Starting phenix.real_space_refine on Sun Dec 17 05:47:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/12_2023/8u81_41996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/12_2023/8u81_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_41996/12_2023/8u81_41996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/12_2023/8u81_41996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/12_2023/8u81_41996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u81_41996/12_2023/8u81_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 18.20, per 1000 atoms: 0.48 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: 16.03 Conformation dependent library (CDL) restraints added in 6.8 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: 4.00 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: 17.26 Time building geometry restraints manager: 17.26 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: 1.580 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: 0.020 Extract box with map and model: 8.040 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 101.170 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.390 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: 117.750 ------------------------------------------------------------------------------- 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 : 3.858 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 outliers start: 25 outliers final: 12 residues processed: 275 average time/residue: 0.4976 time to fit residues: 227.7472 Evaluate side-chains 248 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4713 time to fit residues: 15.2326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 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: 8.9990 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 ** 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 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 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1759 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= 0.403 Angle : 0.771 13.815 51995 Z= 0.411 Chirality : 0.044 0.204 5780 Planarity : 0.005 0.064 6780 Dihedral : 5.709 40.484 5225 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 3.09 % Allowed : 15.35 % Favored : 81.56 % 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: -1.17 (0.12), residues: 4730 helix: 0.53 (0.11), residues: 2079 sheet: -1.58 (0.17), residues: 759 loop : -1.88 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRPC4 34 HIS 0.011 0.002 HISC5 67 PHE 0.029 0.003 PHEG5 61 TYR 0.031 0.003 TYRC2 29 ARG 0.015 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 376 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 247 time to evaluate : 4.802 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 outliers start: 129 outliers final: 63 residues processed: 361 average time/residue: 0.5029 time to fit residues: 303.6978 Evaluate side-chains 283 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 4.431 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.3984 time to fit residues: 52.4321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 287 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 423 optimal weight: 0.8980 chunk 456 optimal weight: 5.9990 chunk 376 optimal weight: 0.9990 chunk 419 optimal weight: 0.0970 chunk 144 optimal weight: 5.9990 chunk 339 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 151 GLN K2 60 GLN ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 192 ASN K3 130 ASN ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 368 GLN C2 222 GLN C4 286 HIS C5 69 HIS ** C5 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 163 GLN ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 220 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 B4 259 GLN ** B4 268 ASN ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38520 Z= 0.164 Angle : 0.609 11.698 51995 Z= 0.320 Chirality : 0.042 0.253 5780 Planarity : 0.004 0.052 6780 Dihedral : 5.142 35.584 5225 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.20 % Allowed : 16.43 % Favored : 82.37 % 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: -0.69 (0.12), residues: 4730 helix: 1.00 (0.11), residues: 2078 sheet: -1.53 (0.17), residues: 790 loop : -1.60 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPK4 45 HIS 0.009 0.001 HISB2 266 PHE 0.023 0.002 PHEB4 199 TYR 0.036 0.001 TYRK5 54 ARG 0.005 0.000 ARGC1 59 *********************** 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 297 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 14 residues processed: 293 average time/residue: 0.4728 time to fit residues: 235.5281 Evaluate side-chains 233 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 4.833 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4560 time to fit residues: 17.3895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 449 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 402 optimal weight: 0.0060 chunk 121 optimal weight: 20.0000 overall best weight: 5.4004 ------------------------------------------------------------------------------- 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 170 GLN ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 195 ASN ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 130 ASN ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 195 ASN K5 75 GLN ** K5 162 GLN ** 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 67 HIS ** 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 142 HIS ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 38520 Z= 0.297 Angle : 0.662 13.388 51995 Z= 0.350 Chirality : 0.042 0.322 5780 Planarity : 0.004 0.048 6780 Dihedral : 5.205 32.166 5225 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 1.97 % Allowed : 17.29 % 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: -0.76 (0.12), residues: 4730 helix: 0.96 (0.11), residues: 2085 sheet: -1.70 (0.17), residues: 799 loop : -1.60 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPK4 45 HIS 0.008 0.002 HISC1 112 PHE 0.021 0.002 PHEB4 199 TYR 0.022 0.002 TYRB4 105 ARG 0.008 0.001 ARGC5 120 *********************** 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 326 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 244 time to evaluate : 4.414 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 outliers start: 82 outliers final: 47 residues processed: 316 average time/residue: 0.4661 time to fit residues: 252.0083 Evaluate side-chains 269 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3692 time to fit residues: 37.