50e-02 1.11e+02 1.82e-01 2.06e+01 pdb=" NE ARGC5 184 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARGC5 184 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARGC5 184 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARGC5 184 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLUC1 258 " 0.066 5.00e-02 4.00e+02 9.89e-02 1.56e+01 pdb=" N PROC1 259 " -0.171 5.00e-02 4.00e+02 pdb=" CA PROC1 259 " 0.050 5.00e-02 4.00e+02 pdb=" CD PROC1 259 " 0.054 5.00e-02 4.00e+02 ... (remaining 6772 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 806 2.68 - 3.24: 40181 3.24 - 3.79: 64283 3.79 - 4.35: 88437 4.35 - 4.90: 138513 Nonbonded interactions: 332220 Sorted by model distance: nonbonded pdb=" OG1 THRC5 293 " pdb=" OG SERC5 359 " model vdw 2.125 2.440 nonbonded pdb=" OG SERC5 221 " pdb=" OE1 GLNC5 222 " model vdw 2.137 2.440 nonbonded pdb=" OH TYRC1 300 " pdb=" OD2 ASPC1 363 " model vdw 2.155 2.440 nonbonded pdb=" O GLUC4 238 " pdb=" ND2 ASNC4 242 " model vdw 2.157 2.520 nonbonded pdb=" O GLUG1 42 " pdb=" NZ LYSG1 46 " model vdw 2.158 2.520 ... (remaining 332215 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 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' } ncs_group { reference = chain 'C1' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' } ncs_group { reference = chain 'G1' selection = chain 'G2' selection = chain 'G3' selection = chain 'G4' selection = chain 'G5' } ncs_group { reference = chain 'K1' selection = chain 'K2' selection = chain 'K3' selection = chain 'K4' selection = chain 'K5' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 9.140 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 94.550 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.004 0.060 38515 Z= 0.229 Angle : 0.838 13.126 51985 Z= 0.474 Chirality : 0.046 0.329 5780 Planarity : 0.008 0.478 6775 Dihedral : 16.816 89.943 14410 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.20 % Favored : 94.55 % Rotamer: Outliers : 0.62 % Allowed : 16.69 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4730 helix: 0.62 (0.11), residues: 2053 sheet: -1.13 (0.20), residues: 661 loop : -1.71 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPC5 109 HIS 0.018 0.002 HISC5 67 PHE 0.051 0.002 PHEC4 377 TYR 0.040 0.002 TYRC2 62 ARG 0.014 0.001 ARGC4 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 292 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K1 69 PHE cc_start: 0.8457 (t80) cc_final: 0.8225 (t80) REVERT: K1 155 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: K1 201 PHE cc_start: 0.8558 (m-80) cc_final: 0.8323 (m-80) REVERT: K2 79 ASP cc_start: 0.4204 (OUTLIER) cc_final: 0.2704 (m-30) REVERT: K2 80 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6890 (pp) REVERT: K3 64 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6961 (ttp80) REVERT: K3 134 LEU cc_start: 0.9166 (mt) cc_final: 0.8797 (pp) REVERT: K4 129 TYR cc_start: 0.6976 (m-80) cc_final: 0.6242 (m-80) REVERT: C3 64 MET cc_start: 0.2495 (tpt) cc_final: 0.2236 (tpt) REVERT: C3 128 ARG cc_start: 0.8571 (ttt180) cc_final: 0.7537 (ptp-170) REVERT: C4 116 MET cc_start: -0.3436 (ttp) cc_final: -0.4280 (tpp) REVERT: C5 124 MET cc_start: 0.8922 (mtm) cc_final: 0.8517 (mtt) REVERT: C5 317 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4811 (mmp) REVERT: B1 217 MET cc_start: 0.8839 (ppp) cc_final: 0.8528 (ppp) REVERT: B5 325 MET cc_start: 0.9008 (tpt) cc_final: 0.8533 (tpp) REVERT: G1 1 MET cc_start: 0.7768 (tpp) cc_final: 0.7464 (tpp) outliers start: 26 outliers final: 7 residues processed: 310 average time/residue: 0.5001 time to fit residues: 255.0080 Evaluate side-chains 272 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 260 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 80 LEU Chi-restraints excluded: chain K2 residue 151 GLN Chi-restraints excluded: chain K2 residue 155 LYS Chi-restraints excluded: chain K3 residue 64 ARG Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 261 VAL Chi-restraints excluded: chain C5 residue 188 GLN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 317 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 422 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 75 GLN K1 151 GLN K1 211 ASN K2 75 GLN ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 162 GLN K5 211 ASN ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 42 GLN ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 132 GLN ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 343 GLN C2 379 ASN ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 324 GLN C5 45 GLN C5 272 HIS ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 313 ASN ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 32 GLN ** B2 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 220 GLN ** B3 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 237 ASN ** B4 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 17 GLN ** B5 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 220 GLN G1 4 ASN ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 38515 Z= 0.339 Angle : 0.742 11.671 51985 Z= 0.397 Chirality : 0.044 0.204 5780 Planarity : 0.005 0.063 6775 Dihedral : 6.408 87.603 5255 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 3.00 % Allowed : 14.94 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4730 helix: 0.74 (0.11), residues: 2117 sheet: -1.34 (0.18), residues: 735 loop : -1.59 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRPC2 109 HIS 0.016 