Starting phenix.real_space_refine on Sat Mar 23 16:38:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/03_2024/8u81_41996.pdb" } resolution = 3.82 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= -0.007 sd= 1.074 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 7345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K1 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 GLU 166": "OE1" <-> "OE2" Residue "K1 GLU 222": "OE1" <-> "OE2" Residue "K1 GLU 229": "OE1" <-> "OE2" Residue "K2 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K3 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K3 ASP 116": "OD1" <-> "OD2" Residue "K3 GLU 127": "OE1" <-> "OE2" Residue "K3 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K3 TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K4 GLU 229": "OE1" <-> "OE2" Residue "K5 ASP 93": "OD1" <-> "OD2" Residue "K5 ASP 95": "OD1" <-> "OD2" Residue "K5 GLU 120": "OE1" <-> "OE2" Residue "K5 GLU 127": "OE1" <-> "OE2" Residue "K5 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 GLU 200": "OE1" <-> "OE2" Residue "C1 GLU 71": "OE1" <-> "OE2" Residue "C1 GLU 79": "OE1" <-> "OE2" Residue "C1 GLU 83": "OE1" <-> "OE2" Residue "C1 GLU 246": "OE1" <-> "OE2" Residue "C1 GLU 278": "OE1" <-> "OE2" Residue "C1 GLU 280": "OE1" <-> "OE2" Residue "C1 TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 79": "OE1" <-> "OE2" Residue "C2 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 176": "OE1" <-> "OE2" Residue "C2 GLU 215": "OE1" <-> "OE2" Residue "C2 GLU 243": "OE1" <-> "OE2" Residue "C2 GLU 265": "OE1" <-> "OE2" Residue "C2 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 55": "OE1" <-> "OE2" Residue "C3 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 ASP 159": "OD1" <-> "OD2" Residue "C3 TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 238": "OE1" <-> "OE2" Residue "C3 GLU 258": "OE1" <-> "OE2" Residue "C3 TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 ASP 373": "OD1" <-> "OD2" Residue "C3 PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 GLU 79": "OE1" <-> "OE2" Residue "C4 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 GLU 202": "OE1" <-> "OE2" Residue "C4 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 GLU 257": "OE1" <-> "OE2" Residue "C4 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 ASP 26": "OD1" <-> "OD2" Residue "C5 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 ASP 35": "OD1" <-> "OD2" Residue "C5 GLU 55": "OE1" <-> "OE2" Residue "C5 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 GLU 91": "OE1" <-> "OE2" Residue "C5 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 GLU 323": "OE1" <-> "OE2" Residue "C5 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 38": "OD1" <-> "OD2" Residue "B1 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 3": "OE1" <-> "OE2" Residue "B2 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 138": "OE1" <-> "OE2" Residue "B2 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 215": "OE1" <-> "OE2" Residue "B2 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 267": "OD1" <-> "OD2" Residue "B2 ASP 312": "OD1" <-> "OD2" Residue "B3 GLU 10": "OE1" <-> "OE2" Residue "B3 ASP 163": "OD1" <-> "OD2" Residue "B3 GLU 226": "OE1" <-> "OE2" Residue "B3 ASP 228": "OD1" <-> "OD2" Residue "B3 PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ASP 267": "OD1" <-> "OD2" Residue "B3 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ASP 312": "OD1" <-> "OD2" Residue "B4 ASP 5": "OD1" <-> "OD2" Residue "B4 GLU 12": "OE1" <-> "OE2" Residue "B4 GLU 130": "OE1" <-> "OE2" Residue "B4 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 3": "OE1" <-> "OE2" Residue "B5 ASP 76": "OD1" <-> "OD2" Residue "B5 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 215": "OE1" <-> "OE2" Residue "B5 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 ASP 26": "OD1" <-> "OD2" Residue "G1 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 GLU 17": "OE1" <-> "OE2" Residue "G2 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 GLU 42": "OE1" <-> "OE2" Residue "G3 GLU 63": "OE1" <-> "OE2" Residue "G4 GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37890 Number of models: 1 Model: "" Number of chains: 20 Chain: "K1" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K2" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K3" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K4" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K5" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} 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: 19.87, per 1000 atoms: 0.52 Number of scatterers: 37890 At special positions: 0 Unit cell: (245.14, 246.17, 135.96, 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 7345 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: 16.49 Conformation dependent library (CDL) restraints added in 5.9 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: 164 helices and 45 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'K1' and resid 59 through 63 Processing helix chain 'K1' and resid 68 through 75 removed outlier: 3.688A pdb=" N ARGK1 72 " --> pdb=" O SERK1 68 " (cutoff:3.500A) Processing helix chain 'K1' and resid 95 through 109 removed outlier: 3.748A pdb=" N GLYK1 100 " --> pdb=" O PROK1 96 " (cutoff:3.500A) Proline residue: K1 101 - end of helix Processing helix chain 'K1' and resid 118 through 129 Processing helix chain 'K1' and resid 131 through 151 removed outlier: 4.230A pdb=" N GLNK1 151 " --> pdb=" O SERK1 147 " (cutoff:3.500A) Processing helix chain 'K1' and resid 164 through 174 removed outlier: 4.622A pdb=" N THRK1 169 " --> pdb=" O GLUK1 165 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLNK1 170 " --> pdb=" O GLUK1 166 " (cutoff:3.500A) Processing helix chain 'K1' and resid 221 through 233 Processing helix chain 'K2' and resid 59 through 63 Processing helix chain 'K2' and resid 70 through 75 removed outlier: 3.692A pdb=" N CYSK2 74 " --> pdb=" O LEUK2 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLNK2 75 " --> pdb=" O TYRK2 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K2' and resid 70 through 75' Processing helix chain 'K2' and resid 95 through 109 Proline residue: K2 101 - end of helix Processing helix chain 'K2' and resid 118 through 129 Processing helix chain 'K2' and resid 131 through 151 Processing helix chain 'K2' and resid 152 through 154 No H-bonds generated for 'chain 'K2' and resid 152 through 154' Processing helix chain 'K2' and resid 164 through 174 removed outlier: 3.511A pdb=" N LEUK2 168 " --> pdb=" O GLNK2 164 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THRK2 169 " --> pdb=" O GLUK2 165 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLNK2 170 " --> pdb=" O GLUK2 166 " (cutoff:3.500A) Processing helix chain 'K2' and resid 221 through 233 removed outlier: 3.686A pdb=" N ARGK2 233 " --> pdb=" O GLUK2 229 " (cutoff:3.500A) Processing helix chain 'K3' and resid 59 through 63 Processing helix chain 'K3' and resid 68 through 75 removed outlier: 3.600A pdb=" N ARGK3 72 " --> pdb=" O SERK3 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLNK3 75 " --> pdb=" O TYRK3 71 " (cutoff:3.500A) Processing helix chain 'K3' and resid 98 through 109 removed outlier: 3.932A pdb=" N VALK3 102 " --> pdb=" O TYRK3 98 " (cutoff:3.500A) Processing helix chain 'K3' and resid 118 through 130 Processing helix chain 'K3' and resid 131 through 150 Processing helix chain 'K3' and resid 164 through 166 No H-bonds generated for 'chain 'K3' and resid 164 through 166' Processing helix chain 'K3' and resid 167 through 174 Processing helix chain 'K3' and resid 191 through 195 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: 3.637A pdb=" N ARGK4 72 " --> pdb=" O SERK4 68 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEUK4 73 " --> pdb=" O PHEK4 69 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLNK4 75 " --> pdb=" O TYRK4 71 " (cutoff:3.500A) Processing helix chain 'K4' and resid 98 through 109 removed outlier: 4.010A pdb=" N VALK4 102 " --> pdb=" O TYRK4 98 " (cutoff:3.500A) Processing helix chain 'K4' and resid 118 through 129 removed outlier: 3.564A pdb=" N VALK4 122 " --> pdb=" O ALAK4 118 " (cutoff:3.500A) Processing helix chain 'K4' and resid 131 through 150 Processing helix chain 'K4' and resid 164 through 174 removed outlier: 4.179A pdb=" N THRK4 169 " --> pdb=" O GLUK4 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLNK4 170 " --> pdb=" O GLUK4 166 " (cutoff:3.500A) Processing helix chain 'K4' and resid 222 through 233 removed outlier: 3.637A pdb=" N ARGK4 233 " --> pdb=" O GLUK4 229 " (cutoff:3.500A) Processing helix chain 'K5' and resid 59 through 63 Processing helix chain 'K5' and resid 68 through 75 removed outlier: 4.529A pdb=" N ARGK5 72 " --> pdb=" O SERK5 68 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEUK5 73 " --> pdb=" O PHEK5 69 " (cutoff:3.500A) Processing helix chain 'K5' and resid 95 through 109 Proline residue: K5 101 - end of helix Processing helix chain 'K5' and resid 118 through 130 Processing helix chain 'K5' and resid 131 through 149 Processing helix chain 'K5' and resid 164 through 174 removed outlier: 4.479A pdb=" N THRK5 169 " --> pdb=" O GLUK5 165 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLNK5 170 " --> pdb=" O GLUK5 166 " (cutoff:3.500A) Processing helix chain 'K5' and resid 210 through 215 removed outlier: 4.007A pdb=" N TYRK5 214 " --> pdb=" O HISK5 210 " (cutoff:3.500A) Processing helix chain 'K5' and resid 221 through 233 Processing helix chain 'C1' and resid 26 through 46 removed outlier: 3.807A pdb=" N SERC1 32 " --> pdb=" O LYSC1 28 " (cutoff:3.500A) Processing helix chain 'C1' and resid 53 through 67 removed outlier: 3.724A pdb=" N LEUC1 57 " --> pdb=" O SERC1 53 " (cutoff:3.500A) removed outlier: 4.087A 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 96 removed outlier: 3.531A pdb=" N ASPC1 92 " --> pdb=" O LYSC1 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SERC1 96 " --> pdb=" O ASPC1 92 " (cutoff:3.500A) Processing helix chain 'C1' and resid 100 through 123 Processing helix chain 'C1' and resid 124 through 135 removed outlier: 3.641A pdb=" N VALC1 129 " --> pdb=" O TYRC1 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VALC1 131 " --> pdb=" O ASPC1 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLNC1 132 " --> pdb=" O ARGC1 128 " (cutoff:3.500A) Processing helix chain 'C1' and resid 138 through 151 Processing helix chain 'C1' and resid 154 through 174 removed outlier: 3.776A pdb=" N HISC1 160 " --> pdb=" O CYSC1 156 " (cutoff:3.500A) Processing helix chain 'C1' and resid 179 through 195 removed outlier: 4.382A pdb=" N ILEC1 183 " --> pdb=" O ASPC1 179 " (cutoff:3.500A) Processing helix chain 'C1' and resid 198 through 