Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 16:34:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/10_2023/6lqj_0947.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 54 5.16 5 C 10791 2.51 5 N 2925 2.21 5 O 3330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E ASP 248": "OD1" <-> "OD2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ASP 248": "OD1" <-> "OD2" Residue "G TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 210": "OD1" <-> "OD2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H ASP 248": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 210": "OD1" <-> "OD2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 236": "OE1" <-> "OE2" Residue "I ASP 248": "OD1" <-> "OD2" Residue "a ASP 58": "OD1" <-> "OD2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "c ASP 58": "OD1" <-> "OD2" Residue "d ASP 58": "OD1" <-> "OD2" Residue "e ASP 58": "OD1" <-> "OD2" Residue "f ASP 58": "OD1" <-> "OD2" Residue "g ASP 58": "OD1" <-> "OD2" Residue "h ASP 58": "OD1" <-> "OD2" Residue "i ASP 58": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 17100 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "B" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "E" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "G" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "H" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "I" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "b" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "c" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "d" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "e" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "f" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "g" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "h" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "i" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Time building chain proxies: 8.71, per 1000 atoms: 0.51 Number of scatterers: 17100 At special positions: 0 Unit cell: (111, 112, 123, 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 54 16.00 O 3330 8.00 N 2925 7.00 C 10791 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: 6.77 Conformation dependent library (CDL) restraints added in 2.4 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 18 sheets defined 26.0% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 37 through 47 Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 37 through 47 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 37 through 47 Processing helix chain 'd' and resid 34 through 36 No H-bonds generated for 'chain 'd' and resid 34 through 36' Processing helix chain 'd' and resid 37 through 47 Processing helix chain 'e' and resid 34 through 36 No H-bonds generated for 'chain 'e' and resid 34 through 36' Processing helix chain 'e' and resid 37 through 47 Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 37 through 47 Processing helix chain 'g' and resid 34 through 36 No H-bonds generated for 'chain 'g' and resid 34 through 36' Processing helix chain 'g' and resid 37 through 47 Processing helix chain 'h' and resid 34 through 36 No H-bonds generated for 'chain 'h' and resid 34 through 36' Processing helix chain 'h' and resid 37 through 47 Processing helix chain 'i' and resid 34 through 36 No H-bonds generated for 'chain 'i' and resid 34 through 36' Processing helix chain 'i' and resid 37 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE A 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 96 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 51 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 57 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 57 current: chain 'H' and resid 162 through 180 removed outlier: 6.269A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE D 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU D 96 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 51 " --> pdb=" O LEU D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE E 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 96 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 51 " --> pdb=" O LEU E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE F 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 96 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 51 " --> pdb=" O LEU F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE H 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 96 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 51 " --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE I 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU I 96 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 51 " --> pdb=" O LEU I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 755 hydrogen bonds defined for protein. 2238 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: 4.77 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5751 1.34 - 1.45: 2233 1.45 - 1.57: 9314 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 17397 Sorted by residual: bond pdb=" CA ASP B 164 " pdb=" CB ASP B 164 " ideal model delta sigma weight residual 1.534 1.512 0.023 1.77e-02 3.19e+03 1.65e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.59e+00 bond pdb=" CA ASP H 164 " pdb=" CB ASP H 164 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.77e-02 3.19e+03 1.58e+00 bond pdb=" CG PRO A 67 " pdb=" CD PRO A 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.57e+00 bond pdb=" CG PRO E 67 " pdb=" CD PRO E 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.55e+00 ... (remaining 17392 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.21: 379 106.21 - 113.19: 9189 113.19 - 120.18: 6639 120.18 - 127.17: 7265 127.17 - 134.16: 126 Bond angle restraints: 23598 Sorted by residual: angle pdb=" CA PHE f 31 " pdb=" CB PHE f 31 " pdb=" CG PHE f 31 " ideal model delta sigma weight residual 113.80 116.91 -3.11 1.00e+00 1.00e+00 9.66e+00 angle pdb=" CA PHE i 31 " pdb=" CB PHE i 31 " pdb=" CG PHE i 31 " ideal model delta sigma weight residual 113.80 116.90 -3.10 1.00e+00 1.00e+00 9.58e+00 angle pdb=" CA PHE a 31 " pdb=" CB PHE a 31 " pdb=" CG PHE a 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.51e+00 angle pdb=" CA PHE d 31 " pdb=" CB PHE d 31 " pdb=" CG PHE d 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.49e+00 angle pdb=" CA PHE e 31 " pdb=" CB PHE e 31 " pdb=" CG PHE e 31 " ideal model delta sigma weight residual 