Starting phenix.real_space_refine on Wed Aug 7 10:44:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/08_2024/8xop_38537.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 12474 2.51 5 N 3304 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "L PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19740 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "B" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "E" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "H" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "N" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 14.17, per 1000 atoms: 0.72 Number of scatterers: 19740 At special positions: 0 Unit cell: (115.92, 116.76, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3857 8.00 N 3304 7.00 C 12474 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.85 Conformation dependent library (CDL) restraints added in 3.6 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 42 sheets defined 51.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 removed outlier: 4.020A pdb=" N ILE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 148 through 174 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.509A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 removed outlier: 3.743A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 149 through 174 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.944A pdb=" N ILE D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.720A pdb=" N GLY E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 removed outlier: 4.175A pdb=" N ILE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.797A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 52 through 59 Processing helix chain 'H' and resid 70 through 87 removed outlier: 3.628A pdb=" N MET H 87 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'H' and resid 130 through 139 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.641A pdb=" N GLU H 204 " --> pdb=" O ARG H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 52 through 59 removed outlier: 3.749A pdb=" N GLU I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 104 through 117 Processing helix chain 'I' and resid 131 through 139 removed outlier: 3.506A pdb=" N VAL I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 191 Processing helix chain 'I' and resid 195 through 204 removed outlier: 4.042A pdb=" N GLU I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 52 through 59 Processing helix chain 'J' and resid 70 through 87 removed outlier: 3.906A pdb=" N MET J 87 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 117 removed outlier: 3.727A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 167 through 192 Processing helix chain 'J' and resid 195 through 204 removed outlier: 3.669A pdb=" N GLU J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.795A pdb=" N GLU K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'K' and resid 104 through 117 Processing helix chain 'K' and resid 131 through 139 Processing helix chain 'K' and resid 167 through 191 removed outlier: 3.548A pdb=" N HIS K 191 " --> pdb=" O MET K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.752A pdb=" N GLU K 204 " --> pdb=" O ARG K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 52 through 59 Processing helix chain 'L' and resid 70 through 87 removed outlier: 3.895A pdb=" N MET L 87 " --> pdb=" O CYS L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 117 removed outlier: 3.664A pdb=" N LEU L 107 " --> pdb=" O SER L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 167 through 191 Processing helix chain 'L' and resid 195 through 204 removed outlier: 3.713A pdb=" N GLU L 204 " --> pdb=" O ARG L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 52 through 59 Processing helix chain 'M' and resid 70 through 87 removed outlier: 3.697A pdb=" N MET M 87 " --> pdb=" O CYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.560A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 167 through 191 Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 52 through 59 Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.699A pdb=" N MET N 87 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 117 removed outlier: 3.593A pdb=" N LEU N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 139 Processing helix chain 'N' and resid 167 through 192 Processing helix chain 'N' and resid 195 through 203 Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.849A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 81 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 110 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.849A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 81 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 110 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG A 127 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.558A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.558A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG B 127 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.521A pdb=" N ALA B 142 " --> pdb=" O GLY J 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.739A pdb=" N GLY B 146 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER J 160 " --> pdb=" O GLY B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.449A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER C 81 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 110 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 134 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 109 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU C 136 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA C 111 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.449A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER C 81 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 110 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 127 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.015A pdb=" N GLY C 146 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER K 160 " --> pdb=" O GLY C 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.521A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.521A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG D 127 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.682A pdb=" N GLY D 146 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER L 160 " --> pdb=" O GLY D 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.383A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.383A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG E 127 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.630A pdb=" N ILE F 46 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN F 80 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 48 " --> pdb=" O ASN F 80 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER F 81 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU F 110 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 134 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY F 109 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU F 136 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA F 111 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.630A pdb=" N ILE F 46 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN F 80 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 48 " --> pdb=" O ASN F 80 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER F 81 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU F 110 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG F 127 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC6, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.415A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU G 134 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY G 109 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU G 136 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA G 111 " --> pdb=" O LEU G 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.415A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG G 127 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AD1, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AD2, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.260A pdb=" N ILE H 63 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN H 98 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU H 65 " --> pdb=" O ASN H 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 124 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 97 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER H 99 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN H 128 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG H 145 " --> pdb=" O GLN H 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'I' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE I 63 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN I 98 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 65 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU I 154 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA I 129 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE I 63 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN I 98 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 65 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG I 145 " --> pdb=" O GLN I 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.583A pdb=" N ILE J 63 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN J 98 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 65 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER J 99 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN J 128 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG J 152 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY J 127 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU J 154 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA J 129 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.583A