Starting phenix.real_space_refine on Thu Feb 22 07:39:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfn_16020/02_2024/8bfn_16020_trim_updated.pdb" } resolution = 3.52 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= 0.001 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 20848 2.51 5 N 6120 2.21 5 O 6360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A ASP 885": "OD1" <-> "OD2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A ASP 968": "OD1" <-> "OD2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1054": "OE1" <-> "OE2" Residue "A GLU 1083": "OE1" <-> "OE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B ASP 854": "OD1" <-> "OD2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 902": "OE1" <-> "OE2" Residue "B PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ASP 278": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E ASP 399": "OD1" <-> "OD2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ASP 130": "OD1" <-> "OD2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F GLU 789": "OE1" <-> "OE2" Residue "F GLU 796": "OE1" <-> "OE2" Residue "F GLU 871": "OE1" <-> "OE2" Residue "F GLU 872": "OE1" <-> "OE2" Residue "F GLU 876": "OE1" <-> "OE2" Residue "F ASP 885": "OD1" <-> "OD2" Residue "F GLU 925": "OE1" <-> "OE2" Residue "F ASP 940": "OD1" <-> "OD2" Residue "F ASP 968": "OD1" <-> "OD2" Residue "F PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1041": "OE1" <-> "OE2" Residue "F PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1054": "OE1" <-> "OE2" Residue "F GLU 1083": "OE1" <-> "OE2" Residue "F GLU 1084": "OE1" <-> "OE2" Residue "F GLU 1086": "OE1" <-> "OE2" Residue "G PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ASP 218": "OD1" <-> "OD2" Residue "G PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G GLU 251": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G ASP 281": "OD1" <-> "OD2" Residue "G GLU 784": "OE1" <-> "OE2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "G GLU 831": "OE1" <-> "OE2" Residue "G ASP 854": "OD1" <-> "OD2" Residue "G GLU 864": "OE1" <-> "OE2" Residue "G GLU 879": "OE1" <-> "OE2" Residue "G PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 885": "OD1" <-> "OD2" Residue "G ASP 895": "OD1" <-> "OD2" Residue "G GLU 902": "OE1" <-> "OE2" Residue "G PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 925": "OE1" <-> "OE2" Residue "G GLU 961": "OE1" <-> "OE2" Residue "G TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1021": "OD1" <-> "OD2" Residue "G PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1054": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J GLU 177": "OE1" <-> "OE2" Residue "J ASP 187": "OD1" <-> "OD2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J GLU 265": "OE1" <-> "OE2" Residue "J ASP 278": "OD1" <-> "OD2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J GLU 334": "OE1" <-> "OE2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "J ASP 379": "OD1" <-> "OD2" Residue "J ASP 386": "OD1" <-> "OD2" Residue "J ASP 399": "OD1" <-> "OD2" Residue "J ASP 400": "OD1" <-> "OD2" Residue "J ASP 403": "OD1" <-> "OD2" Residue "J PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33400 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "F" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "G" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "H" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "I" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "J" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.68, per 1000 atoms: 0.50 Number of scatterers: 33400 At special positions: 0 Unit cell: (163.786, 177.725, 160.301, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 6360 8.00 N 6120 7.00 C 20848 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: 13.10 Conformation dependent library (CDL) restraints added in 6.0 seconds 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 25 sheets defined 55.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.644A pdb=" N GLY A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 6' Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 153 through 174 removed outlier: 8.341A pdb=" N THR A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 199 through 210 removed outlier: 3.981A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 232 through 282 removed outlier: 4.053A pdb=" N ALA A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 783 through 807 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 819 through 834 Proline residue: A 823 - end of helix removed outlier: 4.079A pdb=" N GLU A 834 " --> pdb=" O GLU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.772A pdb=" N ASN A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 883 removed outlier: 3.648A pdb=" N GLU A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 919 removed outlier: 4.082A pdb=" N PHE A 919 " --> pdb=" O ASN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 943 Processing helix chain 'A' and resid 948 through 954 Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 986 through 1005 Processing helix chain 'A' and resid 1029 through 1041 removed outlier: 3.607A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 removed outlier: 4.445A pdb=" N ASP A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.727A pdb=" N GLY B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 10' Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 68 through 71 No H-bonds generated for 'chain 'B' and resid 68 through 71' Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 153 through 174 removed outlier: 8.774A pdb=" N THR B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.834A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 232 through 282 Proline residue: B 264 - end of helix removed outlier: 3.705A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 4.234A pdb=" N ALA B 788 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 789 " --> pdb=" O VAL B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 834 Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 836 through 850 Processing helix chain 'B' and resid 857 through 883 Processing helix chain 'B' and resid 902 through 917 Processing helix chain 'B' and resid 925 through 943 Processing helix chain 'B' and resid 948 through 954 Processing helix chain 'B' and resid 956 through 958 No H-bonds generated for 'chain 'B' and resid 956 through 958' Processing helix chain 'B' and resid 987 through 1005 Processing helix chain 'B' and resid 1029 through 1041 removed outlier: 3.568A pdb=" N ARG B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1060 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 77 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 127 through 145 Processing helix chain 'C' and resid 158 through 169 removed outlier: 3.882A pdb=" N LEU C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 4.038A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 77 through 87 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 127 through 147 Processing helix chain 'D' and resid 158 through 169 Proline residue: D 163 - end of helix removed outlier: 3.792A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 192 Processing helix chain 'D' and resid 208 through 211 Processing helix chain 'D' and resid 216 through 233 Processing helix chain 'E' and resid 3 through 18 removed outlier: 3.753A pdb=" N ARG E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 30 through 43 removed outlier: 4.091A pdb=" N LYS E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 147 through 170 removed outlier: 3.786A pdb=" N ALA E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 196 removed outlier: 3.908A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 219 Processing helix chain 'E' and resid 225 through 231 removed