113.80 116.86 -3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 23593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 8896 15.66 - 31.31: 1010 31.31 - 46.97: 291 46.97 - 62.62: 135 62.62 - 78.28: 18 Dihedral angle restraints: 10350 sinusoidal: 4032 harmonic: 6318 Sorted by residual: dihedral pdb=" CA GLY f 32 " pdb=" C GLY f 32 " pdb=" N GLY f 33 " pdb=" CA GLY f 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY d 32 " pdb=" C GLY d 32 " pdb=" N GLY d 33 " pdb=" CA GLY d 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY e 32 " pdb=" C GLY e 32 " pdb=" N GLY e 33 " pdb=" CA GLY e 33 " ideal model delta harmonic sigma weight residual 180.00 149.02 30.98 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1530 0.036 - 0.072: 831 0.072 - 0.108: 179 0.108 - 0.145: 102 0.145 - 0.181: 13 Chirality restraints: 2655 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PHE i 31 " pdb=" N PHE i 31 " pdb=" C PHE i 31 " pdb=" CB PHE i 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA PHE e 31 " pdb=" N PHE e 31 " pdb=" C PHE e 31 " pdb=" CB PHE e 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 2652 not shown) Planarity restraints: 3123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE g 31 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE g 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE g 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE g 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE g 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE g 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE g 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE e 31 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.27e+00 pdb=" CG PHE e 31 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE e 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE e 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE e 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE e 31 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE e 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 31 " -0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE c 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE c 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE c 31 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE c 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE c 31 " -0.003 2.00e-02 2.50e+03 ... (remaining 3120 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2731 2.75 - 3.29: 16427 3.29 - 3.83: 29104 3.83 - 4.36: 35687 4.36 - 4.90: 64804 Nonbonded interactions: 148753 Sorted by model distance: nonbonded pdb=" OD1 ASN I 224 " pdb=" N MET i 22 " model vdw 2.216 2.520 nonbonded pdb=" O GLN A 102 " pdb=" ND2 ASN A 106 " model vdw 2.226 2.520 nonbonded pdb=" O GLN H 102 " pdb=" ND2 ASN H 106 " model vdw 2.226 2.520 nonbonded pdb=" O GLN G 102 " pdb=" ND2 ASN G 106 " model vdw 2.227 2.520 nonbonded pdb=" O GLN I 102 " pdb=" ND2 ASN I 106 " model vdw 2.227 2.520 ... (remaining 148748 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.730 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.007 0.044 17397 Z= 0.456 Angle : 0.739 6.750 23598 Z= 0.435 Chirality : 0.048 0.181 2655 Planarity : 0.004 0.039 3123 Dihedral : 16.291 78.277 6318 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.34 % Allowed : 15.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -3.28 (0.16), residues: 2178 helix: -1.56 (0.17), residues: 603 sheet: -1.31 (0.21), residues: 693 loop : -3.29 (0.17), residues: 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 287 time to evaluate : 1.970 Fit side-chains outliers start: 99 outliers final: 51 residues processed: 371 average time/residue: 0.3194 time to fit residues: 174.1435 Evaluate side-chains 299 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 248 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.1593 time to fit residues: 17.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 163 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 77 GLN A 148 ASN A 171 GLN A 244 ASN B 77 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 171 GLN B 244 ASN C 62 GLN C 77 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 171 GLN C 244 ASN D 62 GLN D 77 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 148 ASN D 171 GLN D 244 ASN E 62 GLN E 77 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 171 GLN E 244 ASN F 62 GLN F 77 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN F 244 ASN G 62 GLN G 70 ASN G 77 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN G 171 GLN G 244 ASN H 62 GLN H 77 GLN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN H 171 GLN H 244 ASN ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN I 244 ASN a 28 ASN b 28 ASN b 36 ASN c 28 ASN d 28 ASN e 28 ASN f 28 ASN g 28 ASN h 28 ASN i 28 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17397 Z= 0.189 Angle : 0.552 8.680 23598 Z= 0.298 Chirality : 0.044 0.147 2655 Planarity : 0.004 0.038 3123 Dihedral : 5.507 26.761 2385 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.54 % Allowed : 17.37 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.85 (0.18), residues: 2178 helix: 0.10 (0.20), residues: 603 sheet: -0.72 (0.22), residues: 657 loop : -2.54 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 273 time to evaluate : 1.942 Fit side-chains outliers start: 47 outliers final: 22 residues processed: 301 average time/residue: 0.3406 time to fit residues: 149.7336 Evaluate side-chains 263 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1521 time to fit residues: 8.9437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 0.0370 chunk 66 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17397 Z= 0.403 Angle : 0.641 7.295 23598 Z= 0.345 Chirality : 0.048 0.163 2655 Planarity : 0.004 0.041 3123 Dihedral : 5.742 29.054 2385 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.07 % Allowed : 18.28 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.69 (0.18), residues: 2178 helix: 0.38 (0.20), residues: 603 sheet: -0.65 (0.23), residues: 684 loop : -2.57 (0.18), residues: 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 255 time to evaluate : 1.849 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 291 average time/residue: 0.3273 time to fit residues: 137.2856 Evaluate side-chains 289 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1551 time to fit residues: 13.8937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 0.0770 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17397 Z= 0.182 Angle : 0.538 8.409 23598 Z= 0.289 Chirality : 0.044 0.147 2655 Planarity : 0.003 0.037 3123 Dihedral : 5.312 26.786 2385 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.40 % Allowed : 20.77 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.19), residues: 2178 helix: 1.10 (0.21), residues: 603 sheet: -0.47 (0.22), residues: 684 loop : -2.42 (0.19), residues: 891 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 239 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 254 average time/residue: 0.3202 time to fit residues: 119.4373 Evaluate side-chains 226 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1557 time to fit residues: 5.9579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 187 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 overall best weight: 1.