pdb=" N ILE J 63 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN J 98 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 65 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER J 99 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN J 128 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N MET J 146 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR J 123 " --> pdb=" O MET J 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.639A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU K 154 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA K 129 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.639A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG K 145 " --> pdb=" O GLN K 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE L 63 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN L 98 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU L 65 " --> pdb=" O ASN L 98 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N MET L 146 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR L 123 " --> pdb=" O MET L 146 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG L 145 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 153 through 155 Processing sheet with id=AE3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.383A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER M 99 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN M 128 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG M 152 " --> pdb=" O CYS M 125 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY M 127 " --> pdb=" O ARG M 152 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU M 154 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA M 129 " --> pdb=" O LEU M 154 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.383A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER M 99 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN M 128 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG M 145 " --> pdb=" O GLN M 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.362A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ARG N 152 " --> pdb=" O CYS N 125 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY N 127 " --> pdb=" O ARG N 152 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU N 154 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA N 129 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.362A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N MET N 146 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR N 123 " --> pdb=" O MET N 146 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG N 145 " --> pdb=" O GLN N 222 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3255 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: 6.62 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3461 1.32 - 1.44: 4785 1.44 - 1.56: 11599 1.56 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 20041 Sorted by residual: bond pdb=" C3 OTT U 1 " pdb=" C4 OTT U 1 " ideal model delta sigma weight residual 1.445 1.388 0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C3 OTT T 1 " pdb=" C4 OTT T 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C3 OTT S 1 " pdb=" C4 OTT S 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C3 OTT R 1 " pdb=" C4 OTT R 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" C3 OTT W 1 " pdb=" C4 OTT W 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.81e+00 ... (remaining 20036 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.53: 510 105.53 - 112.63: 10677 112.63 - 119.73: 6386 119.73 - 126.84: 9359 126.84 - 133.94: 179 Bond angle restraints: 27111 Sorted by residual: angle pdb=" N GLU J 185 " pdb=" CA GLU J 185 " pdb=" CB GLU J 185 " ideal model delta sigma weight residual 110.28 116.90 -6.62 1.55e+00 4.16e-01 1.82e+01 angle pdb=" C VAL L 77 " pdb=" N MET L 78 " pdb=" CA MET L 78 " ideal model delta sigma weight residual 121.14 113.88 7.26 1.75e+00 3.27e-01 1.72e+01 angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta sigma weight residual 110.12 115.46 -5.34 1.47e+00 4.63e-01 1.32e+01 angle pdb=" C VAL K 77 " pdb=" N MET K 78 " pdb=" CA MET K 78 " ideal model delta sigma weight residual 121.14 114.82 6.32 1.75e+00 3.27e-01 1.31e+01 angle pdb=" N GLU E 156 " pdb=" CA GLU E 156 " pdb=" CB GLU E 156 " ideal model delta sigma weight residual 110.22 115.64 -5.42 1.54e+00 4.22e-01 1.24e+01 ... (remaining 27106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11342 17.94 - 35.89: 699 35.89 - 53.83: 118 53.83 - 71.77: 23 71.77 - 89.71: 19 Dihedral angle restraints: 12201 sinusoidal: 4774 harmonic: 7427 Sorted by residual: dihedral pdb=" CA ARG A 44 " pdb=" C ARG A 44 " pdb=" N ILE A 45 " pdb=" CA ILE A 45 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA b 6 " pdb=" C ALA b 6 " pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " ideal model delta harmonic sigma weight residual 0.00 -26.87 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ALA