outlier: 5.435A pdb=" N ARG E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.874A pdb=" N ASP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 289 Processing helix chain 'E' and resid 291 through 320 removed outlier: 4.496A pdb=" N THR E 319 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY E 320 " --> pdb=" O PHE E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.879A pdb=" N LEU E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 399 through 405 Processing helix chain 'E' and resid 410 through 424 Processing helix chain 'E' and resid 430 through 436 Processing helix chain 'E' and resid 442 through 455 removed outlier: 3.905A pdb=" N ALA E 447 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG E 454 " --> pdb=" O GLY E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N GLY F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 80 through 85 Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 153 through 174 removed outlier: 7.808A pdb=" N THR F 165 " --> pdb=" O HIS F 161 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.921A pdb=" N ALA F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY F 210 " --> pdb=" O ASN F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 Processing helix chain 'F' and resid 232 through 282 removed outlier: 3.868A pdb=" N ALA F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 783 through 806 Processing helix chain 'F' and resid 811 through 813 No H-bonds generated for 'chain 'F' and resid 811 through 813' Processing helix chain 'F' and resid 819 through 834 Proline residue: F 823 - end of helix removed outlier: 3.626A pdb=" N LEU F 826 " --> pdb=" O PRO F 823 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 833 " --> pdb=" O GLN F 830 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 834 " --> pdb=" O GLU F 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 850 removed outlier: 3.506A pdb=" N ASN F 849 " --> pdb=" O LEU F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 857 through 883 removed outlier: 3.919A pdb=" N GLU F 879 " --> pdb=" O ASN F 875 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG F 883 " --> pdb=" O GLU F 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 902 through 919 removed outlier: 4.176A pdb=" N PHE F 919 " --> pdb=" O ASN F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 943 Processing helix chain 'F' and resid 948 through 954 Processing helix chain 'F' and resid 956 through 958 No H-bonds generated for 'chain 'F' and resid 956 through 958' Processing helix chain 'F' and resid 986 through 1005 Processing helix chain 'F' and resid 1029 through 1041 removed outlier: 4.016A pdb=" N ARG F1034 " --> pdb=" O ALA F1030 " (cutoff:3.500A) Processing helix chain 'F' and resid 1055 through 1060 removed outlier: 3.994A pdb=" N ASP F1060 " --> pdb=" O ARG F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1093 Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.802A pdb=" N GLY G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU G 7 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS G 10 " --> pdb=" O GLY G 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 10' Processing helix chain 'G' and resid 49 through 60 Processing helix chain 'G' and resid 68 through 71 No H-bonds generated for 'chain 'G' and resid 68 through 71' Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 153 through 174 removed outlier: 8.652A pdb=" N THR G 165 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 195 removed outlier: 3.545A pdb=" N PHE G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 210 removed outlier: 4.044A pdb=" N GLY G 210 " --> pdb=" O ASN G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 Processing helix chain 'G' and resid 232 through 282 Proline residue: G 264 - end of helix removed outlier: 3.701A pdb=" N TRP G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 807 removed outlier: 4.007A pdb=" N ALA G 788 " --> pdb=" O ARG G 785 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU G 789 " --> pdb=" O VAL G 786 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG G 792 " --> pdb=" O GLU G 789 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 807 " --> pdb=" O ALA G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 819 through 834 Proline residue: G 823 - end of helix Processing helix chain 'G' and resid 836 through 850 Processing helix chain 'G' and resid 857 through 883 Processing helix chain 'G' and resid 902 through 917 Processing helix chain 'G' and resid 925 through 943 Processing helix chain 'G' and resid 948 through 954 Processing helix chain 'G' and resid 956 through 958 No H-bonds generated for 'chain 'G' and resid 956 through 958' Processing helix chain 'G' and resid 987 through 1005 Processing helix chain 'G' and resid 1029 through 1041 removed outlier: 3.944A pdb=" N ARG G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1055 through 1060 Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 77 through 87 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 114 through 116 No H-bonds generated for 'chain 'H' and resid 114 through 116' Processing helix chain 'H' and resid 127 through 145 Processing helix chain 'H' and resid 158 through 169 removed outlier: 3.800A pdb=" N LEU H 162 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Proline residue: H 163 - end of helix removed outlier: 3.580A pdb=" N ILE H 167 " --> pdb=" O PRO H 163 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 192 removed outlier: 3.501A pdb=" N HIS H 192 " --> pdb=" O GLN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 216 through 233 Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 67 through 75 Processing helix chain 'I' and resid 77 through 87 Proline residue: I 86 - end of helix Processing helix chain 'I' and resid 127 through 147 Processing helix chain 'I' and resid 158 through 169 Proline residue: I 163 - end of helix removed outlier: 3.942A pdb=" N TYR I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 192 Processing helix chain 'I' and resid 208 through 211 Processing helix chain 'I' and resid 216 through 233 Processing helix chain 'J' and resid 3 through 18 removed outlier: 3.622A pdb=" N ARG J 8 " --> pdb=" O ASN J 4 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 26 Processing helix chain 'J' and resid 30 through 43 removed outlier: 3.972A pdb=" N LYS J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.704A pdb=" N HIS J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 Processing helix chain 'J' and resid 105 through 117 Processing helix chain 'J' and resid 129 through 141 Processing helix chain 'J' and resid 147 through 169 removed outlier: 3.582A pdb=" N ARG J 156 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG J 157 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 158 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 196 removed outlier: 3.534A pdb=" N VAL J 182 " --> pdb=" O THR J 178 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG J 196 " --> pdb=" O ALA J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 219 removed outlier: 3.546A pdb=" N GLU J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 231 removed outlier: 5.432A pdb=" N ARG J 230 " --> pdb=" O ASP J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 255 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 274 through 279 removed outlier: 3.881A pdb=" N ASP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 289 Processing helix chain 'J' and resid 291 through 320 removed outlier: 4.607A pdb=" N THR J 319 " --> pdb=" O GLY J 315 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY J 320 " --> pdb=" O PHE J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 341 removed outlier: 3.729A pdb=" N LEU J 340 " --> pdb=" O LEU J 336 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS J 341 " --> pdb=" O ASN J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 350 No H-bonds generated for 'chain 'J' and resid 347 through 350' Processing helix chain 'J' and resid 369 through 371 No H-bonds generated for 'chain 'J' and resid 369 through 371' Processing helix chain 'J' and resid 379 through 390 Processing helix chain 'J' and resid 399 through 405 Processing helix chain 'J' and resid 410 through 424 Processing helix chain 'J' and resid 430 through 436 Processing helix chain 'J' and resid 442 through 455 removed outlier: 3.622A pdb=" N ALA J 447 " --> pdb=" O GLU J 444 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE J 450 " --> pdb=" O ALA J 447 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU J 455 " --> pdb=" O MET J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 489 through 494 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.321A pdb=" N THR A 113 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 18 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 111 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A 20 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY A 109 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1075 through 1081 removed outlier: 6.678A pdb=" N ALA A 40 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A1068 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 42 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ARG A1070 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 892 through 895 Processing sheet with id= D, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.695A pdb=" N THR B 113 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 18 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 111 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 20 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 109 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1074 through 1081 removed outlier: 3.839A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B1020 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B1049 " --> pdb=" O LEU B1020 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 893 through 895 removed outlier: 4.120A pdb=" N ALA B 963 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 60 through 62 Processing sheet with id= H, first strand: chain 'C' and resid 155 through 157 Processing sheet with id= I, first strand: chain 'D' and resid 60 through 62 Processing sheet with id= J, first strand: chain 'D' and resid 155 through 157 Processing sheet with id= K, first strand: chain 'E' and resid 94 through 97 Processing sheet with id= L, first strand: chain 'E' and resid 468 through 471 Processing sheet with id= M, first strand: chain 'F' and resid 29 through 33 removed outlier: 6.207A pdb=" N THR F 113 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 18 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA F 111 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU F 20 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY F 109 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 144 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 1075 through 1081 removed outlier: 6.393A pdb=" N ALA F 40 " --> pdb=" O ILE F1066 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F1068 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 42 " --> pdb=" O VAL F1068 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG F1070 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 39 " --> pdb=" O ALA F1046 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 112 through 116 Processing sheet with id= P, first strand: chain 'F' and resid 892 through 895 Processing sheet with id= Q, first strand: chain 'G' and resid 29 through 33 removed outlier: 6.819A pdb=" N THR G 113 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE G 18 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA G 111 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU G 20 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY G 109 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 124 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 1074 through 1081 removed outlier: 3.881A pdb=" N THR G 39 " --> pdb=" O ALA G1046 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G1020 " --> pdb=" O VAL G1047 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G1049 " --> pdb=" O LEU G1020 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 893 through 895 removed outlier: 4.040A pdb=" N ALA G 963 " --> pdb=" O ASP G 895 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 60 through 62 Processing sheet with id= U, first strand: chain 'H' and resid 155 through 157 Processing sheet with id= V, first strand: chain 'I' and resid 60 through 62 Processing sheet with id= W, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= X, first strand: chain 'J' and resid 94 through 97 Processing sheet with id= Y, first strand: chain 'J' and resid 468 through 471 1756 hydrogen bonds defined for protein. 4884 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: 11.02 Time building geometry restraints manager: 13.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9557 1.33 - 1.45: 5161 1.45 - 1.57: 19124 1.57 - 1.69: 16 1.69 - 1.81: 114 Bond restraints: 33972 Sorted by residual: bond pdb=" C5 ADP F1101 " pdb=" C6 ADP F1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C5 ADP A1101 " pdb=" C6 ADP A1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C5 ADP B1101 " pdb=" C6 ADP B1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C5 ADP G1101 " pdb=" C6 ADP G1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C5 ADP B1101 " pdb=" N7 ADP B1101 " ideal model delta sigma weight residual 1.350 1.474 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 33967 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.64: 303 103.64 - 111.36: 15411 111.36 - 119.09: 12539 119.09 - 126.82: 17243 126.82 - 134.54: 468 Bond angle restraints: 45964 Sorted by residual: angle pdb=" CA PRO D 198 " pdb=" N PRO D 198 " pdb=" CD PRO D 198 " ideal model delta sigma weight residual 112.00 101.73 10.27 1.40e+00 5.10e-01 5.38e+01 angle pdb=" O1A ADP G1101 " pdb=" PA ADP G1101 " pdb=" O2A ADP G1101 " ideal model delta sigma weight residual 119.90 101.04 18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" O1A ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sigma weight residual 119.90 101.07 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" O1A ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sigma weight residual 119.90 101.53 18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1A ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sigma weight residual 119.90 101.54 18.36 3.00e+00 1.11e-01 3.74e+01 ... (remaining 45959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 19579 33.17 - 66.33: 976 66.33 - 99.50: 104 99.50 - 132.66: 0 132.66 - 165.83: 5 Dihedral angle restraints: 20664 sinusoidal: 8614 harmonic: 12050 Sorted by residual: dihedral pdb=" C5' ADP F1101 " pdb=" O5' ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sinusoidal sigma weight residual -60.00 105.83 -165.83 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1101 " pdb=" O3A ADP A1101 " pdb=" PB ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 142.55 157.45 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 20661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3453 0.030 - 0.059: 1118 0.059 - 0.089: 372 0.089 - 0.118: 187 0.118 - 0.148: 16 Chirality restraints: 5146 Sorted by residual: chirality pdb=" CG LEU F 224 " pdb=" CB LEU F 224 " pdb=" CD1 LEU F 224 " pdb=" CD2 LEU F 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE E 366 " pdb=" N ILE E 366 " pdb=" C ILE E 366 " pdb=" CB ILE E 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE J 366 " pdb=" N