205 Processing helix chain 'C1' and resid 205 through 228 Processing helix chain 'C1' and resid 229 through 250 Processing helix chain 'C1' and resid 256 through 268 Processing helix chain 'C1' and resid 273 through 278 removed outlier: 3.649A pdb=" N GLUC1 278 " --> pdb=" O THRC1 275 " (cutoff:3.500A) Processing helix chain 'C1' and resid 283 through 291 Processing helix chain 'C1' and resid 292 through 304 removed outlier: 3.511A pdb=" N LEUC1 296 " --> pdb=" O LYSC1 292 " (cutoff:3.500A) Processing helix chain 'C1' and resid 308 through 330 removed outlier: 3.912A pdb=" N THRC1 312 " --> pdb=" O ASNC1 308 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SERC1 330 " --> pdb=" O LYSC1 326 " (cutoff:3.500A) Processing helix chain 'C1' and resid 337 through 342 Processing helix chain 'C1' and resid 343 through 359 Processing helix chain 'C1' and resid 363 through 379 removed outlier: 3.964A pdb=" N ASNC1 379 " --> pdb=" O GLUC1 375 " (cutoff:3.500A) Processing helix chain 'C2' and resid 26 through 46 Processing helix chain 'C2' and resid 53 through 67 Processing helix chain 'C2' and resid 69 through 88 Processing helix chain 'C2' and resid 88 through 95 Processing helix chain 'C2' and resid 100 through 123 removed outlier: 4.100A pdb=" N THRC2 104 " --> pdb=" O ASNC2 100 " (cutoff:3.500A) Processing helix chain 'C2' and resid 124 through 129 Processing helix chain 'C2' and resid 129 through 135 Processing helix chain 'C2' and resid 138 through 151 Processing helix chain 'C2' and resid 154 through 174 Processing helix chain 'C2' and resid 179 through 194 removed outlier: 4.130A 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 251 Processing helix chain 'C2' and resid 256 through 268 removed outlier: 3.511A pdb=" N LYSC2 262 " --> pdb=" O GLUC2 258 " (cutoff:3.500A) Processing helix chain 'C2' and resid 284 through 291 removed outlier: 4.099A pdb=" N LEUC2 288 " --> pdb=" O LEUC2 284 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSC2 289 " --> pdb=" O VALC2 285 " (cutoff:3.500A) Processing helix chain 'C2' and resid 293 through 304 Processing helix chain 'C2' and resid 308 through 330 Processing helix chain 'C2' and resid 343 through 359 removed outlier: 4.038A pdb=" N LYSC2 349 " --> pdb=" O LEUC2 345 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHEC2 355 " --> pdb=" O ARGC2 351 " (cutoff:3.500A) Processing helix chain 'C2' and resid 363 through 379 removed outlier: 3.837A pdb=" N LYSC2 367 " --> pdb=" O ASPC2 363 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASNC2 379 " --> pdb=" O GLUC2 375 " (cutoff:3.500A) Processing helix chain 'C3' and resid 26 through 46 removed outlier: 3.686A pdb=" N VALC3 30 " --> pdb=" O ASPC3 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SERC3 32 " --> pdb=" O LYSC3 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASPC3 35 " --> pdb=" O ASNC3 31 " (cutoff:3.500A) Processing helix chain 'C3' and resid 53 through 67 Processing helix chain 'C3' and resid 69 through 88 removed outlier: 3.669A pdb=" N LYSC3 88 " --> pdb=" O HISC3 84 " (cutoff:3.500A) Processing helix chain 'C3' and resid 88 through 95 Processing helix chain 'C3' and resid 100 through 123 removed outlier: 3.527A pdb=" N THRC3 104 " --> pdb=" O ASNC3 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N METC3 118 " --> pdb=" O THRC3 114 " (cutoff:3.500A) Processing helix chain 'C3' and resid 129 through 135 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: 3.832A pdb=" N ILEC3 183 " --> pdb=" O ASPC3 179 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYC3 194 " --> pdb=" O LEUC3 190 " (cutoff:3.500A) Processing helix chain 'C3' and resid 198 through 205 removed outlier: 3.583A pdb=" N PHEC3 205 " --> pdb=" O TYRC3 201 " (cutoff:3.500A) Processing helix chain 'C3' and resid 205 through 226 removed outlier: 3.663A pdb=" N ALAC3 226 " --> pdb=" O GLNC3 222 " (cutoff:3.500A) Processing helix chain 'C3' and resid 229 through 251 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: 3.970A pdb=" N ILEC3 260 " --> pdb=" O THRC3 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALC3 261 " --> pdb=" O GLUC3 257 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILEC3 269 " --> pdb=" O GLUC3 265 " (cutoff:3.500A) Processing helix chain 'C3' and resid 272 through 278 Processing helix chain 'C3' and resid 283 through 291 Processing helix chain 'C3' and resid 293 through 304 Processing helix chain 'C3' and resid 308 through 330 removed outlier: 4.091A pdb=" N THRC3 312 " --> pdb=" O ASNC3 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N METC3 313 " --> pdb=" O GLYC3 309 " (cutoff:3.500A) Processing helix chain 'C3' and resid 343 through 359 Processing helix chain 'C3' and resid 363 through 377 removed outlier: 3.634A pdb=" N LYSC3 367 " --> pdb=" O ASPC3 363 " (cutoff:3.500A) Processing helix chain 'C4' and resid 27 through 46 Processing helix chain 'C4' and resid 53 through 67 Processing helix chain 'C4' and resid 69 through 88 Processing helix chain 'C4' and resid 88 through 95 Processing helix chain 'C4' and resid 100 through 123 removed outlier: 3.697A pdb=" N METC4 118 " --> pdb=" O THRC4 114 " (cutoff:3.500A) Processing helix chain 'C4' and resid 123 through 129 Processing helix chain 'C4' and resid 129 through 135 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 193 Processing helix chain 'C4' and resid 198 through 205 Processing helix chain 'C4' and resid 205 through 228 Processing helix chain 'C4' and resid 229 through 251 Processing helix chain 'C4' and resid 253 through 255 No H-bonds generated for 'chain 'C4' and resid 253 through 255' Processing helix chain 'C4' and resid 256 through 269 removed outlier: 3.790A pdb=" N ILEC4 260 " --> pdb=" O THRC4 256 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYSC4 262 " --> pdb=" O GLUC4 258 " (cutoff:3.500A) Processing helix chain 'C4' and resid 272 through 278 Processing helix chain 'C4' and resid 283 through 291 Processing helix chain 'C4' and resid 292 through 306 removed outlier: 3.719A pdb=" N ARGC4 305 " --> pdb=" O LYSC4 301 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VALC4 306 " --> pdb=" O LEUC4 302 " (cutoff:3.500A) Processing helix chain 'C4' and resid 308 through 330 Processing helix chain 'C4' and resid 342 through 359 removed outlier: 3.929A pdb=" N LEUC4 346 " --> pdb=" O ILEC4 342 " (cutoff:3.500A) Processing helix chain 'C4' and resid 363 through 379 Processing helix chain 'C5' and resid 26 through 46 removed outlier: 3.715A pdb=" N VALC5 30 " --> pdb=" O ASPC5 26 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SERC5 32 " --> pdb=" O LYSC5 28 " (cutoff:3.500A) Processing helix chain 'C5' and resid 53 through 67 Processing helix chain 'C5' and resid 69 through 88 removed outlier: 3.557A pdb=" N LYSC5 88 " --> pdb=" O HISC5 84 " (cutoff:3.500A) Processing helix chain 'C5' and resid 88 through 97 Processing helix chain 'C5' and resid 100 through 123 removed outlier: 3.691A pdb=" N THRC5 104 " --> pdb=" O ASNC5 100 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N METC5 118 " --> pdb=" O THRC5 114 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEUC5 123 " --> pdb=" O ILEC5 119 " (cutoff:3.500A) Processing helix chain 'C5' and resid 129 through 135 Processing helix chain 'C5' and resid 138 through 149 Processing helix chain 'C5' and resid 154 through 175 Processing helix chain 'C5' and resid 179 through 193 removed outlier: 3.826A 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 228 Processing helix chain 'C5' and resid 229 through 252 Processing helix chain 'C5' and resid 253 through 268 removed outlier: 3.530A pdb=" N GLUC5 257 " --> pdb=" O ASPC5 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLUC5 258 " --> pdb=" O LYSC5 254 " (cutoff:3.500A) Proline residue: C5 259 - end of helix removed outlier: 4.333A pdb=" N LYSC5 262 " --> pdb=" O GLUC5 258 " (cutoff:3.500A) Processing helix chain 'C5' and resid 272 through 279 removed outlier: 3.507A pdb=" N METC5 279 " --> pdb=" O THRC5 275 " (cutoff:3.500A) Processing helix chain 'C5' and resid 282 through 291 removed outlier: 4.240A pdb=" N HISC5 286 " --> pdb=" O SERC5 282 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYSC5 289 " --> pdb=" O VALC5 285 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLYC5 291 " --> pdb=" O METC5 287 " (cutoff:3.500A) Processing helix chain 'C5' and resid 292 through 304 removed outlier: 3.714A pdb=" N LEUC5 296 " --> pdb=" O LYSC5 292 " (cutoff:3.500A) Processing helix chain 'C5' and resid 308 through 330 removed outlier: 4.272A pdb=" N THRC5 312 " --> pdb=" O ASNC5 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N METC5 313 " --> pdb=" O GLYC5 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALAC5 327 " --> pdb=" O GLUC5 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SERC5 330 " --> pdb=" O LYSC5 326 " (cutoff:3.500A) Processing helix chain 'C5' and resid 337 through 342 Processing helix chain 'C5' and resid 343 through 359 Processing helix chain 'C5' and resid 363 through 378 Processing helix chain 'B1' and resid 3 through 25 Processing helix chain 'B1' and resid 29 through 34 removed outlier: 3.994A pdb=" N ILEB1 33 " --> pdb=" O THRB1 29 " (cutoff:3.500A) Processing helix chain 'B2' and resid 3 through 26 Processing helix chain 'B2' and resid 29 through 34 removed outlier: 3.645A pdb=" N ILEB2 33 " --> pdb=" O THRB2 29 " (cutoff:3.500A) Processing helix chain 'B3' and resid 3 through 26 removed outlier: 3.749A pdb=" N LEUB3 7 " --> pdb=" O GLUB3 3 " (cutoff:3.500A) Processing helix chain 'B3' and resid 29 through 34 removed outlier: 3.524A pdb=" N ILEB3 33 " --> pdb=" O THRB3 29 " (cutoff:3.500A) Processing helix chain 'B4' and resid 3 through 26 removed outlier: 3.520A pdb=" N LEUB4 7 " --> pdb=" O GLUB4 3 " (cutoff:3.500A) Processing helix chain 'B4' and resid 29 through 34 Processing helix chain 'B5' and resid 3 through 25 Processing helix chain 'B5' and resid 29 through 34 Processing helix chain 'G1' and resid 1 through 5 Processing helix chain 'G1' and resid 7 through 24 removed outlier: 3.639A pdb=" N GLNG1 11 " --> pdb=" O ALAG1 7 " (cutoff:3.500A) Processing helix chain 'G1' and resid 29 through 44 Processing helix chain 'G1' and resid 48 through 52 Processing helix chain 'G2' and resid 7 through 25 removed outlier: 3.985A pdb=" N GLNG2 11 " --> pdb=" O ALAG2 7 " (cutoff:3.500A) Processing helix chain 'G2' and resid 29 through 44 Processing helix chain 'G3' and resid 1 through 5 Processing helix chain 'G3' and resid 7 through 25 removed outlier: 3.700A pdb=" N GLNG3 11 " --> pdb=" O ALAG3 7 " (cutoff:3.500A) Processing helix chain 'G3' and resid 29 through 45 Processing helix chain 'G3' and resid 46 through 48 No H-bonds generated for 'chain 'G3' and resid 46 through 48' Processing helix