0.002 HISC5 67 PHE 0.040 0.003 PHEC4 377 TYR 0.032 0.002 TYRC4 341 ARG 0.007 0.001 ARGC1 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 266 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K2 79 ASP cc_start: 0.4267 (OUTLIER) cc_final: 0.3665 (m-30) REVERT: K5 171 MET cc_start: 0.9256 (ptp) cc_final: 0.8824 (ptp) REVERT: C1 254 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8473 (mmpt) REVERT: C1 299 MET cc_start: 0.5405 (mmt) cc_final: 0.5158 (mmt) REVERT: C3 64 MET cc_start: 0.2355 (tpt) cc_final: 0.2009 (tpt) REVERT: C3 99 ASN cc_start: 0.8765 (p0) cc_final: 0.8525 (t0) REVERT: C3 118 MET cc_start: 0.9193 (tpt) cc_final: 0.8991 (tpt) REVERT: C3 124 MET cc_start: 0.6922 (mtt) cc_final: 0.6693 (mtt) REVERT: C3 128 ARG cc_start: 0.8682 (ttt180) cc_final: 0.7836 (ptm160) REVERT: C4 63 THR cc_start: 0.8929 (p) cc_final: 0.8168 (p) REVERT: C4 64 MET cc_start: 0.6136 (mmt) cc_final: 0.4776 (ttt) REVERT: C4 126 MET cc_start: 0.6215 (ttm) cc_final: 0.5950 (tpp) REVERT: C4 287 MET cc_start: -0.0582 (mmt) cc_final: -0.1351 (mmt) REVERT: C5 124 MET cc_start: 0.8988 (mtm) cc_final: 0.8622 (mtt) REVERT: C5 317 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5883 (mmp) REVERT: B2 45 MET cc_start: 0.8400 (tpt) cc_final: 0.8093 (tpp) REVERT: B3 225 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7486 (t-90) REVERT: B3 227 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7931 (p) REVERT: B4 36 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B4 183 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.6131 (t-90) REVERT: B4 188 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8358 (ppp) REVERT: B5 36 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7659 (p0) REVERT: G1 21 MET cc_start: 0.9348 (mpp) cc_final: 0.9105 (mpp) REVERT: G2 1 MET cc_start: 0.7933 (tpt) cc_final: 0.6957 (tmm) REVERT: G4 1 MET cc_start: 0.8181 (ppp) cc_final: 0.7893 (ppp) outliers start: 125 outliers final: 59 residues processed: 362 average time/residue: 0.4737 time to fit residues: 287.6154 Evaluate side-chains 310 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 242 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 157 VAL Chi-restraints excluded: chain K2 residue 204 VAL Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 261 VAL Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B2 residue 325 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 74 SER Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 227 SER Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B4 residue 36 ASN Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 266 HIS Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 320 VAL Chi-restraints excluded: chain B5 residue 36 ASN Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G1 residue 38 MET Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 423 optimal weight: 0.7980 chunk 456 optimal weight: 30.0000 chunk 376 optimal weight: 0.5980 chunk 419 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 49 ASN ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 222 GLN C1 272 HIS ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 163 GLN ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 379 ASN ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS C4 324 GLN ** C5 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 361 ASN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 237 ASN B4 259 GLN ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 259 GLN G1 4 ASN G4 18 GLN ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 38515 Z= 0.239 Angle : 0.634 11.878 51985 Z= 0.340 Chirality : 0.041 0.270 5780 Planarity : 0.004 0.072 6775 Dihedral : 5.887 89.605 5236 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 2.64 % Allowed : 17.15 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4730 helix: 0.95 (0.11), residues: 2130 sheet: -1.26 (0.18), residues: 738 loop : -1.51 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPC1 109 HIS 0.015 0.001 HISC5 67 PHE 0.037 0.002 PHEC4 377 TYR 0.026 0.002 TYRC4 341 ARG 0.008 0.001 ARGC1 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 256 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K1 162 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: K2 79 ASP cc_start: 0.4147 (OUTLIER) cc_final: 0.3545 (m-30) REVERT: K4 129 TYR cc_start: 0.6680 (m-80) cc_final: 0.6021 (m-80) REVERT: K5 171 MET cc_start: 0.9215 (ptp) cc_final: 0.8753 (ptp) REVERT: C1 25 MET cc_start: 0.4446 (tpp) cc_final: 0.3586 (tmm) REVERT: C1 109 TRP cc_start: 0.8492 (t60) cc_final: 0.7891 (t60) REVERT: C1 189 MET cc_start: 0.9174 (mtt) cc_final: 0.8521 (mtt) REVERT: C2 64 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.5053 (tpp) REVERT: C3 64 MET cc_start: 0.1850 (tpt) cc_final: 0.1456 (tpt) REVERT: C3 128 ARG cc_start: 0.8781 (ttt180) cc_final: 0.8061 (ptm-80) REVERT: C4 126 MET cc_start: 0.6334 (ttm) cc_final: 0.6033 (tpp) REVERT: C4 287 MET cc_start: -0.0129 (mmt) cc_final: -0.1424 (mmt) REVERT: C5 116 MET cc_start: 0.1002 (ttt) cc_final: 0.0465 (ttm) REVERT: C5 124 MET cc_start: 0.8937 (mtm) cc_final: 0.8532 (mtp) REVERT: C5 317 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6031 (mmp) REVERT: B1 61 MET cc_start: 0.7705 (ppp) cc_final: 0.7462 (ppp) REVERT: B4 36 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7059 (p0) REVERT: B5 325 MET cc_start: 0.9011 (tpt) cc_final: 0.8627 (tpp) REVERT: G1 1 MET cc_start: 0.8343 (tpp) cc_final: 0.8122 (tpp) REVERT: G2 1 MET cc_start: 0.8176 (tpt) cc_final: 0.7232 (tmm) REVERT: G3 21 MET cc_start: 0.9380 (mpp) cc_final: 0.9168 (mpp) REVERT: G4 1 MET cc_start: 0.8318 (ppp) cc_final: 0.8023 (ppp) outliers start: 110 outliers final: 72 residues processed: 342 average time/residue: 0.4587 time to fit residues: 261.3252 Evaluate side-chains 317 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 240 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C2 residue 64 MET Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 163 GLN Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 163 GLN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B2 residue 325 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B4 residue 36 ASN Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 163 ASP Chi-restraints excluded: chain B4 residue 266 HIS Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 9.9990 chunk 318 optimal weight: 0.6980 chunk 219 optimal weight: 40.0000 chunk 46 optimal weight: 9.9990 chunk 201 optimal weight: 0.6980 chunk 284 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 449 optimal weight: 8.9990 chunk 221 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 overall best weight: 6.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 183 GLN K2 130 ASN ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 156 HIS K5 164 GLN ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 103 GLN C1 141 ASN ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 163 GLN ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 106 ASN ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 381 ASN ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 75 GLN ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 11 GLN ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 38515 Z= 0.304 Angle : 0.669 10.713 51985 Z= 0.359 Chirality : 0.042 0.286 5780 Planarity : 0.004 0.063 6775 Dihedral : 5.854 86.775 5235 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.45 % Rotamer: Outliers : 3.62 % Allowed : 16.69 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4730 helix: 0.88 (0.11), residues: 2128 sheet: -1.28 (0.18), residues: 743 loop : -1.45 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPB5 211 HIS 0.017 0.002 HISC5 67 PHE 0.037 0.002 PHEC4 377 TYR 0.025 0.002 TYRC4 341 ARG 0.007 0.001 ARGB2 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 247 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K1 162 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: K2 79 ASP cc_start: 0.4282 (OUTLIER) cc_final: 0.3773 (m-30) REVERT: K4 129 TYR cc_start: 0.6749 (m-80) cc_final: 0.6007 (m-80) REVERT: K5 171 MET cc_start: 0.9290 (ptp) cc_final: 0.8814 (ptp) REVERT: C1 28 LYS cc_start: 0.9672 (tppt) cc_final: 0.9399 (tptp) REVERT: C1 109 TRP cc_start: 0.8481 (t60) cc_final: 0.7403 (t60) REVERT: C2 100 ASN cc_start: 0.8936 (m-40) cc_final: 0.8542 (t0) REVERT: C3 25 MET cc_start: 0.3835 (ppp) cc_final: 0.2729 (pmm) REVERT: C3 64 MET cc_start: 0.1816 (tpt) cc_final: 0.1359 (tpt) REVERT: C3 118 MET cc_start: 0.9469 (mmm) cc_final: 0.8932 (tpt) REVERT: C3 124 MET cc_start: 0.7060 (mtt) cc_final: 0.6285 (mtt) REVERT: C3 128 ARG cc_start: 0.8862 (ttt180) cc_final: 0.7903 (ptm-80) REVERT: C4 287 MET cc_start: -0.0315 (mmt) cc_final: -0.1108 (mmt) REVERT: C5 124 MET cc_start: 0.8955 (mtm) cc_final: 0.8489 (mtp) REVERT: C5 317 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6399 (mmp) REVERT: B4 183 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6307 (t-90) REVERT: B4 200 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7945 (p) REVERT: B4 262 MET cc_start: 0.8155 (tpp) cc_final: 0.7859 (tpp) REVERT: B5 36 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7901 (p0) REVERT: G1 1 MET cc_start: 0.8396 (tpp) cc_final: 0.8027 (ttm) REVERT: G2 1 MET cc_start: 0.8567 (tpt) cc_final: 0.7529 (tmm) REVERT: G4 1 MET cc_start: 0.8537 (ppp) cc_final: 0.8131 (ppp) outliers start: 151 outliers final: 103 residues processed: 367 average time/residue: 0.4663 time to fit residues: 287.5642 Evaluate side-chains 343 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 234 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 204 VAL Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K3 residue 191 TYR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 287 MET Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 163 GLN Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 101 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B2 residue 325 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 74 SER Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 163 ASP Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B5 residue 36 ASN Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G4 residue 57 SER Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 10.0000 chunk 255 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 185 optimal weight: 40.0000 chunk 383 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 229 optimal weight: 30.0000 chunk 403 optimal weight: 3.9990 chunk 113 optimal weight: 0.0570 overall best weight: 5.