ILE J 366 " pdb=" C ILE J 366 " pdb=" CB ILE J 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 5143 not shown) Planarity restraints: 6034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 197 " -0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO D 198 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 887 " 0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO F 888 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 888 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 888 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 887 " -0.057 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO A 888 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " -0.047 5.00e-02 4.00e+02 ... (remaining 6031 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 372 2.52 - 3.11: 28417 3.11 - 3.71: 54540 3.71 - 4.30: 74718 4.30 - 4.90: 122865 Nonbonded interactions: 280912 Sorted by model distance: nonbonded pdb=" OG SER F 971 " pdb=" OD1 ASN F 973 " model vdw 1.921 2.440 nonbonded pdb=" OG SER A 971 " pdb=" OD1 ASN A 973 " model vdw 1.921 2.440 nonbonded pdb=" O ASN B 22 " pdb=" OG1 THR B 108 " model vdw 1.934 2.440 nonbonded pdb=" O LEU B1058 " pdb=" OG1 THR B1062 " model vdw 1.945 2.440 nonbonded pdb=" O SER A 852 " pdb=" OG1 THR A 857 " model vdw 1.949 2.440 ... (remaining 280907 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 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.550 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 83.660 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.250 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 33972 Z= 0.320 Angle : 0.668 18.863 45964 Z= 0.324 Chirality : 0.037 0.148 5146 Planarity : 0.004 0.095 6034 Dihedral : 19.102 165.826 12844 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 45.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 0.48 % Allowed : 33.16 % Favored : 66.36 % 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: 0.87 (0.14), residues: 4136 helix: 1.96 (0.11), residues: 2346 sheet: -0.91 (0.23), residues: 520 loop : -1.44 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 156 HIS 0.007 0.001 HIS G1029 PHE 0.017 0.001 PHE G 194 TYR 0.025 0.001 TYR A 891 ARG 0.009 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 818 time to evaluate : 4.470 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: B 171 MET cc_start: 0.6401 (ptt) cc_final: 0.6042 (ptt) REVERT: F 801 MET cc_start: 0.7293 (mtt) cc_final: 0.6870 (mmt) REVERT: G 34 ILE cc_start: 0.8630 (mp) cc_final: 0.8380 (mp) REVERT: G 172 GLU cc_start: 0.6299 (tt0) cc_final: 0.4556 (tp30) REVERT: G 234 ARG cc_start: 0.3446 (mmm-85) cc_final: 0.2982 (mtt-85) REVERT: G 801 MET cc_start: 0.7427 (ttm) cc_final: 0.7195 (ttt) REVERT: J 211 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7580 (ttm110) REVERT: J 263 MET cc_start: 0.7795 (mtt) cc_final: 0.7258 (mtm) REVERT: J 454 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7199 (ttt180) outliers start: 17 outliers final: 12 residues processed: 829 average time/residue: 0.4783 time to fit residues: 617.6200 Evaluate side-chains 800 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 788 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 372 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS H 218 ASN J 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33972 Z= 0.267 Angle : 0.693 15.407 45964 Z= 0.339 Chirality : 0.043 0.171 5146 Planarity : 0.004 0.058 6034 Dihedral : 7.535 153.257 4661 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.61 % Favored : 94.17 % Rotamer: Outliers : 5.23 % Allowed : 27.37 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4136 helix: 1.72 (0.11), residues: 2352 sheet: -0.75 (0.23), residues: 510 loop : -1.39 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 128 HIS 0.012 0.001 HIS B1029 PHE 0.021 0.002 PHE G 194 TYR 0.023 0.002 TYR F 891 ARG 0.007 0.001 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 894 time to evaluate : 3.990 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: A 801 MET cc_start: 0.6923 (mtt) cc_final: 0.6652 (mtt) REVERT: A 868 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 1054 GLU cc_start: 0.7834 (mp0) cc_final: 0.7343 (mt-10) REVERT: B 219 GLU cc_start: 0.7760 (mp0) cc_final: 0.7182 (tt0) REVERT: B 234 ARG cc_start: 0.3377 (mmm-85) cc_final: 0.2780 (mtp85) REVERT: B 792 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6804 (mtm180) REVERT: B 821 ASP cc_start: 0.6692 (t0) cc_final: 0.6393 (t0) REVERT: B 978 ARG cc_start: 0.1804 (OUTLIER) cc_final: 0.0549 (ptm160) REVERT: B 1029 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.7134 (t-170) REVERT: B 1062 THR cc_start: 0.6778 (p) cc_final: 0.6545 (p) REVERT: C 146 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6262 (tm-30) REVERT: D 54 GLU cc_start: 0.7383 (tp30) cc_final: 0.7048 (mm-30) REVERT: E 461 ILE cc_start: 0.7296 (pt) cc_final: 0.7015 (mp) REVERT: E 494 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5402 (t70) REVERT: F 78 ARG cc_start: 0.8044 (ptp-170) cc_final: 0.7793 (ptp-170) REVERT: F 192 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7671 (mtt180) REVERT: F 1054 GLU cc_start: 0.7856 (mp0) cc_final: 0.7568 (mt-10) REVERT: G 34 ILE cc_start: 0.8684 (mp) cc_final: 0.8387 (mp) REVERT: G 172 GLU cc_start: 0.6221 (tt0) cc_final: 0.4682 (tp30) REVERT: G 234 ARG cc_start: 0.3634 (mmm-85) cc_final: 0.3208 (mtp85) REVERT: G 248 ILE cc_start: 0.7516 (mt) cc_final: 0.7178 (mp) REVERT: G 871 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6302 (tm-30) REVERT: G 978 ARG cc_start: 0.1835 (OUTLIER) cc_final: 0.0349 (ptm160) REVERT: G 1076 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7742 (p0) REVERT: I 215 ASP cc_start: 0.7613 (p0) cc_final: 0.7300 (p0) REVERT: J 161 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5540 (mt) REVERT: J 211 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7685 (ttm110) REVERT: J 263 MET cc_start: 0.7540 (mtt) cc_final: 0.7203 (mtm) outliers start: 186 outliers final: 100 residues processed: 1007 average time/residue: 0.4686 time to fit residues: 735.5485 Evaluate side-chains 905 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 798 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 783 ILE Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 854 ASP Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1002 SER Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1029 HIS Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 328 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 253 optimal weight: 0.0980 chunk 102 optimal weight: 0.0370 chunk 372 optimal weight: 1.9990 chunk 402 optimal weight: 0.8980 chunk 332 optimal weight: 0.5980 chunk 369 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 299 optimal weight: 10.0000 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 275 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 240 ASN E 352 GLN F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1090 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS H 53 GLN J 396 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33972 Z= 0.210 Angle : 0.650 14.252 45964 Z= 0.317 Chirality : 0.041 0.165 5146 Planarity : 0.004 0.056 6034 Dihedral : 7.165 151.490 4644 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Rotamer: Outliers : 5.12 % Allowed : 27.85 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4136 helix: 1.66 (0.11), residues: 2354 sheet: -0.88 (0.22), residues: 532 loop : -1.28 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 128 HIS 0.015 0.001 HIS B1029 PHE 0.027 0.001 PHE A 221 TYR 0.032 0.002 TYR B 891 ARG 0.006 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 861 time to evaluate : 4.213 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: A 192 