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17397 Z= 0.256 Angle : 0.558 7.817 23598 Z= 0.301 Chirality : 0.045 0.177 2655 Planarity : 0.004 0.037 3123 Dihedral : 5.305 27.204 2385 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.89 % Allowed : 21.47 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.12 (0.19), residues: 2178 helix: 1.13 (0.21), residues: 603 sheet: -0.48 (0.22), residues: 684 loop : -2.32 (0.19), residues: 891 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 243 average time/residue: 0.3287 time to fit residues: 116.3458 Evaluate side-chains 237 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1508 time to fit residues: 9.1336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 ASN d 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17397 Z= 0.405 Angle : 0.635 6.996 23598 Z= 0.342 Chirality : 0.048 0.174 2655 Planarity : 0.004 0.038 3123 Dihedral : 5.643 28.997 2385 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.43 % Allowed : 20.77 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.34 (0.18), residues: 2178 helix: 0.94 (0.21), residues: 603 sheet: -0.52 (0.23), residues: 648 loop : -2.45 (0.18), residues: 927 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.871 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 254 average time/residue: 0.3398 time to fit residues: 124.7720 Evaluate side-chains 238 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1523 time to fit residues: 9.2560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17397 Z= 0.226 Angle : 0.561 7.947 23598 Z= 0.302 Chirality : 0.045 0.163 2655 Planarity : 0.003 0.037 3123 Dihedral : 5.404 27.259 2385 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.92 % Allowed : 22.60 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.10 (0.19), residues: 2178 helix: 1.29 (0.21), residues: 603 sheet: -0.46 (0.23), residues: 657 loop : -2.36 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.890 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 244 average time/residue: 0.3494 time to fit residues: 123.1875 Evaluate side-chains 228 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2332 time to fit residues: 5.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 163 optimal weight: 0.0030 chunk 189 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN G 57 GLN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17397 Z= 0.260 Angle : 0.566 7.586 23598 Z= 0.305 Chirality : 0.045 0.156 2655 Planarity : 0.004 0.037 3123 Dihedral : 5.388 27.652 2385 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.92 % Allowed : 22.92 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.01 (0.19), residues: 2178 helix: 1.40 (0.21), residues: 603 sheet: -0.43 (0.23), residues: 657 loop : -2.32 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.714 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 233 average time/residue: 0.3534 time to fit residues: 118.2266 Evaluate side-chains 230 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1551 time to fit residues: 5.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN D 106 ASN D 244 ASN E 106 ASN G 171 GLN H 106 ASN I 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17397 Z= 0.196 Angle : 0.538 8.030 23598 Z= 0.289 Chirality : 0.044 0.149 2655 Planarity : 0.003 0.036 3123 Dihedral : 5.262 26.431 2385 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.38 % Allowed : 23.03 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.19), residues: 2178 helix: 1.71 (0.22), residues: 603 sheet: -0.37 (0.24), residues: 567 loop : -1.87 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 239 average time/residue: 0.3457 time to fit residues: 120.3583 Evaluate side-chains 234 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1761 time to fit residues: 4.9128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 135 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN D 244 ASN G 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17397 Z= 0.407 Angle : 0.643 6.987 23598 Z= 0.346 Chirality : 0.049 0.200 2655 Planarity : 0.004 0.036 3123 Dihedral : 5.680 28.691 2385 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.43 % Allowed : 23.52 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.04 (0.19), residues: 2178 helix: 1.35 (0.21), residues: 603 sheet: -0.44 (0.23), residues: 657 loop : -2.33 (0.19), residues: 918 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 222 time to evaluate : 1.721 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 225 average time/residue: 0.3393 time to fit residues: 109.8716 Evaluate side-chains 226 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1935 time to fit residues: 5.2377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN G 135 ASN G 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117201 restraints weight = 18055.860| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.08 r_work: 0.3190 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17397 Z= 0.205 Angle : 0.552 7.926 23598 Z= 0.297 Chirality : 0.045 0.187 2655 Planarity : 0.003 0.036 3123 Dihedral : 5.373 26.858 2385 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.43 % Allowed : 23.52 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2178 helix: 1.73 (0.22), residues: 603 sheet: -0.34 (0.24), residues: 567 loop : -1.89 (0.19), residues: 1008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3564.33 seconds wall clock time: 65 minutes 34.72 seconds (3934.72 seconds total)