chain 'G4' and resid 7 through 25 removed outlier: 4.223A pdb=" N GLNG4 11 " --> pdb=" O ALAG4 7 " (cutoff:3.500A) Processing helix chain 'G4' and resid 29 through 44 Processing helix chain 'G5' and resid 8 through 25 Processing helix chain 'G5' and resid 29 through 46 removed outlier: 4.246A pdb=" N LYSG5 46 " --> pdb=" O GLUG5 42 " (cutoff:3.500A) Processing helix chain 'G5' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'K1' and resid 53 through 58 removed outlier: 9.621A pdb=" N TYRK1 90 " --> pdb=" O TRPK1 45 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ARGK1 47 " --> pdb=" O TYRK1 90 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILEK1 92 " --> pdb=" O ARGK1 47 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASNK1 49 " --> pdb=" O ILEK1 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K1' and resid 157 through 163 removed outlier: 6.500A pdb=" N LEUK1 202 " --> pdb=" O LEUK1 184 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEUK1 184 " --> pdb=" O LEUK1 202 " (cutoff:3.500A) removed outlier: 6.490A 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: 7.882A pdb=" N ILEK2 92 " --> pdb=" O ARGK2 47 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASNK2 49 " --> pdb=" O ILEK2 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K2' and resid 156 through 163 removed outlier: 6.656A pdb=" N LEUK2 202 " --> pdb=" O LEUK2 184 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEUK2 184 " --> pdb=" O LEUK2 202 " (cutoff:3.500A) removed outlier: 6.812A 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 156 through 163 removed outlier: 6.509A pdb=" N LEUK3 202 " --> pdb=" O LEUK3 184 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEUK3 184 " --> pdb=" O LEUK3 202 " (cutoff:3.500A) removed outlier: 6.779A 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: 9.388A pdb=" N TYRK4 90 " --> pdb=" O TRPK4 45 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARGK4 47 " --> pdb=" O TYRK4 90 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILEK4 92 " --> pdb=" O ARGK4 47 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASNK4 49 " --> pdb=" O ILEK4 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALAK4 89 " --> pdb=" O LYSK4 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K4' and resid 155 through 163 removed outlier: 3.625A pdb=" N LYSK4 155 " --> pdb=" O LEUK4 209 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SERK4 206 " --> pdb=" O PHEK4 181 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHEK4 181 " --> pdb=" O SERK4 206 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLUK4 208 " --> pdb=" O TRPK4 179 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TRPK4 179 " --> pdb=" O GLUK4 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K5' and resid 53 through 58 removed outlier: 10.035A pdb=" N TYRK5 90 " --> pdb=" O TRPK5 45 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARGK5 47 " --> pdb=" O TYRK5 90 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILEK5 92 " --> pdb=" O ARGK5 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASNK5 49 " --> pdb=" O ILEK5 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K5' and resid 157 through 163 removed outlier: 6.664A pdb=" N LEUK5 202 " --> pdb=" O LEUK5 184 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEUK5 184 " --> pdb=" O LEUK5 202 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VALK5 204 " --> pdb=" O GLUK5 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B1' and resid 47 through 52 removed outlier: 6.649A pdb=" N ILEB1 338 " --> pdb=" O ARGB1 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THRB1 50 " --> pdb=" O LEUB1 336 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEUB1 336 " --> pdb=" O THRB1 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B1' and resid 58 through 63 removed outlier: 3.804A pdb=" N ALAB1 60 " --> pdb=" O ALAB1 73 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYSB1 78 " --> pdb=" O SERB1 74 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEUB1 79 " --> pdb=" O ALAB1 92 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALAB1 92 " --> pdb=" O LEUB1 79 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILEB1 81 " --> pdb=" O VALB1 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B1' and resid 100 through 105 removed outlier: 6.001A pdb=" N CYSB1 121 " --> pdb=" O GLUB1 138 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLUB1 138 " --> pdb=" O CYSB1 121 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILEB1 123 " --> pdb=" O SERB1 136 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGB1 134 " --> pdb=" O ASNB1 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B1' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYSB1 148 " --> pdb=" O SERB1 160 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEUB1 168 " --> pdb=" O THRB1 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B1' and resid 191 through 192 removed outlier: 6.146A pdb=" N ASPB1 212 " --> pdb=" O CYSB1 218 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYSB1 218 " --> pdb=" O ASPB1 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B1' and resid 229 through 234 removed outlier: 3.537A pdb=" N ALAB1 231 " --> pdb=" O GLYB1 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYSB1 233 " --> pdb=" O ALAB1 242 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYSB1 250 " --> pdb=" O THRB1 263 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THRB1 263 " --> pdb=" O CYSB1 250 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEUB1 252 " --> pdb=" O LEUB1 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B1' and resid 273 through 278 removed outlier: 3.559A pdb=" N CYSB1 294 " --> pdb=" O LEUB1 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASPB1 298 " --> pdb=" O ARGB1 304 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARGB1 304 " --> pdb=" O ASPB1 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B2' and resid 46 through 50 removed outlier: 6.612A pdb=" N ILEB2 338 " --> pdb=" O ARGB2 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THRB2 50 " --> pdb=" O LEUB2 336 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEUB2 336 " --> pdb=" O THRB2 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYSB2 337 " --> pdb=" O THRB2 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B2' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALAB2 60 " --> pdb=" O ALAB2 73 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEUB2 70 " --> pdb=" O TRPB2 82 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYSB2 78 " --> pdb=" O SERB2 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 100 through 105 removed outlier: 5.664A pdb=" N ASNB2 125 " --> pdb=" O VALB2 135 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VALB2 135 " --> pdb=" O ASNB2 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 148 through 151 removed outlier: 6.235A pdb=" N LEUB2 168 " --> pdb=" O THRB2 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLNB2 175 " --> pdb=" O ASPB2 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B2' and resid 198 through 201 removed outlier: 5.788A pdb=" N ASPB2 212 " --> pdb=" O CYSB2 218 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYSB2 218 " --> pdb=" O ASPB2 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B2' and resid 229 through 234 removed outlier: 3.853A pdb=" N ALAB2 231 " --> pdb=" O GLYB2 244 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYSB2 233 " --> pdb=" O ALAB2 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYSB2 250 " --> pdb=" O THRB2 263 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THRB2 263 " --> pdb=" O CYSB2 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEUB2 252 " --> pdb=" O LEUB2 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B2' and resid 273 through 278 removed outlier: 5.753A pdb=" N ASPB2 298 " --> pdb=" O ARGB2 304 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARGB2 304 " --> pdb=" O ASPB2 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 46 through 50 removed outlier: 6.628A pdb=" N ILEB3 338 " --> pdb=" O ARGB3 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THRB3 50 " --> pdb=" O LEUB3 336 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEUB3 336 " --> pdb=" O THRB3 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSB3 337 " --> pdb=" O THRB3 329 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 58 through 63 removed outlier: 3.526A pdb=" N ALAB3 60 " --> pdb=" O ALAB3 73 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYSB3 78 " --> pdb=" O SERB3 74 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEUB3 79 " --> pdb=" O ALAB3 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALAB3 92 " --> pdb=" O LEUB3 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILEB3 81 " --> pdb=" O VALB3 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 100 through 105 removed outlier: 4.850A pdb=" N GLYB3 116 " --> pdb=" O ILEB3 120 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILEB3 120 " --> pdb=" O GLYB3 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASNB3 125 " --> pdb=" O VALB3 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VALB3 135 " --> pdb=" O ASNB3 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 146 through 151 removed outlier: 7.115A pdb=" N SERB3 160 " --> pdb=" O SERB3 147 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYSB3 149 " --> pdb=" O VALB3 158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VALB3 158 " --> pdb=" O CYSB3 149 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHEB3 151 " --> pdb=" O GLNB3 156 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLNB3 156 " --> pdb=" O PHEB3 151 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEUB3 168 " --> pdb=" O THRB3 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 191 through 192 removed outlier: 3.913A pdb=" N PHEB3 199 " --> pdb=" O TRPB3 211 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASPB3 212 " --> pdb=" O CYSB3 218 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYSB3 218 " --> pdb=" O ASPB3 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 229 through 234 removed outlier: 3.757A pdb=" N ALAB3 231 " --> pdb=" O GLYB3 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYSB3 233 " --> pdb=" O ALAB3 242 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASPB3 254 " --> pdb=" O GLUB3 260 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLUB3 260 " --> pdb=" O ASPB3 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B3' and resid 273 through 278 removed outlier: 6.211A pdb=" N GLYB3 288 " --> pdb=" O THRB3 274 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VALB3 276 " --> pdb=" O LEUB3 286 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEUB3 286 " --> pdb=" O VALB3 