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 185 optimal weight: 30.0000 chunk 383 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 229 optimal weight: 30.0000 chunk 403 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 195 ASN ** C1 100 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 67 HIS ** 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 340 ASN B2 16 ASN ** B2 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 142 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 313 ASN ** B5 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 295 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 38520 Z= 0.418 Angle : 0.772 13.019 51995 Z= 0.409 Chirality : 0.045 0.322 5780 Planarity : 0.005 0.055 6780 Dihedral : 5.684 29.086 5225 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 2.06 % Allowed : 18.56 % 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: -1.19 (0.12), residues: 4730 helix: 0.54 (0.11), residues: 2073 sheet: -1.92 (0.17), residues: 727 loop : -1.75 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPC3 109 HIS 0.010 0.002 HISC2 112 PHE 0.026 0.003 PHEG5 61 TYR 0.027 0.002 TYRB4 105 ARG 0.010 0.001 ARGB4 197 *********************** 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 317 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 231 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 43 residues processed: 312 average time/residue: 0.4833 time to fit residues: 257.0706 Evaluate side-chains 261 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3755 time to fit residues: 35.5839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 6.9990 chunk 404 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 263 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 449 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 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** ** K3 183 GLN ** 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 60 ASN ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 48 ASN ** C2 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 343 GLN ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5 107 GLN ** C5 132 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 340 ASN ** 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 295 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38520 Z= 0.255 Angle : 0.659 14.099 51995 Z= 0.344 Chirality : 0.042 0.351 5780 Planarity : 0.004 0.047 6780 Dihedral : 5.366 27.353 5225 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.92 % Favored : 93.97 % Rotamer: Outliers : 1.10 % Allowed : 19.42 % Favored : 79.47 % 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: 0.78 (0.11), residues: 2082 sheet: -1.86 (0.17), residues: 789 loop : -1.64 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPC3 109 HIS 0.009 0.001 HISC1 250 PHE 0.025 0.002 PHEC2 147 TYR 0.019 0.002 TYRK3 129 ARG 0.008 0.000 ARGC1 59 *********************** 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 283 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 4.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 278 average time/residue: 0.4851 time to fit residues: 228.4140 Evaluate side-chains 245 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 221 time to evaluate : 4.105 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3404 time to fit residues: 20.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 256 optimal weight: 40.0000 chunk 328 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 448 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 273 optimal weight: 0.0030 chunk 206 optimal weight: 20.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 108 HIS ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 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** ** K3 183 GLN ** 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS C2 84 HIS C2 222 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 132 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** B1 125 ASN ** 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** G2 18 GLN ** 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: 0.7571 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38520 Z= 0.215 Angle : 0.648 14.716 51995 Z= 0.337 Chirality : 0.042 0.371 5780 Planarity : 0.004 0.044 6780 Dihedral : 5.180 26.915 5225 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 0.74 % Allowed : 20.50 % Favored : 78.75 % 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: -0.75 (0.12), residues: 4730 helix: 0.91 (0.11), residues: 2076 sheet: -1.82 (0.17), residues: 799 loop : -1.45 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRPC3 109 HIS 0.016 0.001 HISC1 69 PHE 0.026 0.002 PHEC2 147 TYR 0.015 0.001 TYRC2 29 ARG 0.007 0.000 ARGC1 59 *********************** 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 255 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 4.325 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 outliers start: 31 outliers final: 12 residues processed: 254 average time/residue: 0.4893 time to fit residues: 210.4926 Evaluate side-chains 228 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 4.181 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3372 time to fit residues: 13.3136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 267 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 162 GLN ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 162 GLN ** K2 170 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** ** K3 183 GLN ** 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 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** 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 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** 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** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 132 GLN C4 133 GLN C5 84 HIS ** C5 132 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** ** 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 295 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: 0.7586 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38520 Z= 0.264 Angle : 0.675 13.097 51995 Z= 0.353 Chirality : 0.042 0.328 5780 Planarity : 0.004 0.041 6780 Dihedral : 5.213 26.829 5225 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 1.06 % Allowed : 21.06 % Favored : 77.89 % 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: 0.86 (0.11), residues: 2076 sheet: -1.82 (0.17), residues: 799 loop : -1.46 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPC3 109 HIS 0.007 0.001 HISB1 142 PHE 0.022 0.002 PHEC5 366 TYR 0.025 0.002 TYRK3 129 ARG 0.006 0.000 ARGK2 72 *********************** 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 268 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 5.