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 104 ASN ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 130 ASN ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 343 GLN ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 222 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38515 Z= 0.275 Angle : 0.663 11.488 51985 Z= 0.351 Chirality : 0.042 0.255 5780 Planarity : 0.004 0.061 6775 Dihedral : 5.755 84.304 5231 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 3.72 % Allowed : 17.79 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4730 helix: 0.86 (0.11), residues: 2141 sheet: -1.44 (0.18), residues: 728 loop : -1.33 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPB5 211 HIS 0.019 0.002 HISC5 67 PHE 0.041 0.002 PHEC4 377 TYR 0.024 0.002 TYRC4 341 ARG 0.008 0.001 ARGC1 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 248 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K4 129 TYR cc_start: 0.6808 (m-80) cc_final: 0.6095 (m-80) REVERT: K5 171 MET cc_start: 0.9282 (ptp) cc_final: 0.8813 (ptp) REVERT: C1 28 LYS cc_start: 0.9685 (tppt) cc_final: 0.9475 (tptp) REVERT: C1 254 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8532 (mmpt) REVERT: C1 299 MET cc_start: 0.5581 (tpt) cc_final: 0.5309 (tpt) REVERT: C2 64 MET cc_start: 0.5680 (ttt) cc_final: 0.5130 (tpp) REVERT: C2 100 ASN cc_start: 0.8966 (m-40) cc_final: 0.8529 (t0) REVERT: C2 191 MET cc_start: 0.8370 (mmm) cc_final: 0.7910 (mmm) REVERT: C3 25 MET cc_start: 0.3811 (ppp) cc_final: 0.2750 (pmm) REVERT: C3 64 MET cc_start: 0.1729 (tpt) cc_final: 0.1273 (tpt) REVERT: C3 118 MET cc_start: 0.9429 (mmm) cc_final: 0.8870 (tpt) REVERT: C3 124 MET cc_start: 0.6820 (mtt) cc_final: 0.6459 (mtt) REVERT: C3 128 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8010 (ptm-80) REVERT: C4 64 MET cc_start: 0.5977 (mmt) cc_final: 0.5063 (mmm) REVERT: C4 126 MET cc_start: 0.6316 (tpp) cc_final: 0.5883 (tpp) REVERT: C4 287 MET cc_start: 0.0373 (mmt) cc_final: -0.0624 (mmt) REVERT: C5 116 MET cc_start: 0.2464 (ttt) cc_final: 0.2001 (ttm) REVERT: C5 124 MET cc_start: 0.8965 (mtm) cc_final: 0.8491 (mtp) REVERT: C5 317 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6526 (mmp) REVERT: B2 125 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8092 (p0) REVERT: B2 188 MET cc_start: 0.9109 (ppp) cc_final: 0.8509 (ppp) REVERT: B4 183 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6278 (t-90) REVERT: B4 188 MET cc_start: 0.8753 (ptm) cc_final: 0.8204 (ppp) REVERT: B4 200 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (p) REVERT: B5 36 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B5 119 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.6669 (m-40) REVERT: B5 146 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7883 (mp) REVERT: G1 1 MET cc_start: 0.8422 (tpp) cc_final: 0.8041 (ttm) REVERT: G4 1 MET cc_start: 0.8546 (ppp) cc_final: 0.8051 (ppp) outliers start: 155 outliers final: 106 residues processed: 374 average time/residue: 0.4969 time to fit residues: 313.9659 Evaluate side-chains 349 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 235 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 205 VAL Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K3 residue 191 TYR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 181 THR Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 246 ASP Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 125 ASN Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B2 residue 325 MET Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 338 ILE Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B4 residue 303 ASP Chi-restraints excluded: chain B5 residue 36 ASN Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 187 VAL Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G3 residue 26 ASP Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 40.0000 chunk 404 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 449 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 151 GLN K4 49 ASN K4 75 GLN ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 103 GLN C2 106 ASN ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 185 ASN ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4 362 ASN ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 150 GLN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 222 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 38515 Z= 0.353 Angle : 0.729 11.517 51985 Z= 0.386 Chirality : 0.043 0.230 5780 Planarity : 0.005 0.071 6775 Dihedral : 5.898 84.639 5227 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.19 % Favored : 92.71 % Rotamer: Outliers : 4.00 % Allowed : 18.35 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4730 helix: 0.63 (0.11), residues: 2147 sheet: -1.48 (0.18), residues: 737 loop : -1.47 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPB5 99 HIS 0.019 0.002 HISC5 67 PHE 0.040 0.003 PHEC4 377 TYR 0.023 0.002 TYRC4 341 ARG 0.010 0.001 ARGC1 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 243 time to evaluate : 4.