276 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHEB3 278 " --> pdb=" O LEUB3 284 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEUB3 284 " --> pdb=" O PHEB3 278 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASPB3 298 " --> pdb=" O ARGB3 304 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARGB3 304 " --> pdb=" O ASPB3 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 46 through 50 removed outlier: 6.451A pdb=" N ILEB4 338 " --> pdb=" O ARGB4 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THRB4 50 " --> pdb=" O LEUB4 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEUB4 336 " --> pdb=" O THRB4 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYSB4 337 " --> pdb=" O THRB4 329 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B4' and resid 58 through 62 removed outlier: 3.761A pdb=" N ALAB4 60 " --> pdb=" O ALAB4 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYSB4 78 " --> pdb=" O SERB4 74 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEUB4 79 " --> pdb=" O ALAB4 92 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALAB4 92 " --> pdb=" O LEUB4 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILEB4 81 " --> pdb=" O VALB4 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B4' and resid 100 through 105 removed outlier: 6.082A pdb=" N CYSB4 121 " --> pdb=" O GLUB4 138 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUB4 138 " --> pdb=" O CYSB4 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILEB4 123 " --> pdb=" O SERB4 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARGB4 134 " --> pdb=" O ASNB4 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B4' and resid 146 through 151 Processing sheet with id=AD9, first strand: chain 'B4' and resid 187 through 192 removed outlier: 5.685A pdb=" N ASPB4 212 " --> pdb=" O CYSB4 218 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYSB4 218 " --> pdb=" O ASPB4 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 229 through 234 removed outlier: 6.581A pdb=" N CYSB4 250 " --> pdb=" O THRB4 263 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THRB4 263 " --> pdb=" O CYSB4 250 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUB4 252 " --> pdb=" O LEUB4 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B4' and resid 273 through 278 removed outlier: 5.423A pdb=" N ASPB4 298 " --> pdb=" O ARGB4 304 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARGB4 304 " --> pdb=" O ASPB4 298 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B5' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARGB5 46 " --> pdb=" O ASNB5 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILEB5 338 " --> pdb=" O ARGB5 48 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THRB5 50 " --> pdb=" O LEUB5 336 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEUB5 336 " --> pdb=" O THRB5 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSB5 337 " --> pdb=" O THRB5 329 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B5' and resid 58 through 63 removed outlier: 3.677A pdb=" N ALAB5 60 " --> pdb=" O ALAB5 73 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SERB5 74 " --> pdb=" O LYSB5 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYSB5 78 " --> pdb=" O SERB5 74 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEUB5 79 " --> pdb=" O ALAB5 92 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALAB5 92 " --> pdb=" O LEUB5 79 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILEB5 81 " --> pdb=" O VALB5 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASNB5 88 " --> pdb=" O ASPB5 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B5' and resid 100 through 105 removed outlier: 5.892A pdb=" N CYSB5 121 " --> pdb=" O GLUB5 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLUB5 138 " --> pdb=" O CYSB5 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILEB5 123 " --> pdb=" O SERB5 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARGB5 134 " --> pdb=" O ASNB5 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 146 through 151 removed outlier: 6.617A pdb=" N LEUB5 168 " --> pdb=" O THRB5 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLNB5 175 " --> pdb=" O ASPB5 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B5' and resid 191 through 192 removed outlier: 5.954A pdb=" N ASPB5 212 " --> pdb=" O CYSB5 218 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYSB5 218 " --> pdb=" O ASPB5 212 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 229 through 231 removed outlier: 6.916A pdb=" N GLYB5 244 " --> pdb=" O ASNB5 230 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASPB5 254 " --> pdb=" O GLUB5 260 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLUB5 260 " --> pdb=" O ASPB5 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 273 through 278 removed outlier: 4.274A pdb=" N CYSB5 294 " --> pdb=" O LEUB5 308 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASPB5 298 " --> pdb=" O ARGB5 304 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARGB5 304 " --> pdb=" O ASPB5 298 " (cutoff:3.500A) 1972 hydrogen bonds defined for protein. 5742 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: 13.47 Time building geometry restraints manager: 17.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12615 1.34 - 1.46: 7162 1.46 - 1.58: 18317 1.58 - 1.70: 1 1.70 - 1.82: 425 Bond restraints: 38520 Sorted by residual: bond pdb=" N VALK3 154 " pdb=" CA VALK3 154 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.80e+00 bond pdb=" N ILEK5 92 " pdb=" CA ILEK5 92 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N ARGK5 94 " pdb=" CA ARGK5 94 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N ILEB4 269 " pdb=" CA ILEB4 269 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.17e-02 7.31e+03 7.05e+00 bond pdb=" N GLYB3 202 " pdb=" CA GLYB3 202 " ideal model delta sigma weight residual 1.447 1.477 -0.030 1.17e-02 7.31e+03 6.70e+00 ... (remaining 38515 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.11: 449 105.11 - 112.39: 19284 112.39 - 119.67: 13692 119.67 - 126.95: 18226 126.95 - 134.22: 344 Bond angle restraints: 51995 Sorted by residual: angle pdb=" N LYSK2 44 " pdb=" CA LYSK2 44 " pdb=" C LYSK2 44 " ideal model delta sigma weight residual 114.75 103.04 11.71 1.26e+00 6.30e-01 8.64e+01 angle pdb=" C TYRK4 193 " pdb=" CA TYRK4 193 " pdb=" CB TYRK4 193 " ideal model delta sigma weight residual 116.54 109.72 6.82 1.15e+00 7.56e-01 3.52e+01 angle pdb=" C ASNK2 130 " pdb=" N ILEK2 131 " pdb=" CA ILEK2 131 " ideal model delta sigma weight residual 122.37 115.50 6.87 1.25e+00 6.40e-01 3.02e+01 angle pdb=" C LEUC1 195 " pdb=" CA LEUC1 195 " pdb=" CB LEUC1 195 " ideal model delta sigma weight residual 116.63 110.38 6.25 1.16e+00 7.43e-01 2.90e+01 angle pdb=" N ASPB3 118 " pdb=" CA ASPB3 118 " pdb=" C ASPB3 118 " ideal model delta sigma weight residual 114.56 108.28 6.28 1.27e+00 6.20e-01 2.44e+01 ... (remaining 51990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20760 17.99 - 35.99: 1934 35.99 - 53.98: 376 53.98 - 71.98: 187 71.98 - 89.97: 128 Dihedral angle restraints: 23385 sinusoidal: 9500 harmonic: 13885 Sorted by residual: dihedral pdb=" CD ARGK5 94 " pdb=" NE ARGK5 94 " pdb=" CZ ARGK5 94 " pdb=" NH1 ARGK5 94 " ideal model delta sinusoidal sigma weight residual 0.00 -79.89 79.89 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARGK4 72 " pdb=" NE ARGK4 72 " pdb=" CZ ARGK4 72 " pdb=" NH1 ARGK4 72 " ideal model delta sinusoidal sigma weight residual 0.00 -52.92 52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CG ARGK5 94 " pdb=" CD ARGK5 94 " pdb=" NE ARGK5 94 " pdb=" CZ ARGK5 94 " ideal model delta sinusoidal sigma weight residual -90.00 -19.02 -70.98 2 1.50e+01 4.44e-03 1.91e+01 ... (remaining 23382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4417 0.049 - 0.099: 1152 0.099 - 0.148: 189 0.148 - 0.197: 19 0.197 - 0.247: 3 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CA ILEB4 270 " pdb=" N ILEB4 270 " pdb=" C ILEB4 270 " pdb=" CB ILEB4 270 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILEC1 33 " pdb=" CA ILEC1 33 " pdb=" CG1 ILEC1 33 " pdb=" CG2 ILEC1 33 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA METG3 21 " pdb=" N METG3 21 " pdb=" C METG3 21 " pdb=" CB METG3 21 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 5777 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGK5 94 " 1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARGK5 94 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARGK5 94 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARGK5 94 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARGK5 94 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGK4 72 " 0.867 9.50e-02 1.11e+02 3.89e-01 9.17e+01 pdb=" NE ARGK4 72 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARGK4 72 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGK4 72 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARGK4 72 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPC4 109 " 0.023 2.00e-02 2.50e+03 1.89e-02 8.93e+00 pdb=" CG TRPC4 109 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRPC4 109 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRPC4 109 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRPC4 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRPC4 109 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRPC4 109 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRPC4 109 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRPC4 109 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRPC4 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 664 2.66 - 3.22: 39180 3.22 - 3.78: 64235 3.78 - 4.34: 88904 4.34 - 4.90: 139762 Nonbonded interactions: 332745 Sorted by model distance: nonbonded pdb=" OG1 THRB2 321 " pdb=" OD1 ASPB2 323 " model vdw 2.097 2.440 nonbonded pdb=" O THRK5 58 " pdb=" OG1 THRK5 61 " model vdw 2.125 2.440 nonbonded pdb=" OG SERC5 53 " pdb=" OE1 GLUC5 55 " model vdw 2.144 2.440 nonbonded pdb=" OD2 ASPK1 95 " pdb=" OG1 THRK1 97 " model vdw 2.169 2.440 nonbonded pdb=" O CYSB3 148 " pdb=" OG SERB3 160 " model vdw 2.178 2.440 ... (remaining 332740 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.260 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 94.390 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.340 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.105 38520 Z= 0.245 Angle : 0.799 13.730 51995 Z= 0.455 Chirality : 0.044 0.247 5780 Planarity : 0.009 0.483 6780 Dihedral : 17.065 89.971 14415 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer: Outliers : 0.60 % Allowed : 16.57 % Favored : 82.83 % 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: -1.07 (0.12), residues: 4730 helix: 0.59 (0.11), residues: 2057 sheet: -1.54 (0.17), residues: 802 loop : -1.75 