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7674 (mtt180) REVERT: A 976 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: A 1054 GLU cc_start: 0.7826 (mp0) cc_final: 0.7412 (mt-10) REVERT: B 219 GLU cc_start: 0.7774 (mp0) cc_final: 0.7265 (tt0) REVERT: B 248 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7157 (mt) REVERT: B 978 ARG cc_start: 0.1814 (OUTLIER) cc_final: 0.0584 (ptm160) REVERT: B 1062 THR cc_start: 0.6765 (p) cc_final: 0.6478 (p) REVERT: C 146 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 54 GLU cc_start: 0.7420 (tp30) cc_final: 0.7150 (mm-30) REVERT: E 196 ARG cc_start: 0.7659 (tmt-80) cc_final: 0.7274 (tmt-80) REVERT: E 198 ASP cc_start: 0.7543 (m-30) cc_final: 0.7118 (m-30) REVERT: E 263 MET cc_start: 0.7225 (mtt) cc_final: 0.7005 (mtm) REVERT: E 461 ILE cc_start: 0.7342 (pt) cc_final: 0.7024 (mp) REVERT: E 494 ASP cc_start: 0.5867 (OUTLIER) cc_final: 0.5407 (t70) REVERT: F 192 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7617 (mtt180) REVERT: F 893 ARG cc_start: 0.7300 (ttp-170) cc_final: 0.7061 (ttp-170) REVERT: F 976 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6695 (tp30) REVERT: F 1056 ARG cc_start: 0.7045 (mtt180) cc_final: 0.6759 (tpp80) REVERT: G 172 GLU cc_start: 0.5994 (tt0) cc_final: 0.4566 (tp30) REVERT: G 219 GLU cc_start: 0.7789 (mp0) cc_final: 0.7372 (tt0) REVERT: G 234 ARG cc_start: 0.3613 (mmm-85) cc_final: 0.2952 (mtp85) REVERT: G 253 GLU cc_start: 0.4900 (mm-30) cc_final: 0.3431 (mm-30) REVERT: G 270 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: G 871 GLU cc_start: 0.6294 (tm-30) cc_final: 0.5995 (tm-30) REVERT: G 875 ASN cc_start: 0.8065 (m-40) cc_final: 0.7718 (m-40) REVERT: G 978 ARG cc_start: 0.1807 (OUTLIER) cc_final: 0.0624 (ptm160) REVERT: H 146 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6225 (tm-30) REVERT: I 100 LEU cc_start: 0.8699 (mt) cc_final: 0.8471 (mt) REVERT: I 215 ASP cc_start: 0.7596 (p0) cc_final: 0.7128 (p0) REVERT: J 134 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6342 (mtm180) REVERT: J 161 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5556 (mt) REVERT: J 211 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7598 (ttm110) REVERT: J 230 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7301 (ttp-110) REVERT: J 263 MET cc_start: 0.7635 (mtt) cc_final: 0.7273 (mtm) REVERT: J 494 ASP cc_start: 0.5955 (OUTLIER) cc_final: 0.5424 (t70) outliers start: 182 outliers final: 105 residues processed: 973 average time/residue: 0.4791 time to fit residues: 731.7084 Evaluate side-chains 911 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 797 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 881 MET Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 250 optimal weight: 0.0980 chunk 374 optimal weight: 0.7980 chunk 396 optimal weight: 0.3980 chunk 195 optimal weight: 4.9990 chunk 354 optimal weight: 0.3980 chunk 106 optimal weight: 0.0170 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 396 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1090 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33972 Z= 0.178 Angle : 0.631 13.781 45964 Z= 0.306 Chirality : 0.040 0.307 5146 Planarity : 0.004 0.054 6034 Dihedral : 6.852 155.174 4642 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.68 % Favored : 94.12 % Rotamer: Outliers : 4.86 % Allowed : 27.99 % Favored : 67.14 % 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 (0.13), residues: 4136 helix: 1.67 (0.11), residues: 2354 sheet: -0.90 (0.22), residues: 496 loop : -1.18 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 128 HIS 0.005 0.001 HIS G1029 PHE 0.022 0.001 PHE G 194 TYR 0.024 0.001 TYR B 891 ARG 0.007 0.000 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 905 time to evaluate : 3.617 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: A 67 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.6310 (m110) REVERT: A 192 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7648 (mtt180) REVERT: B 219 GLU cc_start: 0.7759 (mp0) cc_final: 0.7264 (tt0) REVERT: B 253 GLU cc_start: 0.4843 (mm-30) cc_final: 0.3918 (mm-30) REVERT: B 270 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: B 1062 THR cc_start: 0.6758 (p) cc_final: 0.6493 (p) REVERT: C 146 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6734 (tm-30) REVERT: C 159 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: E 80 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6869 (tp-100) REVERT: E 196 ARG cc_start: 0.7432 (tmt-80) cc_final: 0.7198 (tmt-80) REVERT: E 220 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7000 (pp20) REVERT: E 230 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.7227 (ttp-110) REVERT: E 263 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6839 (mtt) REVERT: E 294 ARG cc_start: 0.7175 (ptp-110) cc_final: 0.6483 (mtm180) REVERT: E 304 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: E 461 ILE cc_start: 0.7359 (pt) cc_final: 0.7050 (mp) REVERT: E 494 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5462 (t70) REVERT: F 192 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7655 (mtt180) REVERT: F 794 ASN cc_start: 0.8347 (t0) cc_final: 0.8030 (t0) REVERT: G 172 GLU cc_start: 0.6339 (tt0) cc_final: 0.4568 (tp30) REVERT: G 219 GLU cc_start: 0.7677 (mp0) cc_final: 0.7413 (tt0) REVERT: G 234 ARG cc_start: 0.3428 (mmm-85) cc_final: 0.3215 (mtp85) REVERT: G 237 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7304 (mm-30) REVERT: G 253 GLU cc_start: 0.4940 (mm-30) cc_final: 0.4670 (mm-30) REVERT: G 270 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: G 785 ARG cc_start: 0.6384 (mtm110) cc_final: 0.6073 (mtm110) REVERT: G 789 GLU cc_start: 0.6767 (tt0) cc_final: 0.6492 (tt0) REVERT: G 871 GLU cc_start: 0.6356 (tm-30) cc_final: 0.5972 (tm-30) REVERT: G 967 MET cc_start: 0.4980 (mtp) cc_final: 0.4390 (mtp) REVERT: H 45 LEU cc_start: 0.8866 (mp) cc_final: 0.8259 (tp) REVERT: H 121 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7505 (mtm-85) REVERT: H 146 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6542 (tm-30) REVERT: I 101 TYR cc_start: 0.9088 (p90) cc_final: 0.8839 (p90) REVERT: I 215 ASP cc_start: 0.7645 (p0) cc_final: 0.7253 (p0) REVERT: J 134 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: J 161 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5565 (mt) REVERT: J 201 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: J 211 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7588 (ttm110) REVERT: J 411 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7051 (pp20) REVERT: J 418 LEU cc_start: 0.7202 (pp) cc_final: 0.6889 (pp) REVERT: J 494 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5402 (t70) outliers start: 173 outliers final: 102 residues processed: 1007 average time/residue: 0.4765 time to fit residues: 751.4551 Evaluate side-chains 940 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 827 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 982 GLN Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 273 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 355 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 396 GLN F 22 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 927 HIS G1029 HIS J 396 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33972 Z= 0.199 Angle : 0.637 12.672 45964 Z= 0.310 Chirality : 0.041 0.334 5146 Planarity : 0.004 0.058 6034 Dihedral : 6.716 157.299 4640 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.71 % Favored : 94.10 % Rotamer: Outliers : 4.89 % Allowed : 28.81 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 4136 helix: 1.59 (0.11), residues: 2366 sheet: -0.88 (0.22), residues: 512 loop : -1.19 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 128 HIS 0.006 0.001 HIS G1029 PHE 0.017 0.001 PHE J 467 TYR 0.024 