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K4 71 TYR cc_start: 0.8656 (t80) cc_final: 0.8176 (m-80) REVERT: K5 171 MET cc_start: 0.9319 (ptp) cc_final: 0.8857 (ptp) REVERT: C1 254 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8518 (mmpt) REVERT: C1 287 MET cc_start: 0.5925 (mmp) cc_final: 0.5660 (mmp) REVERT: C2 100 ASN cc_start: 0.9005 (m-40) cc_final: 0.8587 (t0) REVERT: C3 25 MET cc_start: 0.3920 (ppp) cc_final: 0.2694 (pmm) REVERT: C3 64 MET cc_start: 0.2103 (tpt) cc_final: 0.1813 (tpt) REVERT: C3 118 MET cc_start: 0.9392 (mmm) cc_final: 0.8820 (tpt) REVERT: C3 124 MET cc_start: 0.6769 (mtt) cc_final: 0.6552 (mtt) REVERT: C4 64 MET cc_start: 0.6083 (mmt) cc_final: 0.5134 (mmm) REVERT: C4 287 MET cc_start: 0.1326 (mmt) cc_final: 0.0055 (mmt) REVERT: C5 124 MET cc_start: 0.9054 (mtm) cc_final: 0.8662 (mtp) REVERT: C5 317 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7068 (mmt) REVERT: C5 351 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6495 (ttt90) REVERT: B1 325 MET cc_start: 0.8568 (ppp) cc_final: 0.7428 (ppp) REVERT: B2 125 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7949 (p0) REVERT: B2 188 MET cc_start: 0.9153 (ppp) cc_final: 0.8609 (ppp) REVERT: B4 105 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7329 (t80) REVERT: B4 183 HIS cc_start: 0.6560 (OUTLIER) cc_final: 0.6335 (t-90) REVERT: B4 200 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7874 (p) REVERT: B4 325 MET cc_start: 0.8427 (ttt) cc_final: 0.7924 (ptm) REVERT: B5 36 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7841 (p0) REVERT: B5 119 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.6644 (m-40) REVERT: B5 146 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7834 (mp) REVERT: B5 325 MET cc_start: 0.9035 (tpt) cc_final: 0.8811 (tpp) REVERT: G4 1 MET cc_start: 0.8651 (ppp) cc_final: 0.8127 (ppp) outliers start: 167 outliers final: 114 residues processed: 384 average time/residue: 0.4664 time to fit residues: 298.4590 Evaluate side-chains 348 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 224 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K3 residue 191 TYR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 48 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 132 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 293 THR Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 192 ILE Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 100 ASN Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 67 HIS Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 351 ARG Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 181 THR Chi-restraints excluded: chain B1 residue 246 ASP Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 101 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 125 ASN Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 293 ASN Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B3 residue 338 ILE Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B4 residue 303 ASP Chi-restraints excluded: chain B5 residue 36 ASN Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 274 THR Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G2 residue 9 ILE Chi-restraints excluded: chain G3 residue 26 ASP Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 chunk 378 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 448 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 206 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 151 GLN ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 222 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN B3 266 HIS ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38515 Z= 0.272 Angle : 0.681 13.592 51985 Z= 0.359 Chirality : 0.042 0.239 5780 Planarity : 0.004 0.058 6775 Dihedral : 5.680 83.586 5223 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 3.74 % Allowed : 19.33 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4730 helix: 0.77 (0.11), residues: 2139 sheet: -1.48 (0.18), residues: 737 loop : -1.37 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPC1 109 HIS 0.018 0.002 HISC5 67 PHE 0.044 0.002 PHEC4 377 TYR 0.034 0.002 TYRB3 85 ARG 0.009 0.001 ARGC1 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 244 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K4 71 TYR cc_start: 0.8739 (t80) cc_final: 0.8270 (m-80) REVERT: K5 171 MET cc_start: 0.9276 (ptp) cc_final: 0.8817 (ptp) REVERT: C1 64 MET cc_start: 0.7734 (ttm) cc_final: 0.7368 (tpp) REVERT: C1 254 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8559 (mmpt) REVERT: C2 100 ASN cc_start: 0.9005 (m-40) cc_final: 0.8591 (t0) REVERT: C2 180 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8288 (mtt90) REVERT: C3 25 MET cc_start: 0.3842 (ppp) cc_final: 0.2754 (pmm) REVERT: C3 64 MET cc_start: 0.2057 (tpt) cc_final: 0.1527 (tpt) REVERT: C3 118 MET cc_start: 0.9403 (mmm) cc_final: 0.8819 (tpt) REVERT: C3 219 MET cc_start: 0.8776 (tmm) cc_final: 0.8539 (tmm) REVERT: C4 64 MET cc_start: 0.6367 (mmt) cc_final: 0.5509 (mmm) REVERT: C4 126 MET cc_start: 0.6034 (tpp) cc_final: 0.5565 (tpp) REVERT: C4 287 MET cc_start: 0.1360 (mmt) cc_final: 0.0376 (mmt) REVERT: C5 116 MET cc_start: 0.3238 (ttt) cc_final: 0.2855 (ttm) REVERT: C5 124 MET cc_start: 0.9032 (mtm) cc_final: 0.8627 (mtp) REVERT: C5 168 MET cc_start: 0.8669 (ttt) cc_final: 0.8449 (ttt) REVERT: C5 254 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9235 (mmpt) REVERT: C5 317 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7065 (mmt) REVERT: B1 325 MET cc_start: 0.8428 (ppp) cc_final: 0.7012 (ppp) REVERT: B2 125 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B2 188 MET cc_start: 0.9141 (ppp) cc_final: 0.8583 (ppp) REVERT: B3 44 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.5549 (mp10) REVERT: B4 105 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B4 183 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.6285 (t-90) REVERT: B4 188 MET cc_start: 0.8890 (ptm) cc_final: 0.8614 (ppp) REVERT: B4 200 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7881 (p) REVERT: B4 262 MET cc_start: 0.8229 (tpp) cc_final: 0.7815 (tpp) REVERT: B5 36 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8009 (p0) REVERT: B5 146 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B5 