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRPC4 109 HIS 0.011 0.002 HISC5 67 PHE 0.033 0.002 PHEC3 54 TYR 0.037 0.002 TYRC5 376 ARG 0.012 0.001 ARGB2 46 *********************** 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 278 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 4.450 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: K2 129 TYR cc_start: 0.8411 (m-80) cc_final: 0.7350 (m-80) REVERT: K2 171 MET cc_start: 0.9222 (ptp) cc_final: 0.9011 (ptp) REVERT: K2 198 GLN cc_start: 0.3998 (tp40) cc_final: 0.2981 (pp30) REVERT: K4 72 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7830 (mmm160) REVERT: C1 184 ARG cc_start: 0.9174 (mtm180) cc_final: 0.8602 (ptt-90) REVERT: C1 279 MET cc_start: 0.7670 (mtt) cc_final: 0.7185 (ptp) REVERT: C1 317 MET cc_start: 0.5619 (tpt) cc_final: 0.4705 (tmm) REVERT: C4 191 MET cc_start: 0.9508 (tpp) cc_final: 0.9216 (mmm) REVERT: C5 55 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8776 (mp0) REVERT: B2 61 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7451 (ptm) REVERT: B2 312 ASP cc_start: 0.9016 (p0) cc_final: 0.8719 (p0) REVERT: B4 45 MET cc_start: 0.8091 (mpp) cc_final: 0.7746 (mmt) REVERT: B4 188 MET cc_start: 0.8708 (ppp) cc_final: 0.8247 (ppp) outliers start: 25 outliers final: 12 residues processed: 275 average time/residue: 0.5100 time to fit residues: 232.3847 Evaluate side-chains 254 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K2 residue 44 LYS Chi-restraints excluded: chain K2 residue 77 ASP Chi-restraints excluded: chain K4 residue 72 ARG Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C2 residue 28 LYS Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C5 residue 55 GLU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain B1 residue 276 VAL Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B5 residue 82 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 364 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 221 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 422 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 151 GLN K2 108 HIS ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 170 GLN ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 195 ASN ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 164 GLN ** K4 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 192 ASN ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 211 ASN C1 60 ASN ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 133 GLN C1 218 GLN ** C1 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 368 GLN C2 222 GLN C2 290 ASN C3 185 ASN ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 150 GLN C4 228 ASN C4 281 ASN C5 98 ASN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 9 GLN B3 142 HIS ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN B3 340 ASN B5 36 ASN ** B5 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 88 ASN B5 125 ASN G1 18 GLN ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 24 ASN ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 38520 Z= 0.406 Angle : 0.767 15.910 51995 Z= 0.408 Chirality : 0.044 0.222 5780 Planarity : 0.005 0.112 6780 Dihedral : 6.273 59.143 5262 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 3.19 % Allowed : 15.47 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4730 helix: 0.54 (0.11), residues: 2079 sheet: -1.55 (0.17), residues: 755 loop : -1.88 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRPB1 211 HIS 0.011 0.002 HISC5 67 PHE 0.029 0.003 PHEG5 61 TYR 0.030 0.003 TYRC2 29 ARG 0.018 0.001 ARGC1 180 *********************** 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 380 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 247 time to evaluate : 4.376 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: K1 60 GLN cc_start: 0.9165 (mp10) cc_final: 0.8961 (mp10) REVERT: K1 155 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9036 (mtmm) REVERT: K2 198 GLN cc_start: 0.4659 (tp40) cc_final: 0.3056 (pp30) REVERT: K3 129 TYR cc_start: 0.6748 (m-10) cc_final: 0.6280 (m-10) REVERT: K4 47 ARG cc_start: 0.7607 (ttt90) cc_final: 0.7355 (ptt-90) REVERT: C1 212 MET cc_start: 0.4167 (ptm) cc_final: 0.3675 (ptt) REVERT: C1 317 MET cc_start: 0.5572 (tpt) cc_final: 0.4623 (tmm) REVERT: C3 29 TYR cc_start: 0.2317 (OUTLIER) cc_final: 0.0697 (p90) REVERT: C3 287 MET cc_start: -0.2277 (mtt) cc_final: -0.2600 (mtt) REVERT: C5 25 MET cc_start: 0.3131 (tpp) cc_final: 0.2877 (tpp) REVERT: C5 59 ARG cc_start: 0.9346 (ttt180) cc_final: 0.8952 (mpt180) REVERT: C5 128 ARG cc_start: 0.9042 (tmt170) cc_final: 0.8617 (ttt-90) REVERT: C5 168 MET cc_start: 0.8715 (mmm) cc_final: 0.8436 (mmm) REVERT: B1 262 MET cc_start: 0.8944 (mmm) cc_final: 0.8723 (mmm) REVERT: B1 285 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B1 325 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8462 (ptm) REVERT: B2 217 MET cc_start: 0.8120 (ppp) cc_final: 0.7796 (ppp) REVERT: B2 262 MET cc_start: 0.8561 (tpp) cc_final: 0.8311 (tpp) REVERT: B3 267 ASP cc_start: 0.8766 (p0) cc_final: 0.8448 (p0) REVERT: B4 188 MET cc_start: 0.8721 (ppp) cc_final: 0.8209 (ppp) REVERT: B4 273 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B5 102 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7593 (t) REVERT: B5 325 MET cc_start: 0.9476 (tpp) cc_final: 0.9171 (tpp) REVERT: G4 9 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6977 (pt) REVERT: G4 21 MET cc_start: 0.9337 (mpp) cc_final: 0.9108 (mpp) REVERT: G5 1 MET cc_start: 0.8695 (ppp) cc_final: 0.8289 (tmm) outliers start: 133 outliers final: 66 residues processed: 364 average time/residue: 0.4753 time to fit residues: 287.9350 Evaluate side-chains 298 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 225 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 175 MET Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 112 HIS Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C4 residue 206 GLU Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain C5 residue 367 LYS Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 285 LEU Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 101 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 323 ASP Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 423 optimal weight: 0.9990 chunk 456 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 130 ASN ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 195 ASN K4 60 GLN ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5 104 ASN ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS C2 222 GLN ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 286 HIS C5 69 HIS ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 220 GLN ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38520 Z= 0.213 Angle : 0.613 11.793 51995 Z= 0.326 Chirality : 0.041 0.219 5780 Planarity : 0.004 0.052 6780 Dihedral : 5.590 58.206 5240 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.80 % Rotamer: Outliers : 2.33 % Allowed : 16.93 % Favored : 80.74 % 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: -0.84 (0.12), residues: 4730 helix: 0.88 (0.11), residues: 2084 sheet: -1.62 (0.17), residues: 787 loop : -1.69 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPK4 45 HIS 0.008 0.001 HISB2 266 PHE 0.024 0.002 PHEB4 199 TYR 0.038 0.002 TYRK5 54 ARG 0.007 0.000 ARGC5 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 340 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 243 time to evaluate : 4.563 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: K2 198 GLN cc_start: 0.4019 (tp40) cc_final: 0.2602 (pp30) REVERT: K3 129 TYR cc_start: 0.6591 (m-10) cc_final: 0.6320 (m-10) REVERT: K4 47 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7315 (ptt-90) REVERT: C1 201 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6347 (t80) REVERT: C1 212 MET cc_start: 0.4181 (ptm) cc_final: 0.3451 (ptt) REVERT: C1 250 HIS cc_start: 0.7881 (t70) cc_final: 0.7610 (t-170) REVERT: C1 279 MET cc_start: 0.8049 (mtt) cc_final: 0.7658 (ptp) REVERT: C1 317 MET cc_start: 0.5458 (tpt) cc_final: 0.4514 (tmm) REVERT: C2 212 MET cc_start: 0.8626 (ppp) cc_final: 0.8403 (ppp) REVERT: C3 126 MET cc_start: 0.5843 (ppp) cc_final: 0.5514 (ppp) REVERT: C3 287 MET cc_start: -0.2436 (mtt) cc_final: -0.2711 (mtt) REVERT: C4 73 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6732 (mt) REVERT: C4 124 MET cc_start: 0.8226 (mtt) cc_final: 0.7933 (mmt) REVERT: C4 126 MET cc_start: 0.7808 (ppp) cc_final: 0.7606 (ppp) REVERT: C5 25 MET cc_start: 0.2860 (tpp) cc_final: 0.2604 (tpp) REVERT: C5 128 ARG cc_start: 0.9002 (tmt170) cc_final: 0.8577 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6808 (tp) REVERT: B1 172 GLU cc_start: 0.8695 (tp30) cc_final: 0.8421 (tp30) REVERT: B2 217 MET cc_start: 0.8204 (ppp) cc_final: 0.8001 (ppp) REVERT: B3 188 MET cc_start: 0.8699 (ppp) cc_final: 0.8322 (ppp) REVERT: B3 267 ASP cc_start: 0.8799 (p0) cc_final: 0.8540 (p0) REVERT: B4 101 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8270 (pmm) REVERT: B4 188 MET cc_start: 0.8766 (ppp) cc_final: 0.8204 (ppp) REVERT: B4 325 MET cc_start: 0.8254 (tpp) cc_final: 0.7940 (tpp) REVERT: B5 325 MET cc_start: 0.9373 (tpp) cc_final: 0.9053 (tpp) REVERT: G2 28 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7389 (tp) REVERT: G4 9 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6898 (pt) REVERT: G4 21 MET cc_start: 0.9319 (mpp) cc_final: 0.9038 (mpp) REVERT: G5 1 MET cc_start: 0.8558 (ppp) cc_final: 0.8251 (tmm) outliers start: 97 outliers final: 56 residues processed: 325 average time/residue: 0.4861 time to fit residues: 265.3676 Evaluate side-chains 286 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 111 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C4 residue 73 LEU Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 120 ILE Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 101 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 259 GLN Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 chunk 449 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 402 optimal weight: 0.0980 chunk 121 optimal weight: 20.