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 259 average time/residue: 0.4862 time to fit residues: 215.2927 Evaluate side-chains 237 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 4.204 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3537 time to fit residues: 17.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 391 optimal weight: 5.9990 chunk 417 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 377 optimal weight: 0.0970 chunk 395 optimal weight: 0.9980 chunk 416 optimal weight: 9.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** K3 183 GLN ** 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** 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 C2 222 GLN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 272 HIS ** 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 218 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** ** 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** ** 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: 0.7569 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38520 Z= 0.212 Angle : 0.673 14.764 51995 Z= 0.345 Chirality : 0.042 0.316 5780 Planarity : 0.004 0.083 6780 Dihedral : 5.114 26.547 5225 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 0.41 % Allowed : 21.68 % Favored : 77.91 % 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: -0.66 (0.12), residues: 4730 helix: 0.96 (0.11), residues: 2077 sheet: -1.73 (0.17), residues: 798 loop : -1.37 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPC3 109 HIS 0.008 0.001 HISC1 69 PHE 0.021 0.002 PHEC2 147 TYR 0.016 0.001 TYRK1 71 ARG 0.007 0.000 ARGK5 107 *********************** 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 248 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 245 average time/residue: 0.4917 time to fit residues: 205.5148 Evaluate side-chains 232 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 4.389 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3745 time to fit residues: 10.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 4.9990 chunk 441 optimal weight: 8.9990 chunk 269 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 463 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 284 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** K2 170 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** K3 183 GLN ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 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 69 HIS ** 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 48 ASN C2 110 ASN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 135 ASN C3 141 ASN ** C3 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 142 HIS ** 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 295 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** ** 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: 0.7609 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 38520 Z= 0.334 Angle : 0.744 12.722 51995 Z= 0.385 Chirality : 0.043 0.279 5780 Planarity : 0.004 0.047 6780 Dihedral : 5.374 26.784 5225 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 29.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.19 % Favored : 92.71 % Rotamer: Outliers : 0.26 % Allowed : 22.04 % Favored : 77.70 % 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: -0.90 (0.12), residues: 4730 helix: 0.74 (0.11), residues: 2095 sheet: -1.82 (0.17), residues: 736 loop : -1.54 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRPC3 109 HIS 0.009 0.002 HISB1 142 PHE 0.027 0.003 PHEC5 366 TYR 0.027 0.002 TYRK3 129 ARG 0.008 0.001 ARGC4 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 234 average time/residue: 0.4834 time to fit residues: 194.0691 Evaluate side-chains 228 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 4.418 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3966 time to fit residues: 11.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 113 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 369 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 379 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 104 ASN ** K2 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 170 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** 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 48 ASN C2 110 ASN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 141 ASN ** C3 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 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** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.077705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.058458 restraints weight = 425648.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.058615 restraints weight = 252834.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.058659 restraints weight = 177267.482| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38520 Z= 0.220 Angle : 0.689 12.903 51995 Z= 0.353 Chirality : 0.043 0.285 5780 Planarity : 0.004 0.040 6780 Dihedral : 5.205 27.793 5225 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.60 % Favored : 94.29 % Rotamer: Outliers : 0.22 % Allowed : 22.25 % Favored : 77.53 % 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: 0.86 (0.11), residues: 2097 sheet: -1.68 (0.17), residues: 781 loop : -1.40 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRPC3 109 HIS 0.009 0.001 HISC1 69 PHE 0.042 0.002 PHEC3 374 TYR 0.018 0.002 TYRK5 71 ARG 0.006 0.000 ARGC5 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7308.13 seconds wall clock time: 142 minutes 45.89 seconds (8565.89 seconds total)