0.002 TYR B 891 ARG 0.008 0.000 ARG J 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 872 time to evaluate : 3.838 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: A 67 ASN cc_start: 0.6669 (OUTLIER) cc_final: 0.6439 (m110) REVERT: A 192 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7679 (mtt180) REVERT: A 1020 LEU cc_start: 0.8933 (mt) cc_final: 0.8696 (mt) REVERT: B 171 MET cc_start: 0.6277 (ptt) cc_final: 0.6028 (ptt) REVERT: B 219 GLU cc_start: 0.7726 (mp0) cc_final: 0.7281 (tt0) REVERT: B 270 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: B 978 ARG cc_start: 0.1365 (OUTLIER) cc_final: 0.0500 (ptm160) REVERT: B 1062 THR cc_start: 0.6810 (p) cc_final: 0.6590 (p) REVERT: C 146 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6808 (tm-30) REVERT: C 159 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: D 103 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8366 (ptpp) REVERT: E 134 ARG cc_start: 0.6700 (mtm180) cc_final: 0.6290 (mtm180) REVERT: E 198 ASP cc_start: 0.7537 (m-30) cc_final: 0.7101 (m-30) REVERT: E 294 ARG cc_start: 0.7211 (ptp-110) cc_final: 0.6572 (mtm180) REVERT: E 304 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: E 461 ILE cc_start: 0.7365 (pt) cc_final: 0.7101 (mp) REVERT: E 494 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.5428 (t70) REVERT: F 192 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7664 (mtt180) REVERT: F 794 ASN cc_start: 0.8375 (t0) cc_final: 0.8107 (t0) REVERT: F 921 ASP cc_start: 0.7650 (t0) cc_final: 0.7321 (t0) REVERT: F 976 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6456 (tp30) REVERT: G 31 GLN cc_start: 0.5679 (pt0) cc_final: 0.5380 (pt0) REVERT: G 172 GLU cc_start: 0.6480 (tt0) cc_final: 0.4734 (tp30) REVERT: G 219 GLU cc_start: 0.7664 (mp0) cc_final: 0.7431 (tt0) REVERT: G 237 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7267 (mm-30) REVERT: G 270 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: G 819 LEU cc_start: 0.7103 (pt) cc_final: 0.6171 (mm) REVERT: G 996 VAL cc_start: 0.9023 (t) cc_final: 0.8816 (t) REVERT: H 45 LEU cc_start: 0.8792 (mp) cc_final: 0.8235 (tp) REVERT: H 121 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7501 (mtm-85) REVERT: H 146 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6705 (tm-30) REVERT: I 54 GLU cc_start: 0.7371 (tp30) cc_final: 0.7078 (tp30) REVERT: I 215 ASP cc_start: 0.7704 (p0) cc_final: 0.7312 (p0) REVERT: J 122 MET cc_start: 0.5509 (mmt) cc_final: 0.3701 (mmt) REVERT: J 201 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7831 (ttp80) REVERT: J 411 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6832 (pp20) REVERT: J 494 ASP cc_start: 0.5982 (OUTLIER) cc_final: 0.5462 (t70) outliers start: 174 outliers final: 121 residues processed: 980 average time/residue: 0.4869 time to fit residues: 744.6466 Evaluate side-chains 941 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 810 time to evaluate : 4.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 0.9980 chunk 356 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 396 optimal weight: 0.4980 chunk 329 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 208 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 278 GLN B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN E 11 ASN E 74 GLN E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G1029 HIS J 11 ASN J 396 GLN J 415 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.045 33972 Z= 0.233 Angle : 0.649 12.692 45964 Z= 0.317 Chirality : 0.041 0.243 5146 Planarity : 0.004 0.064 6034 Dihedral : 6.676 158.551 4640 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 5.34 % Allowed : 29.09 % Favored : 65.57 % 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: 0.58 (0.13), residues: 4136 helix: 1.53 (0.11), residues: 2368 sheet: -0.90 (0.22), residues: 512 loop : -1.21 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 128 HIS 0.006 0.001 HIS G1029 PHE 0.023 0.002 PHE J 405 TYR 0.024 0.002 TYR A 891 ARG 0.007 0.000 ARG H 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 839 time to evaluate : 4.147 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: A 67 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6588 (m110) REVERT: A 192 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7652 (mtt180) REVERT: A 976 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6589 (tp30) REVERT: B 173 LYS cc_start: 0.5694 (ptpt) cc_final: 0.5071 (ptmm) REVERT: B 219 GLU cc_start: 0.7682 (mp0) cc_final: 0.7260 (tt0) REVERT: B 270 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: B 819 LEU cc_start: 0.7126 (pt) cc_final: 0.6197 (mm) REVERT: B 978 ARG cc_start: 0.0864 (OUTLIER) cc_final: 0.0192 (ptm160) REVERT: C 106 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6441 (mp) REVERT: D 103 LYS cc_start: 0.8600 (ptpp) cc_final: 0.7957 (ptpp) REVERT: E 80 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6840 (tp-100) REVERT: E 134 ARG cc_start: 0.6732 (mtm180) cc_final: 0.6288 (mtm180) REVERT: E 163 ARG cc_start: 0.7311 (mtm110) cc_final: 0.7052 (mtm110) REVERT: E 198 ASP cc_start: 0.7512 (m-30) cc_final: 0.7119 (m-30) REVERT: E 227 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7812 (mm) REVERT: E 304 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: E 461 ILE cc_start: 0.7390 (pt) cc_final: 0.7125 (mp) REVERT: E 494 ASP cc_start: 0.5977 (OUTLIER) cc_final: 0.5421 (t70) REVERT: F 56 LEU cc_start: 0.9042 (tt) cc_final: 0.8695 (tt) REVERT: F 192 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7662 (mtt180) REVERT: F 921 ASP cc_start: 0.7770 (t0) cc_final: 0.7408 (t0) REVERT: F 976 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6569 (tp30) REVERT: G 31 GLN cc_start: 0.5506 (pt0) cc_final: 0.5001 (pt0) REVERT: G 219 GLU cc_start: 0.7681 (mp0) cc_final: 0.7476 (tt0) REVERT: G 237 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7267 (mm-30) REVERT: G 270 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: G 819 LEU cc_start: 0.7129 (pt) cc_final: 0.6185 (mm) REVERT: G 870 ILE cc_start: 0.9122 (mm) cc_final: 0.8871 (mt) REVERT: G 978 ARG cc_start: 0.1197 (OUTLIER) cc_final: 0.0403 (ptm160) REVERT: H 45 LEU cc_start: 0.8855 (mp) cc_final: 0.8277 (tp) REVERT: H 106 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6482 (mp) REVERT: H 121 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7555 (mtm-85) REVERT: H 146 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6766 (tm-30) REVERT: J 122 MET cc_start: 0.5550 (OUTLIER) cc_final: 0.3863 (mmt) REVERT: J 134 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6320 (mtm180) REVERT: J 201 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7794 (ttp80) REVERT: J 494 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5445 (t70) outliers start: 190 outliers final: 142 residues processed: 951 average time/residue: 0.4864 time to fit residues: 724.8696 Evaluate side-chains 956 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 798 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 333 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 395 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 240 optimal weight: 0.0770 chunk 182 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 74 GLN E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 396 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33972 Z= 0.279 Angle : 0.675 12.773 45964 Z= 0.332 Chirality : 0.042 0.286 5146 Planarity : 0.004 0.072 6034 Dihedral : 6.733 159.269 4640 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 5.54 % Allowed : 29.09 % Favored : 65.37 % 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: 0.43 (0.13), residues: 4136 helix: 1.44 (0.11), residues: 2354 sheet: -0.92 (0.22), residues: 522 loop : -1.35 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 