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38520 Z= 0.288 Angle : 0.641 11.802 51995 Z= 0.341 Chirality : 0.041 0.192 5780 Planarity : 0.004 0.050 6780 Dihedral : 5.550 58.967 5236 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 3.79 % Allowed : 16.83 % Favored : 79.38 % 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: -0.84 (0.12), residues: 4730 helix: 0.90 (0.11), residues: 2091 sheet: -1.64 (0.17), residues: 775 loop : -1.73 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPK4 45 HIS 0.008 0.001 HISC1 112 PHE 0.023 0.002 PHEB4 199 TYR 0.021 0.002 TYRB4 105 ARG 0.015 0.001 ARGK5 94 *********************** 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 397 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 239 time to evaluate : 4.621 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: K1 183 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8687 (tm-30) REVERT: K2 198 GLN cc_start: 0.4393 (tp40) cc_final: 0.2756 (pp30) REVERT: K3 129 TYR cc_start: 0.6739 (m-10) cc_final: 0.6450 (m-10) REVERT: K3 168 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9295 (tt) REVERT: K5 175 MET cc_start: 0.7980 (tmm) cc_final: 0.7589 (tmm) REVERT: C1 201 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6565 (t80) REVERT: C1 212 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3907 (ptt) REVERT: C1 317 MET cc_start: 0.5338 (tpt) cc_final: 0.4326 (tmm) REVERT: C3 25 MET cc_start: 0.2167 (pmm) cc_final: 0.1929 (pmm) REVERT: C3 124 MET cc_start: 0.7636 (mpp) cc_final: 0.7338 (mpt) REVERT: C3 126 MET cc_start: 0.5800 (ppp) cc_final: 0.5389 (ppp) REVERT: C4 124 MET cc_start: 0.8024 (mtt) cc_final: 0.7692 (mmt) REVERT: C4 126 MET cc_start: 0.7926 (ppp) cc_final: 0.7648 (ppp) REVERT: C4 249 MET cc_start: 0.8646 (mmp) cc_final: 0.8429 (mmp) REVERT: C4 299 MET cc_start: -0.3855 (tpt) cc_final: -0.4352 (tpt) REVERT: C5 59 ARG cc_start: 0.9329 (ttt180) cc_final: 0.9055 (mpt180) REVERT: C5 128 ARG cc_start: 0.9020 (tmt170) cc_final: 0.8581 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6693 (tt) REVERT: B1 262 MET cc_start: 0.9124 (mmm) cc_final: 0.8844 (mmm) REVERT: B1 285 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8570 (pp) REVERT: B3 119 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B3 188 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8310 (ppp) REVERT: B3 260 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B3 267 ASP cc_start: 0.8801 (p0) cc_final: 0.8464 (p0) REVERT: B4 61 MET cc_start: 0.8087 (tmm) cc_final: 0.7830 (tmm) REVERT: B4 101 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8189 (pmm) REVERT: B4 188 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: B4 273 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B5 102 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7584 (t) REVERT: B5 325 MET cc_start: 0.9415 (tpp) cc_final: 0.9096 (tpp) REVERT: G4 9 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6885 (pt) REVERT: G4 21 MET cc_start: 0.9399 (mpp) cc_final: 0.9081 (mpp) REVERT: G5 1 MET cc_start: 0.8652 (ppp) cc_final: 0.8298 (tmm) outliers start: 158 outliers final: 96 residues processed: 373 average time/residue: 0.4635 time to fit residues: 291.8690 Evaluate side-chains 336 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 226 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 183 GLN Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 168 LEU Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 175 MET Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 111 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 191 MET Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C2 residue 345 LEU Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 61 MET Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 285 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 303 ASP Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 101 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 119 ASN Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G3 residue 32 LYS Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 9.9990 chunk 255 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 334 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 chunk 383 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 229 optimal weight: 30.0000 chunk 403 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 195 ASN ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 195 ASN C1 60 ASN ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 222 GLN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38520 Z= 0.235 Angle : 0.618 12.111 51995 Z= 0.327 Chirality : 0.041 0.268 5780 Planarity : 0.004 0.048 6780 Dihedral : 5.323 57.463 5231 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 3.45 % Allowed : 17.51 % Favored : 79.04 % 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: -0.71 (0.12), residues: 4730 helix: 1.00 (0.11), residues: 2084 sheet: -1.62 (0.17), residues: 767 loop : -1.63 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPC3 109 HIS 0.013 0.001 HISC3 84 PHE 0.022 0.002 PHEB4 199 TYR 0.033 0.002 TYRC4 62 ARG 0.007 0.000 ARGC5 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 379 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 235 time to evaluate : 4.429 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: K2 198 GLN cc_start: 0.4299 (tp40) cc_final: 0.2937 (pp30) REVERT: K3 124 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9086 (tt0) REVERT: K3 129 TYR cc_start: 0.6754 (m-10) cc_final: 0.6394 (m-10) REVERT: K5 183 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: C1 201 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6645 (t80) REVERT: C1 212 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.3959 (ptt) REVERT: C1 279 MET cc_start: 0.8012 (mtm) cc_final: 0.7715 (mtm) REVERT: C3 124 MET cc_start: 0.7655 (mpp) cc_final: 0.7444 (mpp) REVERT: C3 126 MET cc_start: 0.5820 (ppp) cc_final: 0.5404 (ppp) REVERT: C3 189 MET cc_start: 0.7654 (ptp) cc_final: 0.6890 (ptp) REVERT: C3 287 MET cc_start: -0.2083 (mtt) cc_final: -0.2312 (mtt) REVERT: C4 126 MET cc_start: 0.7966 (ppp) cc_final: 0.7701 (ppp) REVERT: C4 273 MET cc_start: 0.6355 (pmm) cc_final: 0.6110 (mtm) REVERT: C4 276 ILE cc_start: 0.2930 (OUTLIER) cc_final: 0.2621 (tp) REVERT: C5 128 ARG cc_start: 0.8960 (tmt170) cc_final: 0.8515 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6684 (tt) REVERT: C5 168 MET cc_start: 0.8592 (mmm) cc_final: 0.8376 (mmm) REVERT: B1 262 MET cc_start: 0.9167 (mmm) cc_final: 0.8763 (mmm) REVERT: B2 188 MET cc_start: 0.9168 (ppp) cc_final: 0.8961 (ppp) REVERT: B3 188 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8413 (ppp) REVERT: B3 260 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: B3 267 ASP cc_start: 0.8837 (p0) cc_final: 0.8491 (p0) REVERT: B4 61 MET cc_start: 0.8173 (tmm) cc_final: 0.7848 (tmm) REVERT: B4 188 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8360 (ppp) REVERT: B4 273 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B4 325 MET cc_start: 0.8318 (tpp) cc_final: 0.7985 (tpp) REVERT: B5 325 MET cc_start: 0.9349 (tpp) cc_final: 0.9043 (tpp) REVERT: G3 38 MET cc_start: 0.7232 (mtm) cc_final: 0.6832 (mtm) REVERT: G4 9 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6661 (pt) REVERT: G4 21 MET cc_start: 0.9392 (mpp) cc_final: 0.9185 (mpp) REVERT: G5 1 MET cc_start: 0.8613 (ppp) cc_final: 0.8258 (tmm) outliers start: 144 outliers final: 100 residues processed: 358 average time/residue: 0.4715 time to fit residues: 287.4810 Evaluate side-chains 334 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 224 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 183 GLN Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 112 HIS Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 276 ILE Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 61 MET Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 303 ASP Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 327 VAL Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G3 residue 32 LYS Chi-restraints excluded: chain G4 residue 9 ILE 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: 10.0000 chunk 88 optimal weight: 5.9990 chunk 263 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 449 optimal weight: 5.9990 chunk 373 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 183 GLN ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 60 ASN ** C1 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 222 GLN C2 48 ASN C2 222 GLN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 343 GLN ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 340 ASN B2 16 ASN ** B2 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 75 GLN B4 259 GLN B4 313 ASN ** B5 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 38520 Z= 0.388 Angle : 0.741 13.199 51995 Z= 0.389 Chirality : 0.043 0.260 5780 Planarity : 0.005 0.051 6780 Dihedral : 5.666 53.690 5231 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 4.41 % Allowed : 18.01 % Favored : 77.58 % 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: -1.05 (0.12), residues: 4730 helix: 0.69 (0.11), residues: 2075 sheet: -1.85 (0.18), residues: 712 loop : -1.73 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRPC3 109 HIS 0.012 0.002 HISB1 142 PHE 0.029 0.003 PHEC2 147 TYR 0.022 0.002 TYRK1 71 ARG 0.009 0.001 ARGC5 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 418 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 234 time to evaluate : 4.495 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: K1 183 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: K2 45 TRP cc_start: 0.8755 (OUTLIER) cc_final: 0.7556 (m-90) REVERT: K2 171 MET cc_start: 0.9259 (ptp) cc_final: 0.8850 (ptp) REVERT: K2 198 GLN cc_start: 0.4840 (tp40) cc_final: 0.3234 (pp30) REVERT: K3 129 TYR cc_start: 0.7047 (m-10) cc_final: 0.6734 (m-10) REVERT: C1 69 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.6412 (t-90) REVERT: C1 201 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6721 (t80) REVERT: C1 212 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4792 (ptt) REVERT: C2 187 CYS cc_start: 0.5988 (m) cc_final: 0.5773 (m) REVERT: C3 29 TYR cc_start: 0.2188 (OUTLIER) cc_final: 0.0480 (p90) REVERT: C3 126 MET cc_start: 0.6081 (ppp) cc_final: 0.5617 (ppp) REVERT: C3 317 MET cc_start: 0.3419 (mmm) cc_final: 0.3154 (mmm) REVERT: C4 126 MET cc_start: 0.7996 (ppp) cc_final: 0.7678 (ppp) REVERT: C4 273 MET cc_start: 0.6406 (pmm) cc_final: 0.6179 (mtm) REVERT: C4 321 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5026 (tt) REVERT: C4 366 PHE cc_start: -0.0154 (OUTLIER) cc_final: -0.0511 (m-10) REVERT: C5 128 ARG cc_start: 0.9167 (tmt170) cc_final: 0.8747 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6860 (tt) REVERT: C5 168 MET cc_start: 0.8737 (mmm) cc_final: 0.8430 (mmm) REVERT: B1 285 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8628 (pp) REVERT: B1 325 MET cc_start: 0.8904 (ptm) cc_final: 0.8669 (ptm) REVERT: B3 188 MET cc_start: 0.8823 (ppp) cc_final: 0.8293 (ppp) REVERT: B3 260 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B3 267 ASP cc_start: 0.8877 (p0) cc_final: 0.8539 (p0) REVERT: B4 43 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6629 (tp) REVERT: B4 61 MET cc_start: 0.8186 (tmm) cc_final: 0.7939 (tmm) REVERT: B4 188 MET cc_start: 0.8903 (ppp) cc_final: 0.8350 (tmm) REVERT: B4 273 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B5 119 