W 6 " pdb=" C ALA W 6 " pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " ideal model delta harmonic sigma weight residual 0.00 -26.59 26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 12198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2253 0.040 - 0.080: 600 0.080 - 0.120: 257 0.120 - 0.160: 26 0.160 - 0.200: 14 Chirality restraints: 3150 Sorted by residual: chirality pdb=" CG MP8 b 7 " pdb=" CB MP8 b 7 " pdb=" CD MP8 b 7 " pdb=" CE MP8 b 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CG MP8 V 7 " pdb=" CB MP8 V 7 " pdb=" CD MP8 V 7 " pdb=" CE MP8 V 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CG MP8 X 7 " pdb=" CB MP8 X 7 " pdb=" CD MP8 X 7 " pdb=" CE MP8 X 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3147 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 OTT b 1 " 0.075 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C6 OTT b 1 " -0.075 2.00e-02 2.50e+03 pdb=" C7 OTT b 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 OTT b 1 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 OTT Y 1 " 0.072 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" C6 OTT Y 1 " -0.073 2.00e-02 2.50e+03 pdb=" C7 OTT Y 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 OTT Y 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 OTT a 1 " -0.037 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C2 OTT a 1 " 0.036 2.00e-02 2.50e+03 pdb=" C3 OTT a 1 " 0.041 2.00e-02 2.50e+03 pdb=" C4 OTT a 1 " -0.040 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 417 2.68 - 3.23: 19673 3.23 - 3.79: 31202 3.79 - 4.34: 40491 4.34 - 4.90: 67808 Nonbonded interactions: 159591 Sorted by model distance: nonbonded pdb=" OE1 GLN C 139 " pdb=" NE2 GLN K 166 " model vdw 2.120 3.120 nonbonded pdb=" NH2 ARG A 164 " pdb=" OE1 GLU A 167 " model vdw 2.182 3.120 nonbonded pdb=" NH2 ARG F 164 " pdb=" OE1 GLU F 167 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG D 164 " pdb=" OE1 GLU D 167 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG E 164 " pdb=" OE1 GLU E 167 " model vdw 2.197 3.120 ... (remaining 159586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 60.530 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 0.057 20041 Z= 0.303 Angle : 0.691 8.958 27111 Z= 0.356 Chirality : 0.045 0.200 3150 Planarity : 0.006 0.074 3556 Dihedral : 12.473 89.713 7399 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2464 helix: 1.54 (0.15), residues: 1358 sheet: 1.74 (0.34), residues: 245 loop : -0.21 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.002 0.000 HIS G 138 PHE 0.022 0.001 PHE I 104 TYR 0.020 0.001 TYR H 51 ARG 0.009 0.001 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8779 (mm-40) REVERT: B 50 GLN cc_start: 0.9261 (pt0) cc_final: 0.9036 (pt0) REVERT: C 43 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8965 (mm-30) REVERT: C 73 LYS cc_start: 0.9319 (mttm) cc_final: 0.9090 (mtpp) REVERT: C 97 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8778 (mm-40) REVERT: D 43 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8917 (mm-30) REVERT: D 100 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8722 (mptt) REVERT: E 43 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8983 (mm-30) REVERT: E 97 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8855 (mm-40) REVERT: E 114 MET cc_start: 0.9055 (tpp) cc_final: 0.8804 (mmm) REVERT: F 43 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9036 (mm-30) REVERT: F 50 GLN cc_start: 0.9307 (pt0) cc_final: 0.9070 (pt0) REVERT: F 73 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9220 (mtpp) REVERT: G 50 GLN cc_start: 0.9253 (pt0) cc_final: 0.9035 (pt0) REVERT: G 97 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8988 (mm110) REVERT: H 166 GLN cc_start: 0.7993 (pt0) cc_final: 0.7516 (pt0) REVERT: H 222 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8689 (tp-100) REVERT: I 85 GLU cc_start: 0.8169 (pp20) cc_final: 0.7940 (pp20) REVERT: I 91 ARG cc_start: 0.9309 (mtp85) cc_final: 0.9107 (mtp-110) REVERT: I 203 ILE cc_start: 0.9556 (tp) cc_final: 0.9349 (tp) REVERT: I 222 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8749 (tp-100) REVERT: J 60 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8877 (mm-30) REVERT: K 91 ARG cc_start: 0.9271 (ttm110) cc_final: 0.8793 (ttm110) REVERT: K 197 GLU cc_start: 0.9012 (pm20) cc_final: 0.8761 (pm20) REVERT: K 201 GLU cc_start: 0.9059 (mp0) cc_final: 0.8501 (mp0) REVERT: K 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7962 (tm-30) REVERT: L 185 GLU cc_start: 0.8351 (pt0) cc_final: 0.8097 (pt0) REVERT: L 200 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8560 (ttm110) REVERT: M 60 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8894 (mm-30) REVERT: M 185 GLU cc_start: 0.8531 (pt0) cc_final: 0.8244 (pt0) REVERT: N 91 ARG cc_start: 0.9068 (ptp90) cc_final: 0.8712 (pmm-80) REVERT: N 122 GLN cc_start: 0.7402 (mt0) cc_final: 0.7059 (mt0) REVERT: N 204 GLU cc_start: 0.8697 (tp30) cc_final: 0.8024 (tp30) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 1.6054 time to fit residues: 939.6276 Evaluate side-chains 427 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 50 GLN D 58 ASN D 63 GLN E 50 GLN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 122 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 80 GLN L 122 GLN N 175 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20041 Z= 0.289 Angle : 0.646 8.001 27111 Z= 0.334 Chirality : 0.043 0.171 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.281 34.174 2800 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.85 % Allowed : 14.72 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2464 helix: 1.91 (0.14), residues: 1358 sheet: 1.69 (0.34), residues: 245 loop : -0.21 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.026 0.001 PHE L 58 TYR 0.018 0.001 TYR H 51 ARG 0.009 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 487 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8712 (mm-40) REVERT: A 171 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8805 (tm-30) REVERT: B 50 GLN cc_start: 0.9241 (pt0) cc_final: 0.8974 (pt0) REVERT: B 97 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: B 100 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8474 (mmtt) REVERT: B 194 GLU cc_start: 0.8830 (pt0) cc_final: 0.8429 (pt0) REVERT: B 205 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: C 43 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8971 (mm-30) REVERT: C 73 LYS cc_start: 0.9253 (mttm) cc_final: 0.9052 (mtpp) REVERT: C 97 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8754 (mm-40) REVERT: C 134 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8487 (mt-10) REVERT: D 43 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8960 (mm-30) REVERT: D 100 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8696 (mptt) REVERT: D 134 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8420 (mt-10) REVERT: D 194 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8354 (mt-10) REVERT: E 43 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8952 (mm-30) REVERT: E 97 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8893 (mm-40) REVERT: E 134 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8548 (mt-10) REVERT: F 43 GLU cc_start: 0.9244 (mm-30) cc_final: 0.9003 (mm-30) REVERT: F 50 GLN cc_start: 0.9265 (pt0) cc_final: 0.8979 (pt0) REVERT: F 100 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8455 (mmtt) REVERT: F 108 MET cc_start: 0.8474 (ptp) cc_final: 0.8072 (ptp) REVERT: F 194 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8385 (mt-10) REVERT: G 50 GLN cc_start: 0.9218 (pt0) cc_final: 0.8929 (pt0) REVERT: G 97 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8856 (mm-40) REVERT: H 59 GLU cc_start: 0.8879 (mp0) cc_final: 0.8556 (mp0) REVERT: H 204 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8049 (tm-30) REVERT: H 222 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8710 (tp-100) REVERT: I 157 GLN cc_start: 0.9242 (pt0) cc_final: 0.8860 (pt0) REVERT: I 181 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8407 (ttm-80) REVERT: I 222 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8764 (tp-100) REVERT: J 200 ARG cc_start: 0.8652 (mpp80) cc_final: 0.8397 (mpp80) REVERT: J 203 ILE cc_start: 0.9397 (tp) cc_final: 0.9174 (tp) REVERT: J 204 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7941 (tm-30) REVERT: K 87 MET cc_start: 0.6963 (mtt) cc_final: 0.6712 (mtm) REVERT: K 91 ARG cc_start: 0.9221 (ttm110) cc_final: 0.8617 (ttm110) REVERT: K 166 GLN cc_start: 0.8236 (tt0) cc_final: 0.7827 (tt0) REVERT: K 197 GLU cc_start: 0.9082 (pm20) cc_final: 0.8742 (pm20) REVERT: K 200 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8393 (mmm160) REVERT: K 201 GLU cc_start: 0.8952 (mp0) cc_final: 0.8601 (mp0) REVERT: K 203 ILE cc_start: 0.9590 (tp) cc_final: 0.9264 (tp) REVERT: K 204 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8126 (tm-30) REVERT: L 91 ARG cc_start: 0.9347 (mtp-110) cc_final: 0.9101 (mtp85) REVERT: L 166 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: L 198 LYS cc_start: 0.9425 (tppp) cc_final: 0.9108 (tppp) REVERT: L 204 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7936 (tm-30) REVERT: M 51 TYR cc_start: 0.8257 (t80) cc_final: 0.8028 (t80) REVERT: M 60 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8920 (mm-30) REVERT: M 185 GLU cc_start: 0.8582 (pt0) cc_final: 0.8285 (pt0) REVERT: M 204 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8115 (tm-30) REVERT: N 122 GLN cc_start: 0.7250 (mt0) cc_final: 0.6917 (mt0) REVERT: N 198 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9076 (tptp) REVERT: N 204 GLU cc_start: 0.8872 (tp30) cc_final: 0.8059 (tp30) outliers start: 59 outliers final: 10 residues processed: 500 average time/residue: 1.8623 time to fit residues: 1010.6587 Evaluate side-chains 460 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 446 