195 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B5 325 MET cc_start: 0.9035 (tpt) cc_final: 0.8756 (tpp) REVERT: G1 1 MET cc_start: 0.8395 (tpp) cc_final: 0.8068 (ttm) REVERT: G4 1 MET cc_start: 0.8608 (ppp) cc_final: 0.8063 (ppp) outliers start: 156 outliers final: 115 residues processed: 370 average time/residue: 0.4540 time to fit residues: 282.6862 Evaluate side-chains 366 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 240 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K3 residue 191 TYR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 48 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 132 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 293 THR Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 221 SER Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 275 THR Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 100 ASN Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 157 ILE Chi-restraints excluded: chain B1 residue 181 THR Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 125 ASN Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 303 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 29 THR Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B3 residue 338 ILE Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 36 ASN Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 187 VAL Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 294 CYS Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G2 residue 9 ILE Chi-restraints excluded: chain G3 residue 26 ASP Chi-restraints excluded: chain G3 residue 38 MET Chi-restraints excluded: chain G3 residue 54 VAL Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 163 GLN ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 106 ASN ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 188 GLN ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4 272 HIS ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 60 ASN C5 150 GLN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 188 GLN C5 324 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN B3 340 ASN ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38515 Z= 0.197 Angle : 0.650 13.399 51985 Z= 0.340 Chirality : 0.042 0.265 5780 Planarity : 0.004 0.050 6775 Dihedral : 5.417 85.695 5223 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 2.93 % Allowed : 20.07 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4730 helix: 0.93 (0.11), residues: 2150 sheet: -1.35 (0.18), residues: 738 loop : -1.27 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPC1 109 HIS 0.021 0.001 HISC5 67 PHE 0.045 0.002 PHEC4 377 TYR 0.026 0.002 TYRB3 85 ARG 0.007 0.000 ARGC3 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 254 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K3 134 LEU cc_start: 0.9384 (mt) cc_final: 0.8932 (pp) REVERT: K4 71 TYR cc_start: 0.8731 (t80) cc_final: 0.8286 (m-80) REVERT: K4 129 TYR cc_start: 0.6894 (m-80) cc_final: 0.6220 (m-80) REVERT: C1 64 MET cc_start: 0.7589 (ttm) cc_final: 0.7226 (tpp) REVERT: C1 254 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8538 (mmpt) REVERT: C2 25 MET cc_start: -0.0165 (tpt) cc_final: -0.0376 (tpp) REVERT: C2 100 ASN cc_start: 0.9004 (m-40) cc_final: 0.8574 (t0) REVERT: C2 180 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8303 (mtt90) REVERT: C3 25 MET cc_start: 0.3688 (ppp) cc_final: 0.2567 (pmm) REVERT: C3 64 MET cc_start: 0.1893 (tpt) cc_final: 0.1400 (tpt) REVERT: C3 118 MET cc_start: 0.9360 (mmm) cc_final: 0.8794 (tpt) REVERT: C4 64 MET cc_start: 0.6462 (mmt) cc_final: 0.4618 (tpp) REVERT: C4 126 MET cc_start: 0.6117 (tpp) cc_final: 0.5639 (tpp) REVERT: C4 287 MET cc_start: 0.1289 (mmt) cc_final: 0.0409 (mmt) REVERT: C5 116 MET cc_start: 0.2758 (ttt) cc_final: 0.2370 (ttm) REVERT: C5 124 MET cc_start: 0.8989 (mtm) cc_final: 0.8590 (mtp) REVERT: C5 168 MET cc_start: 0.8655 (ttt) cc_final: 0.8424 (ttt) REVERT: C5 254 LYS cc_start: 0.9505 (tmtt) cc_final: 0.9272 (tppt) REVERT: C5 317 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6637 (mmp) REVERT: B1 325 MET cc_start: 0.8414 (ppp) cc_final: 0.6966 (ppp) REVERT: B2 147 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7880 (p) REVERT: B2 188 MET cc_start: 0.9032 (ppp) cc_final: 0.8531 (tmm) REVERT: B2 217 MET cc_start: 0.8770 (ppp) cc_final: 0.7966 (ppp) REVERT: B3 44 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5916 (mp10) REVERT: B4 105 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7452 (t80) REVERT: B4 183 HIS cc_start: 0.6528 (OUTLIER) cc_final: 0.6195 (t-90) REVERT: B4 262 MET cc_start: 0.8091 (tpp) cc_final: 0.7749 (tpp) REVERT: B5 146 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8045 (mt) REVERT: B5 195 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8801 (p0) REVERT: B5 325 MET cc_start: 0.8855 (tpt) cc_final: 0.8551 (tpp) REVERT: G4 1 MET cc_start: 0.8549 (ppp) cc_final: 0.7988 (ppp) REVERT: G5 1 MET cc_start: 0.4513 (OUTLIER) cc_final: 0.4296 (ptt) outliers start: 122 outliers final: 90 residues processed: 349 average time/residue: 0.4621 time to fit residues: 270.3474 Evaluate side-chains 346 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 246 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 323 GLU Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 163 GLN Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 221 SER Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 100 ASN Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 157 ILE Chi-restraints excluded: chain B1 residue 211 TRP Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 147 SER Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 293 ASN Chi-restraints excluded: chain B2 residue 303 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 29 THR Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B4 residue 303 ASP Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 294 CYS Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G5 residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 391 optimal weight: 20.0000 chunk 417 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 327 optimal weight: 30.0000 chunk 128 optimal weight: 30.0000 chunk 377 optimal weight: 0.8980 chunk 395 optimal weight: 5.9990 chunk 416 optimal weight: 1.