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7738 (m-40) REVERT: B5 325 MET cc_start: 0.9471 (tpp) cc_final: 0.9122 (tpp) REVERT: G3 27 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.7455 (mmt90) REVERT: G4 9 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6769 (pt) REVERT: G5 1 MET cc_start: 0.8737 (ppp) cc_final: 0.8402 (tmm) outliers start: 184 outliers final: 123 residues processed: 399 average time/residue: 0.4695 time to fit residues: 313.5259 Evaluate side-chains 365 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 226 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 183 GLN Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 45 TRP Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K2 residue 132 THR Chi-restraints excluded: chain K2 residue 191 TYR Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 112 VAL Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 69 HIS Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 112 HIS Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C4 residue 321 LEU Chi-restraints excluded: chain C4 residue 366 PHE Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 67 HIS Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 225 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 61 MET Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 285 LEU Chi-restraints excluded: chain B1 residue 303 ASP Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 307 VAL Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 214 ARG Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 43 ILE Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 293 ASN Chi-restraints excluded: chain B4 residue 317 CYS Chi-restraints excluded: chain B4 residue 327 VAL Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 70 LEU Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain B5 residue 338 ILE Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G3 residue 27 ARG Chi-restraints excluded: chain G3 residue 32 LYS Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 328 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 206 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 60 GLN ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 48 ASN C2 103 GLN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 125 ASN ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38520 Z= 0.266 Angle : 0.664 14.824 51995 Z= 0.347 Chirality : 0.042 0.334 5780 Planarity : 0.004 0.074 6780 Dihedral : 5.480 54.011 5231 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 3.57 % Allowed : 19.28 % Favored : 77.15 % 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: -0.89 (0.12), residues: 4730 helix: 0.79 (0.11), residues: 2092 sheet: -1.81 (0.18), residues: 727 loop : -1.60 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRPC3 109 HIS 0.007 0.001 HISB1 142 PHE 0.030 0.002 PHEC3 224 TYR 0.018 0.002 TYRC2 29 ARG 0.014 0.000 ARGC2 247 *********************** 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 375 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 226 time to evaluate : 5.071 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: K2 171 MET cc_start: 0.9070 (ptp) cc_final: 0.8827 (ptp) REVERT: K2 198 GLN cc_start: 0.4708 (tp40) cc_final: 0.3076 (pp30) REVERT: K3 129 TYR cc_start: 0.6941 (m-10) cc_final: 0.6591 (m-10) REVERT: C1 69 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.6068 (t-90) REVERT: C1 201 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6677 (t80) REVERT: C1 212 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4533 (ptt) REVERT: C2 317 MET cc_start: 0.3066 (mmp) cc_final: 0.2856 (mmm) REVERT: C3 126 MET cc_start: 0.6070 (ppp) cc_final: 0.5509 (ppp) REVERT: C3 287 MET cc_start: -0.1516 (mtt) cc_final: -0.1755 (mtt) REVERT: C4 126 MET cc_start: 0.7980 (ppp) cc_final: 0.7651 (ppp) REVERT: C4 273 MET cc_start: 0.6336 (pmm) cc_final: 0.6092 (mtm) REVERT: C4 321 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4837 (tt) REVERT: C5 128 ARG cc_start: 0.9131 (tmt170) cc_final: 0.8669 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6894 (tt) REVERT: C5 168 MET cc_start: 0.8705 (mmm) cc_final: 0.8412 (mmm) REVERT: B1 262 MET cc_start: 0.9215 (mmm) cc_final: 0.8906 (mmm) REVERT: B1 285 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (pp) REVERT: B1 325 MET cc_start: 0.8795 (ptm) cc_final: 0.8591 (ptm) REVERT: B3 188 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: B3 267 ASP cc_start: 0.8812 (p0) cc_final: 0.8473 (p0) REVERT: B4 61 MET cc_start: 0.8215 (tmm) cc_final: 0.7867 (tmm) REVERT: B4 188 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8324 (tmm) REVERT: B4 273 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B4 325 MET cc_start: 0.8283 (tpp) cc_final: 0.7936 (tpp) REVERT: B5 102 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7511 (t) REVERT: B5 119 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7650 (m-40) REVERT: B5 325 MET cc_start: 0.9385 (tpp) cc_final: 0.9025 (tpp) REVERT: G3 38 MET cc_start: 0.7309 (mtm) cc_final: 0.6919 (mtm) REVERT: G4 9 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6810 (pt) REVERT: G5 1 MET cc_start: 0.8753 (ppp) cc_final: 0.8427 (tmm) outliers start: 149 outliers final: 109 residues processed: 355 average time/residue: 0.4659 time to fit residues: 278.8463 Evaluate side-chains 340 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 219 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 102 VAL Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 123 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 69 HIS Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C4 residue 321 LEU Chi-restraints excluded: chain C5 residue 39 ASN Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 225 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 136 SER Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 285 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 273 ILE Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 317 CYS Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 267 optimal weight: 40.0000 chunk 135 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 305 optimal weight: 0.0570 chunk 221 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 60 GLN ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 60 ASN ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 84 HIS ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 160 HIS ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 84 HIS C5 107 GLN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 18 GLN ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38520 Z= 0.240 Angle : 0.654 14.920 51995 Z= 0.340 Chirality : 0.042 0.336 5780 Planarity : 0.004 0.073 6780 Dihedral : 5.363 53.668 5231 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 3.53 % Allowed : 19.66 % Favored : 76.81 % 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: -0.79 (0.12), residues: 4730 helix: 0.90 (0.11), residues: 2099 sheet: -1.81 (0.17), residues: 767 loop : -1.55 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPC3 109 HIS 0.007 0.001 HISB1 142 PHE 0.022 0.002 PHEC2 147 TYR 0.018 0.002 TYRC2 29 ARG 0.008 0.000 ARGC2 247 *********************** 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 377 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 230 time to evaluate : 4.392 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: K1 183 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8574 (tm-30) REVERT: K2 171 MET cc_start: 0.9066 (ptp) cc_final: 0.8831 (ptp) REVERT: K2 198 GLN cc_start: 0.4586 (tp40) cc_final: 0.2789 (pp30) REVERT: K3 129 TYR cc_start: 0.7049 (m-10) cc_final: 0.6705 (m-10) REVERT: C1 69 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5927 (t-90) REVERT: C1 201 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6733 (t80) REVERT: C1 212 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4427 (ptt) REVERT: C1 279 MET cc_start: 0.8253 (mtm) cc_final: 0.8012 (ptp) REVERT: C3 29 TYR cc_start: 0.1513 (OUTLIER) cc_final: -0.0326 (p90) REVERT: C3 64 MET cc_start: 0.6860 (mtp) cc_final: 0.6551 (mtm) REVERT: C3 287 MET cc_start: -0.1228 (mtt) cc_final: -0.1485 (mtt) REVERT: C4 126 MET cc_start: 0.8035 (ppp) cc_final: 0.7701 (ppp) REVERT: C4 273 MET cc_start: 0.6110 (pmm) cc_final: 0.5859 (mtm) REVERT: C4 321 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4692 (tt) REVERT: C5 128 ARG cc_start: 0.9109 (tmt170) cc_final: 0.8659 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7024 (tt) REVERT: C5 168 MET cc_start: 0.8719 (mmm) cc_final: 0.8421 (mmm) REVERT: B1 262 MET cc_start: 0.9210 (mmm) cc_final: 0.8894 (mmm) REVERT: B1 285 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8525 (pp) REVERT: B3 188 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8331 (ppp) REVERT: B3 267 ASP cc_start: 0.8797 (p0) cc_final: 0.8443 (p0) REVERT: B4 61 MET cc_start: 0.8184 (tmm) cc_final: 0.7844 (tmm) REVERT: B4 188 MET cc_start: 0.8886 (ppp) cc_final: 0.8342 (tmm) REVERT: B4 273 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B4 325 MET cc_start: 0.8288 (tpp) cc_final: 0.7949 (tpp) REVERT: B5 102 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7480 (t) REVERT: B5 119 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7668 (m-40) REVERT: B5 325 MET cc_start: 0.9386 (tpp) cc_final: 0.9055 (tpp) REVERT: G3 38 MET cc_start: 0.7240 (mtm) cc_final: 0.6813 (mtm) REVERT: G4 9 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6827 (pt) REVERT: G5 1 MET cc_start: 0.8728 (ppp) cc_final: 0.8419 (tmm) outliers start: 147 outliers final: 108 residues processed: 356 average time/residue: 0.4533 time to fit residues: 273.9883 Evaluate side-chains 342 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 221 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 183 GLN Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 69 HIS Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 201 TYR Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 233 TYR Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C4 residue 321 LEU Chi-restraints excluded: chain C5 residue 39 ASN Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 136 SER Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 285 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 273 ILE Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 317 CYS Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 262 MET Chi-restraints excluded: chain B5 residue 263 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 5.9990 chunk 429 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 417 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 327 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 395 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 104 ASN ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 48 ASN ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 135 ASN ** C3 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 132 GLN C4 133 GLN ** C5 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 176 GLN ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38520 Z= 0.300 Angle : 0.698 14.786 51995 Z= 0.362 Chirality : 0.042 0.365 5780 Planarity : 0.004 0.068 6780 Dihedral : 5.480 51.863 5231 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 28.