115 HIS 0.006 0.001 HIS J 19 PHE 0.022 0.002 PHE J 405 TYR 0.026 0.002 TYR G 187 ARG 0.010 0.001 ARG E 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 824 time to evaluate : 3.786 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: A 192 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7704 (mtt180) REVERT: A 976 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: B 171 MET cc_start: 0.6292 (ptt) cc_final: 0.5627 (ptt) REVERT: B 219 GLU cc_start: 0.7664 (mp0) cc_final: 0.7299 (tt0) REVERT: B 270 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: B 819 LEU cc_start: 0.7063 (pt) cc_final: 0.6119 (mm) REVERT: B 1003 TYR cc_start: 0.7271 (t80) cc_final: 0.7006 (t80) REVERT: C 146 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6743 (pp20) REVERT: E 134 ARG cc_start: 0.6662 (mtm180) cc_final: 0.6269 (mtm180) REVERT: E 198 ASP cc_start: 0.7530 (m-30) cc_final: 0.7184 (m-30) REVERT: E 227 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7975 (mm) REVERT: E 304 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: E 376 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: E 461 ILE cc_start: 0.7418 (pt) cc_final: 0.7171 (mp) REVERT: E 494 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5431 (t70) REVERT: F 56 LEU cc_start: 0.9012 (tt) cc_final: 0.8672 (tt) REVERT: F 192 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7710 (mtt180) REVERT: F 976 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: G 219 GLU cc_start: 0.7695 (mp0) cc_final: 0.7448 (tt0) REVERT: G 237 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7285 (mm-30) REVERT: G 270 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: G 819 LEU cc_start: 0.7050 (pt) cc_final: 0.6135 (mm) REVERT: G 866 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7172 (mm-30) REVERT: G 978 ARG cc_start: 0.0877 (OUTLIER) cc_final: -0.0145 (ptm160) REVERT: H 45 LEU cc_start: 0.8875 (mp) cc_final: 0.8296 (tp) REVERT: H 121 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7680 (mtm-85) REVERT: H 146 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6874 (tm-30) REVERT: J 122 MET cc_start: 0.5696 (mmt) cc_final: 0.4224 (mmt) REVERT: J 201 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7730 (ttp80) REVERT: J 494 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5451 (t70) outliers start: 197 outliers final: 155 residues processed: 938 average time/residue: 0.4804 time to fit residues: 707.6067 Evaluate side-chains 949 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 783 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain F residue 1029 HIS Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 HIS B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN E 11 ASN E 74 GLN E 396 GLN F 67 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS H 201 HIS J 396 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 33972 Z= 0.395 Angle : 0.741 13.424 45964 Z= 0.369 Chirality : 0.046 0.376 5146 Planarity : 0.005 0.074 6034 Dihedral : 7.139 169.747 4640 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.29 % Favored : 93.52 % Rotamer: Outliers : 6.24 % Allowed : 28.95 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4136 helix: 1.15 (0.11), residues: 2346 sheet: -1.04 (0.22), residues: 502 loop : -1.47 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 115 HIS 0.008 0.001 HIS J 19 PHE 0.023 0.002 PHE F 886 TYR 0.028 0.002 TYR G 891 ARG 0.008 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 814 time to evaluate : 3.928 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: A 233 ASP cc_start: 0.7387 (p0) cc_final: 0.7125 (p0) REVERT: A 976 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6463 (tp30) REVERT: B 144 LEU cc_start: 0.7985 (mp) cc_final: 0.7582 (pp) REVERT: B 219 GLU cc_start: 0.7663 (mp0) cc_final: 0.7366 (tt0) REVERT: B 256 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6307 (ptm160) REVERT: B 270 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: B 819 LEU cc_start: 0.7045 (pt) cc_final: 0.6165 (mm) REVERT: B 978 ARG cc_start: 0.0867 (OUTLIER) cc_final: 0.0292 (ppt170) REVERT: C 106 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6684 (mp) REVERT: E 96 GLU cc_start: 0.6625 (tp30) cc_final: 0.6405 (tm-30) REVERT: E 125 THR cc_start: 0.8850 (p) cc_final: 0.8648 (p) REVERT: E 198 ASP cc_start: 0.7600 (m-30) cc_final: 0.7228 (m-30) REVERT: E 227 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7992 (mm) REVERT: E 304 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: E 376 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: E 494 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5507 (t70) REVERT: F 56 LEU cc_start: 0.8993 (tt) cc_final: 0.8682 (tt) REVERT: F 192 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7742 (mtt180) REVERT: F 929 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: F 931 LEU cc_start: 0.9340 (tp) cc_final: 0.9119 (tp) REVERT: F 976 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6462 (tp30) REVERT: G 219 GLU cc_start: 0.7697 (mp0) cc_final: 0.7488 (tt0) REVERT: G 253 GLU cc_start: 0.4921 (mm-30) cc_final: 0.3860 (mm-30) REVERT: G 270 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: G 819 LEU cc_start: 0.7043 (pt) cc_final: 0.6149 (mm) REVERT: G 978 ARG cc_start: 0.0894 (OUTLIER) cc_final: 0.0369 (ppt90) REVERT: H 146 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6994 (tm-30) REVERT: I 103 LYS cc_start: 0.8883 (pttm) cc_final: 0.8295 (pttm) REVERT: J 50 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7820 (tp) REVERT: J 96 GLU cc_start: 0.6549 (tm-30) cc_final: 0.6267 (tm-30) REVERT: J 122 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.4222 (mmt) REVERT: J 201 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: J 467 PHE cc_start: 0.6207 (m-80) cc_final: 0.5778 (m-80) REVERT: J 494 ASP cc_start: 0.5982 (OUTLIER) cc_final: 0.5478 (t70) outliers start: 222 outliers final: 165 residues processed: 958 average time/residue: 0.4959 time to fit residues: 739.6389 Evaluate side-chains 969 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 788 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 813 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 THR Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 0.7980 chunk 378 optimal weight: 0.7980 chunk 345 optimal weight: 0.9990 chunk 368 optimal weight: 0.2980 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 289 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 332 optimal weight: 0.5980 chunk 348 optimal weight: 0.6980 chunk 366 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 396 GLN F 67 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G1029 HIS H 201 HIS J 396 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33972 Z= 0.211 Angle : 0.689 12.578 45964 Z= 0.339 Chirality : 0.042 0.308 5146 Planarity : 0.004 0.069 6034 Dihedral : 6.878 168.493 4640 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.02 % Favored : 93.81 % Rotamer: Outliers : 4.50 % Allowed : 31.08 % Favored : 64.42 % 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: 0.26 (0.13), residues: 4136 helix: 1.30 (0.11), residues: 2356 sheet: -1.06 (0.22), residues: 512 loop : -1.38 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 449 HIS 0.006 0.001 HIS B 249 PHE 0.028 0.001 PHE B 194 TYR 0.025 0.002 TYR G 187 ARG 0.012 0.001 ARG E 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 835 time to evaluate : 3.930 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: A 233 ASP cc_start: 0.7429 (p0) cc_final: 0.7176 (p0) REVERT: A 830 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7399 (tm130) REVERT: A 921 ASP cc_start: 0.7730 (t0) cc_final: 0.7435 (t0) REVERT: A 976 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: B 141 ARG cc_start: 0.5487 (ptt90) cc_final: 0.5180 (ptt-90) REVERT: B 144 LEU cc_start: 0.7970 (mp) cc_final: 0.7582 (pp) REVERT: B 171 MET cc_start: 0.6262 (ptt) cc_final: 0.6011 (ptt) REVERT: B 219 GLU cc_start: 0.7672 (mp0) cc_final: 0.7359 (tt0) REVERT: B 256 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6300 (ptm160) REVERT: B 270 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: B 819 LEU cc_start: 0.6733 (pt) cc_final: 0.5936 (mm) REVERT: B 978 ARG cc_start: 0.0844 (OUTLIER) cc_final: 0.0248 (ppt170) REVERT: B 1003 TYR cc_start: 0.7181 (t80) cc_final: 0.6859 (t80) REVERT: D 168 TYR cc_start: 0.8510 (m-80) cc_final: 0.8166 (m-80) REVERT: E 134 ARG cc_start: 0.7055 (mtm-85) cc_final: 0.6297 (mtm180) REVERT: E 220 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7294 (pp20) REVERT: E 227 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7973 (mm) REVERT: E 304 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: E 461 ILE cc_start: 0.7412 (pt) cc_final: 0.7072 (mp) REVERT: E 494 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5579 (t70) REVERT: F 56 LEU cc_start: 0.8974 (tt) cc_final: 0.8702 (tt) REVERT: F 192 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7596 (mtt180) REVERT: F 921 ASP cc_start: 0.7782 (t0) cc_final: 0.7482 (t0) REVERT: F 931 LEU cc_start: 0.9223 (tp) cc_final: 0.8977 (tp) REVERT: F 976 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6396 (tp30) REVERT: G 156 TRP cc_start: 0.7675 (m-10) cc_final: 0.7297 (m-90) REVERT: G 219 GLU cc_start: 0.7700 (mp0) cc_final: 0.7475 (tt0) REVERT: G 253 GLU cc_start: 0.4956 (mm-30) cc_final: 0.4416 (mm-30) REVERT: G 270 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: G 819 LEU cc_start: 0.6934 (pt) cc_final: 0.6215 (mm) REVERT: G 866 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7253 (mm-30) REVERT: G 978 ARG cc_start: 0.0824 (OUTLIER) cc_final: 0.0287 (ppt170) REVERT: H 146 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6929 (tm-30) REVERT: I 103 LYS cc_start: 0.8824 (pttm) cc_final: 0.8170 (pttm) REVERT: I 226 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (tt) REVERT: J 467 PHE cc_start: 0.6123 (m-80) cc_final: 0.5735 (m-80) REVERT: J 494 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5490 (t70) outliers start: 160 outliers final: 122 residues processed: 936 average time/residue: 0.4911 time to fit residues: 720.1355 Evaluate side-chains 933 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 799 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 977 SER Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 813 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 1.9990 chunk 389 optimal weight: 1.9990 chunk 237 optimal weight: 0.0270 chunk 184 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 408 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 325 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 199 optimal weight: 0.1980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 74 GLN J 396 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33972 Z= 0.197 Angle : 0.688 12.901 45964 Z= 0.339 Chirality : 0.041 0.224 5146 Planarity : 0.004 0.068 6034 Dihedral : 6.723 178.340 4640 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 3.79 % Allowed : 31.70 % Favored : 64.50 % 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: 0.34 (0.13), residues: 4136 helix: 1.33 (0.11), residues: 2360 sheet: -1.03 (0.23), residues: 500 loop : -1.29 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 402 HIS 0.006 0.001 HIS G1029 PHE 0.025 0.001 PHE B 194 TYR 0.035 0.001 TYR G 187 ARG 0.011 0.001 ARG F1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 834 time to evaluate : 3.781 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: A 233 ASP cc_start: 0.7407 (p0) cc_final: 0.7148 (p0) REVERT: A 830 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7739 (tm130) REVERT: A 921 ASP cc_start: 0.7777 (t0) cc_final: 0.7488 (t0) REVERT: A 976 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6513 (tp30) REVERT: B 141 ARG cc_start: 0.5103 (ptt90) cc_final: 0.4791 (ptt-90) REVERT: B 144 LEU cc_start: 0.7909 (mp) cc_final: 0.7519 (pp) REVERT: B 171 MET cc_start: 0.6252 (ptt) cc_final: 0.5979 (ptt) REVERT: B 219 GLU cc_start: 0.7674 (mp0) cc_final: 0.7369 (tt0) REVERT: B 256 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6328 (ptm160) REVERT: B 270 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: B 819 LEU cc_start: 0.6621 (pt) cc_final: 0.5937 (mm) REVERT: E 220 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7289 (pp20) REVERT: E 227 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7914 (mm) REVERT: E 304 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: E 461 ILE cc_start: 0.7333 (pt) cc_final: 0.6965 (mp) REVERT: F 56 LEU cc_start: 0.8982 (tt) cc_final: 0.8700 (tt) REVERT: F 192 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7631 (mtt180) REVERT: F 921 ASP cc_start: 0.7726 (t0) cc_final: 0.7452 (t0) REVERT: F 931 LEU cc_start: 0.9203 (tp) cc_final: 0.8976 (tp) REVERT: F 976 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6500 (tp30) REVERT: F 1091 ARG cc_start: 0.7092 (mtm180) cc_final: 0.6704 (ptp-170) REVERT: G 156 TRP cc_start: 0.7597 (m-10) cc_final: 0.7115 (m-90) REVERT: G 219 GLU cc_start: 0.7686 (mp0) cc_final: 0.7457 (tt0) REVERT: G 237 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7175 (mm-30) REVERT: G 270 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: G 819 LEU cc_start: 0.6875 (pt) cc_final: 0.6112 (mm) REVERT: G 989 LYS cc_start: 0.7949 (tptp) cc_final: 0.7594 (tttt) REVERT: H 146 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6965 (tm-30) REVERT: I 103 LYS cc_start: 0.8784 (pttm) cc_final: 0.8154 (pttm) REVERT: J 122 MET cc_start: 0.5228 (mmp) cc_final: 0.3856 (mmt) REVERT: J 134 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6196 (mtm180) REVERT: J 304 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (mp10) outliers start: 135 outliers final: 114 residues processed: 919 average time/residue: 0.4708 time to fit residues: 680.2952 Evaluate side-chains 928 residues out of total 3558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 806 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 785 ARG Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 813 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1080 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 76 HIS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 299 SER Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 299 optimal weight: 10.0000 chunk 48 optimal weight: 0.0000 chunk 90 optimal weight: 9.9990 chunk 325 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 334 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 396 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 11 ASN J 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126903 restraints weight = 52249.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125137 restraints weight = 29649.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125872 restraints weight = 26991.346| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33972 Z= 0.208 Angle : 0.692 12.951 45964 Z= 0.341 Chirality : 0.042 0.352 5146 Planarity : 0.004 0.068 6034 Dihedral : 6.626 173.814 4640 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.74 % Rotamer: Outliers : 3.71 % Allowed : 31.96 % Favored : 64.33 % 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: 0.33 (0.13), residues: 4136 helix: 1.30 (0.11), residues: 2368 sheet: -1.03 (0.23), residues: 500 loop : -1.26 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 402 HIS 0.006 0.001 HIS G1029 PHE 0.023 0.001 PHE B 194 TYR 0.030 0.002 TYR D 70 ARG 0.018 0.001 ARG G 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10503.36 seconds wall clock time: 187 minutes 56.72 seconds (11276.72 seconds total)