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 60 ASN C5 150 GLN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38515 Z= 0.269 Angle : 0.689 12.727 51985 Z= 0.360 Chirality : 0.042 0.258 5780 Planarity : 0.004 0.053 6775 Dihedral : 5.499 82.952 5223 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 2.97 % Allowed : 20.60 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4730 helix: 0.87 (0.11), residues: 2138 sheet: -1.44 (0.18), residues: 742 loop : -1.27 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPC1 109 HIS 0.022 0.002 HISC5 67 PHE 0.047 0.002 PHEC4 377 TYR 0.028 0.002 TYRC5 62 ARG 0.010 0.001 ARGC5 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 252 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K3 175 MET cc_start: 0.8397 (tpt) cc_final: 0.8182 (tpt) REVERT: K4 71 TYR cc_start: 0.8861 (t80) cc_final: 0.8438 (m-80) REVERT: C1 25 MET cc_start: 0.4992 (tpp) cc_final: 0.4490 (tmm) REVERT: C1 64 MET cc_start: 0.7721 (ttm) cc_final: 0.7375 (tpp) REVERT: C1 254 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8555 (mmpt) REVERT: C2 100 ASN cc_start: 0.9044 (m-40) cc_final: 0.8606 (t0) REVERT: C2 180 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8326 (mtt90) REVERT: C3 25 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.2930 (pmm) REVERT: C3 64 MET cc_start: 0.1979 (tpt) cc_final: 0.1491 (tpt) REVERT: C3 118 MET cc_start: 0.9375 (mmm) cc_final: 0.8796 (tpt) REVERT: C4 64 MET cc_start: 0.6624 (mmt) cc_final: 0.5249 (tpp) REVERT: C4 126 MET cc_start: 0.6332 (tpp) cc_final: 0.5971 (tpp) REVERT: C4 287 MET cc_start: 0.1697 (mmt) cc_final: 0.0668 (mmp) REVERT: C5 124 MET cc_start: 0.8969 (mtm) cc_final: 0.8531 (mtp) REVERT: C5 125 TYR cc_start: 0.8275 (t80) cc_final: 0.8037 (t80) REVERT: C5 168 MET cc_start: 0.8729 (ttt) cc_final: 0.8506 (ttt) REVERT: C5 254 LYS cc_start: 0.9537 (tmtt) cc_final: 0.9317 (tppt) REVERT: C5 317 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6890 (mmt) REVERT: B1 59 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: B1 325 MET cc_start: 0.8487 (ppp) cc_final: 0.7209 (ppp) REVERT: B2 188 MET cc_start: 0.9154 (ppp) cc_final: 0.8610 (ppp) REVERT: B2 217 MET cc_start: 0.8799 (ppp) cc_final: 0.8475 (ppp) REVERT: B3 44 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5864 (mp10) REVERT: B4 105 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B4 183 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.6135 (t-90) REVERT: B4 188 MET cc_start: 0.9008 (ptm) cc_final: 0.8155 (ppp) REVERT: B4 262 MET cc_start: 0.8136 (tpp) cc_final: 0.7724 (tpp) REVERT: B5 146 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8132 (mt) REVERT: B5 195 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8814 (p0) REVERT: B5 325 MET cc_start: 0.8967 (tpt) cc_final: 0.8634 (tpp) REVERT: G4 1 MET cc_start: 0.8596 (ppp) cc_final: 0.8034 (ppp) outliers start: 124 outliers final: 101 residues processed: 351 average time/residue: 0.4586 time to fit residues: 271.8222 Evaluate side-chains 354 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 243 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 132 THR Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 145 ILE Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 323 GLU Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 145 ILE Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 221 SER Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 275 THR Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 100 ASN Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 59 TYR Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 293 ASN Chi-restraints excluded: chain B2 residue 303 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 29 THR Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B4 residue 303 ASP Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 294 CYS Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G2 residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 7.9990 chunk 441 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 307 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 426 optimal weight: 20.0000 chunk 368 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 192 ASN ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 60 ASN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 38515 Z= 0.284 Angle : 0.712 13.570 51985 Z= 0.373 Chirality : 0.043 0.271 5780 Planarity : 0.004 0.053 6775 Dihedral : 5.568 79.583 5223 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 2.83 % Allowed : 20.89 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4730 helix: 0.73 (0.11), residues: 2140 sheet: -1.45 (0.18), residues: 731 loop : -1.29 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPC1 109 HIS 0.020 0.002 HISC5 67 PHE 0.046 0.002 PHEC4 377 TYR 0.023 0.002 TYRC4 341 ARG 0.008 0.001 ARGC1 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 244 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K3 175 MET cc_start: 0.8528 (tpt) cc_final: 0.8328 (tpt) REVERT: K4 71 TYR cc_start: 0.8928 (t80) cc_final: 0.8525 (m-80) REVERT: C1 25 MET cc_start: 0.5112 (tpp) cc_final: 0.4614 (tmm) REVERT: C1 64 MET cc_start: 0.7608 (ttm) cc_final: 0.7329 (tpp) REVERT: C2 100 ASN cc_start: 0.9017 (m-40) cc_final: 0.8600 (t0) REVERT: C2 180 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8296 (mpt180) REVERT: C3 25 MET cc_start: 0.3740 (OUTLIER) cc_final: 0.2614 (pmm) REVERT: C3 64 MET cc_start: 0.2042 (tpt) cc_final: 0.1755 (tpt) REVERT: C3 118 MET cc_start: 0.9363 (mmm) cc_final: 0.8755 (tpt) REVERT: C3 124 MET cc_start: 0.7639 (mtt) cc_final: 0.7407 (mpp) REVERT: C4 64 MET cc_start: 0.6611 (mmt) cc_final: 0.5279 (tpp) REVERT: C4 126 MET cc_start: 0.6615 (tpp) cc_final: 0.6030 (tpp) REVERT: C4 287 MET cc_start: 0.2020 (mmt) cc_final: 0.0981 (mmp) REVERT: C5 124 MET cc_start: 0.8983 (mtm) cc_final: 0.8582 (mtp) REVERT: C5 168 MET cc_start: 0.8774 (ttt) cc_final: 0.8554 (ttt) REVERT: C5 254 LYS cc_start: 0.9538 (tmtt) cc_final: 0.9337 (mmmt) REVERT: C5 317 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: B1 59 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: B1 325 MET cc_start: 0.8473 (ppp) cc_final: 0.7293 (ppp) REVERT: B2 188 MET cc_start: 0.9344 (ppp) cc_final: 0.8974 (ppp) REVERT: B3 44 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5778 (mp10) REVERT: B4 105 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7230 (t80) REVERT: B4 183 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.6186 (t-90) REVERT: B4 188 MET cc_start: 0.9074 (ptm) cc_final: 0.8258 (ppp) REVERT: B5 45 MET cc_start: 0.8409 (mtt) cc_final: 0.8156 (mmm) REVERT: B5 146 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B5 195 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8820 (p0) REVERT: B5 325 MET cc_start: 0.9009 (tpt) cc_final: 0.8667 (tpp) REVERT: G2 5 ASN cc_start: 0.8625 (t0) cc_final: 0.8017 (m110) REVERT: G4 1 MET cc_start: 0.8613 (ppp) cc_final: 0.7483 (ppp) outliers start: 118 outliers final: 103 residues processed: 337 average time/residue: 0.4744 time to fit residues: 269.8558 Evaluate side-chains 346 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 234 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 67 LYS Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 175 MET Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K3 residue 171 MET Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 48 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 132 THR Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 145 ILE Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 164 THR Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 323 GLU Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 145 ILE Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 221 SER Chi-restraints excluded: chain C2 residue 272 HIS Chi-restraints excluded: chain C2 residue 275 THR Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 100 ASN Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain C5 residue 369 THR Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 59 TYR Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 228 ASP Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 274 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B2 residue 293 ASN Chi-restraints excluded: chain B2 residue 303 ASP Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 29 THR Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 153 ASP Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 200 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 274 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 303 ASP Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B4 residue 303 ASP Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 187 VAL Chi-restraints excluded: chain B5 residue 195 ASP Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 294 CYS Chi-restraints excluded: chain B5 residue 321 THR Chi-restraints excluded: chain G3 residue 26 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 369 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 268 ASN ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.063599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.046911 restraints weight = 472677.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.046509 restraints weight = 296314.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.046786 restraints weight = 209043.324| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38515 Z= 0.233 Angle : 0.694 15.001 51985 Z= 0.360 Chirality : 0.043 0.319 5780 Planarity : 0.004 0.050 6775 Dihedral : 5.469 83.435 5223 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 2.81 % Allowed : 20.91 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4730 helix: 0.83 (0.11), residues: 2140 sheet: -1.41 (0.18), residues: 732 loop : -1.25 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPC4 109 HIS 0.018 0.002 HISC5 67 PHE 0.047 0.002 PHEC4 377 TYR 0.023 0.002 TYRC4 341 ARG 0.009 0.000 ARGC5 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7942.29 seconds wall clock time: 146 minutes 17.68 seconds (8777.68 seconds total)