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.87 % Favored : 93.02 % Rotamer: Outliers : 3.24 % Allowed : 20.07 % Favored : 76.69 % 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: -0.89 (0.12), residues: 4730 helix: 0.80 (0.11), residues: 2092 sheet: -1.81 (0.18), residues: 707 loop : -1.62 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPC3 109 HIS 0.008 0.001 HISC1 112 PHE 0.022 0.002 PHEG1 61 TYR 0.021 0.002 TYRK1 71 ARG 0.007 0.001 ARGC2 247 *********************** 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 359 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 224 time to evaluate : 4.669 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: K1 183 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: K2 45 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.7673 (m-90) REVERT: K2 198 GLN cc_start: 0.4576 (tp40) cc_final: 0.2570 (pp30) REVERT: K3 129 TYR cc_start: 0.7125 (m-10) cc_final: 0.6766 (m-10) REVERT: C1 69 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5920 (t-90) REVERT: C1 212 MET cc_start: 0.5279 (OUTLIER) cc_final: 0.4709 (ptt) REVERT: C1 279 MET cc_start: 0.8310 (mtm) cc_final: 0.8033 (ptp) REVERT: C3 29 TYR cc_start: 0.1774 (OUTLIER) cc_final: -0.0046 (p90) REVERT: C3 64 MET cc_start: 0.6893 (mtp) cc_final: 0.6556 (mtm) REVERT: C3 126 MET cc_start: 0.6174 (ppp) cc_final: 0.5789 (ppp) REVERT: C3 287 MET cc_start: -0.1114 (mtt) cc_final: -0.1325 (mtt) REVERT: C4 126 MET cc_start: 0.7995 (ppp) cc_final: 0.7651 (ppp) REVERT: C4 321 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4910 (tt) REVERT: C5 128 ARG cc_start: 0.9192 (tmt170) cc_final: 0.8760 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6844 (tt) REVERT: B1 262 MET cc_start: 0.9247 (mmm) cc_final: 0.8937 (mmm) REVERT: B3 188 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8329 (ppp) REVERT: B3 267 ASP cc_start: 0.8838 (p0) cc_final: 0.8473 (p0) REVERT: B4 45 MET cc_start: 0.8378 (mpp) cc_final: 0.7976 (mmp) REVERT: B4 61 MET cc_start: 0.8156 (tmm) cc_final: 0.7858 (tmm) REVERT: B4 188 MET cc_start: 0.8884 (ppp) cc_final: 0.8331 (tmm) REVERT: B4 273 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B5 102 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7509 (t) REVERT: B5 119 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7651 (m-40) REVERT: B5 325 MET cc_start: 0.9443 (tpp) cc_final: 0.9099 (tpp) REVERT: G3 38 MET cc_start: 0.7268 (mtm) cc_final: 0.6834 (mtm) REVERT: G4 9 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6928 (pt) REVERT: G5 1 MET cc_start: 0.8723 (ppp) cc_final: 0.8415 (tmm) outliers start: 135 outliers final: 110 residues processed: 342 average time/residue: 0.4593 time to fit residues: 265.9523 Evaluate side-chains 343 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 221 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 62 LEU Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 104 ASN Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 183 GLN Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 45 TRP Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 102 VAL Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 69 HIS Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 233 TYR Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C4 residue 321 LEU Chi-restraints excluded: chain C5 residue 39 ASN Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 273 ILE Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 317 CYS Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 263 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 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: 5.9990 chunk 441 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 463 optimal weight: 20.0000 chunk 426 optimal weight: 9.9990 chunk 368 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 284 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 48 ASN ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 132 GLN C4 242 ASN ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 38520 Z= 0.313 Angle : 0.719 14.217 51995 Z= 0.372 Chirality : 0.043 0.354 5780 Planarity : 0.004 0.069 6780 Dihedral : 5.523 50.909 5231 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.19 % Favored : 92.71 % Rotamer: Outliers : 3.21 % Allowed : 20.38 % Favored : 76.40 % 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: -0.95 (0.12), residues: 4730 helix: 0.72 (0.11), residues: 2095 sheet: -1.82 (0.18), residues: 707 loop : -1.62 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPC3 109 HIS 0.008 0.001 HISK1 108 PHE 0.045 0.002 PHEC3 374 TYR 0.024 0.002 TYRK1 71 ARG 0.007 0.001 ARGK1 107 ********************** 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 357 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 223 time to evaluate : 4.899 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: K1 183 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8538 (tm-30) REVERT: K2 198 GLN cc_start: 0.4626 (tp40) cc_final: 0.2623 (pp30) REVERT: K3 129 TYR cc_start: 0.7089 (m-10) cc_final: 0.6703 (m-10) REVERT: C1 212 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.4650 (ptt) REVERT: C1 279 MET cc_start: 0.8349 (mtm) cc_final: 0.8069 (ptp) REVERT: C3 25 MET cc_start: 0.1885 (pmm) cc_final: 0.1677 (pmm) REVERT: C3 29 TYR cc_start: 0.1786 (OUTLIER) cc_final: 0.0149 (p90) REVERT: C3 126 MET cc_start: 0.6258 (ppp) cc_final: 0.5871 (ppp) REVERT: C3 287 MET cc_start: -0.0851 (mtt) cc_final: -0.1053 (mtt) REVERT: C4 25 MET cc_start: 0.8162 (ttt) cc_final: 0.7540 (tpp) REVERT: C4 124 MET cc_start: 0.7881 (mmm) cc_final: 0.7670 (mmt) REVERT: C4 126 MET cc_start: 0.8069 (ppp) cc_final: 0.7675 (ppp) REVERT: C4 273 MET cc_start: 0.6063 (pmm) cc_final: 0.5841 (mtm) REVERT: C4 321 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4934 (tt) REVERT: C5 128 ARG cc_start: 0.9234 (tmt170) cc_final: 0.8928 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6941 (tt) REVERT: B1 262 MET cc_start: 0.9244 (mmm) cc_final: 0.8966 (mmm) REVERT: B3 188 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8381 (ppp) REVERT: B3 267 ASP cc_start: 0.8849 (p0) cc_final: 0.8481 (p0) REVERT: B4 45 MET cc_start: 0.8366 (mpp) cc_final: 0.7981 (mmp) REVERT: B4 61 MET cc_start: 0.8115 (tmm) cc_final: 0.7823 (tmm) REVERT: B4 188 MET cc_start: 0.8884 (ppp) cc_final: 0.8314 (tmm) REVERT: B4 273 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B5 102 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7493 (t) REVERT: B5 119 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: B5 325 MET cc_start: 0.9411 (tpp) cc_final: 0.9051 (tpp) REVERT: G3 27 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.7662 (mmt90) REVERT: G3 38 MET cc_start: 0.7299 (mtm) cc_final: 0.6860 (mtm) REVERT: G4 9 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6910 (pt) REVERT: G5 1 MET cc_start: 0.8758 (ppp) cc_final: 0.8474 (tmm) outliers start: 134 outliers final: 115 residues processed: 341 average time/residue: 0.4618 time to fit residues: 267.0004 Evaluate side-chains 346 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 220 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 43 SER Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 62 LEU Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 183 GLN Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 102 VAL Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 173 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 95 ASP Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 180 ARG Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 113 GLN Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 233 TYR Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C3 residue 178 VAL Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C4 residue 321 LEU Chi-restraints excluded: chain C5 residue 39 ASN Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 63 THR Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 313 MET Chi-restraints excluded: chain C5 residue 314 CYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 232 ILE Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 333 ASP Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 66 ASP Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 143 THR Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 273 ILE Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 246 ASP Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B4 residue 317 CYS Chi-restraints excluded: chain B5 residue 5 ASP Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 119 ASN Chi-restraints excluded: chain B5 residue 128 THR Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 263 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 1 MET Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G3 residue 27 ARG Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 9.9990 chunk 392 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 369 optimal weight: 0.0270 chunk 154 optimal weight: 40.0000 chunk 379 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 195 ASN ** K5 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 110 ASN ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.077241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.057931 restraints weight = 426941.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 86)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.054404 restraints weight = 249364.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.054650 restraints weight = 175751.882| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38520 Z= 0.238 Angle : 0.683 14.259 51995 Z= 0.352 Chirality : 0.043 0.351 5780 Planarity : 0.004 0.066 6780 Dihedral : 5.392 52.110 5231 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 94.00 % Rotamer: Outliers : 2.95 % Allowed : 20.62 % 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: -0.79 (0.12), residues: 4730 helix: 0.84 (0.11), residues: 2099 sheet: -1.85 (0.18), residues: 742 loop : -1.47 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRPC4 34 HIS 0.007 0.001 HISC1 69 PHE 0.046 0.002 PHEC3 224 TYR 0.019 0.002 TYRK1 71 ARG 0.007 0.000 ARGC2 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8695.33 seconds wall clock time: 160 minutes 37.40 seconds (9637.40 seconds total)