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN C 58 ASN D 97 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN N 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20041 Z= 0.401 Angle : 0.675 9.638 27111 Z= 0.350 Chirality : 0.044 0.168 3150 Planarity : 0.005 0.049 3556 Dihedral : 4.553 54.067 2800 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 2.75 % Allowed : 18.63 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2464 helix: 1.90 (0.14), residues: 1358 sheet: 1.77 (0.32), residues: 259 loop : -0.38 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.023 0.001 PHE M 58 TYR 0.018 0.001 TYR H 51 ARG 0.012 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 471 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8804 (mm-40) REVERT: A 156 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: B 39 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8856 (mtp-110) REVERT: B 50 GLN cc_start: 0.9247 (pt0) cc_final: 0.8992 (pt0) REVERT: B 100 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8460 (mmtt) REVERT: B 156 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: B 163 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8689 (tmmm) REVERT: B 205 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8056 (mtp) REVERT: C 39 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8658 (mtp-110) REVERT: C 43 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8983 (mm-30) REVERT: C 73 LYS cc_start: 0.9194 (mttm) cc_final: 0.8914 (mtpp) REVERT: C 97 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8896 (mm110) REVERT: C 134 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8475 (mt-10) REVERT: C 156 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: C 163 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8731 (tmmm) REVERT: D 39 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8639 (mtp-110) REVERT: D 43 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8975 (mm-30) REVERT: D 100 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8682 (mptt) REVERT: D 156 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: D 194 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8413 (mt-10) REVERT: E 43 GLU cc_start: 0.9221 (mm-30) cc_final: 0.9016 (mm-30) REVERT: E 50 GLN cc_start: 0.9386 (pt0) cc_final: 0.9134 (pt0) REVERT: E 97 GLN cc_start: 0.9309 (mm-40) cc_final: 0.9083 (mm110) REVERT: E 134 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8496 (mt-10) REVERT: E 156 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: F 39 ARG cc_start: 0.9173 (ttp80) cc_final: 0.8847 (mtp-110) REVERT: F 43 GLU cc_start: 0.9259 (mm-30) cc_final: 0.9023 (mm-30) REVERT: F 50 GLN cc_start: 0.9245 (pt0) cc_final: 0.8976 (pt0) REVERT: F 134 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8514 (mt-10) REVERT: F 156 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: F 194 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8801 (mt-10) REVERT: G 50 GLN cc_start: 0.9259 (pt0) cc_final: 0.8989 (pt0) REVERT: G 156 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: G 163 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8706 (tmmm) REVERT: H 91 ARG cc_start: 0.9329 (ptm160) cc_final: 0.9016 (ptp90) REVERT: H 203 ILE cc_start: 0.9513 (tp) cc_final: 0.9269 (tp) REVERT: H 204 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8284 (tp30) REVERT: H 222 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8729 (tp-100) REVERT: I 222 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8730 (tp-100) REVERT: J 59 GLU cc_start: 0.8857 (mp0) cc_final: 0.8490 (mp0) REVERT: J 144 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8277 (ptpp) REVERT: J 170 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8893 (mp) REVERT: J 204 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7916 (tm-30) REVERT: K 91 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8678 (ttm110) REVERT: K 166 GLN cc_start: 0.8258 (tt0) cc_final: 0.7671 (tt0) REVERT: K 198 LYS cc_start: 0.9249 (tppp) cc_final: 0.9025 (tppp) REVERT: K 201 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: K 203 ILE cc_start: 0.9592 (tp) cc_final: 0.9388 (tp) REVERT: K 204 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8118 (tm-30) REVERT: L 59 GLU cc_start: 0.9080 (mp0) cc_final: 0.8737 (mp0) REVERT: L 91 ARG cc_start: 0.9324 (mtp-110) cc_final: 0.8996 (mtp85) REVERT: L 122 GLN cc_start: 0.8082 (pt0) cc_final: 0.7462 (pm20) REVERT: L 166 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: L 200 ARG cc_start: 0.8988 (ttm110) cc_final: 0.8502 (mtm110) REVERT: L 204 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8127 (tm-30) REVERT: M 51 TYR cc_start: 0.8315 (t80) cc_final: 0.8041 (t80) REVERT: M 60 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8942 (mm-30) REVERT: M 185 GLU cc_start: 0.8635 (pt0) cc_final: 0.8327 (pt0) REVERT: M 204 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8033 (tm-30) REVERT: N 122 GLN cc_start: 0.7351 (mt0) cc_final: 0.7102 (mt0) REVERT: N 152 ARG cc_start: 0.7412 (ttt180) cc_final: 0.6473 (ttt-90) REVERT: N 166 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8022 (mm-40) REVERT: N 197 GLU cc_start: 0.9255 (mp0) cc_final: 0.9018 (pm20) REVERT: N 204 GLU cc_start: 0.8903 (tp30) cc_final: 0.8066 (tp30) outliers start: 57 outliers final: 13 residues processed: 488 average time/residue: 1.9300 time to fit residues: 1020.6046 Evaluate side-chains 475 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 445 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 5.9990 chunk 162 optimal weight: 0.0570 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 113 optimal weight: 0.0170 chunk 205 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN G 35 GLN H 157 GLN I 80 GLN I 150 ASN I 166 GLN J 175 ASN K 80 GLN N 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20041 Z= 0.181 Angle : 0.618 9.166 27111 Z= 0.316 Chirality : 0.042 0.163 3150 Planarity : 0.005 0.066 3556 Dihedral : 4.294 55.096 2800 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.75 % Allowed : 20.37 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.18), residues: 2464 helix: 2.06 (0.15), residues: 1379 sheet: 1.95 (0.31), residues: 224 loop : -0.16 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.002 0.000 HIS G 138 PHE 0.026 0.001 PHE L 58 TYR 0.018 0.001 TYR N 159 ARG 0.011 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 494 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8684 (mm-40) REVERT: A 100 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8480 (mmtt) REVERT: A 108 MET cc_start: 0.8483 (ptp) cc_final: 0.7908 (ptp) REVERT: A 156 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: A 176 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8791 (t) REVERT: A 178 GLU cc_start: 0.9237 (pm20) cc_final: 0.8918 (pm20) REVERT: B 39 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8819 (mtp-110) REVERT: B 50 GLN cc_start: 0.9256 (pt0) cc_final: 0.9000 (pt0) REVERT: B 100 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8483 (mmtt) REVERT: B 156 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: C 43 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8964 (mm-30) REVERT: C 73 LYS cc_start: 0.9213 (mttm) cc_final: 0.8937 (mtpp) REVERT: C 97 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8884 (mm110) REVERT: C 100 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8513 (mmtt) REVERT: C 134 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8438 (mt-10) REVERT: C 139 GLN cc_start: 0.8108 (tt0) cc_final: 0.7486 (tt0) REVERT: C 156 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: C 163 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8720 (tmmm) REVERT: D 42 ASN cc_start: 0.9567 (m-40) cc_final: 0.9111 (m110) REVERT: D 43 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8956 (mm-30) REVERT: D 100 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8738 (mptt) REVERT: D 152 LYS cc_start: 0.8405 (tttt) cc_final: 0.8145 (tttm) REVERT: D 156 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: D 194 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8404 (mt-10) REVERT: E 39 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8747 (mtp-110) REVERT: E 43 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8933 (mm-30) REVERT: E 50 GLN cc_start: 0.9339 (pt0) cc_final: 0.9084 (pt0) REVERT: E 97 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8909 (mm-40) REVERT: E 134 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8386 (mt-10) REVERT: E 156 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: E 163 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8708 (tmmm) REVERT: F 39 ARG cc_start: 0.9172 (ttp80) cc_final: 0.8779 (mtp-110) REVERT: F 50 GLN cc_start: 0.9229 (pt0) cc_final: 0.8973 (pt0) REVERT: F 100 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8484 (mmtt) REVERT: F 156 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: F 194 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8675 (mt-10) REVERT: G 50 GLN cc_start: 0.9239 (pt0) cc_final: 0.8948 (pt0) REVERT: G 97 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8800 (mm-40) REVERT: G 100 LYS cc_start: 0.8736 (mptt) cc_final: 0.8491 (mptt) REVERT: G 156 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: G 163 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8704 (tmmm) REVERT: H 91 ARG cc_start: 0.9330 (ptm160) cc_final: 0.9026 (ptp90) REVERT: H 128 GLN cc_start: 0.8883 (tp40) cc_final: 0.8227 (tp40) REVERT: H 144 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8773 (ttmp) REVERT: H 203 ILE cc_start: 0.9498 (tp) cc_final: 0.9267 (tp) REVERT: H 204 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7871 (tm-30) REVERT: H 222 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8741 (tp-100) REVERT: I 122 GLN cc_start: 0.7788 (pt0) cc_final: 0.7250 (pm20) REVERT: I 150 ASN cc_start: 0.9280 (m-40) cc_final: 0.8941 (m110) REVERT: I 157 GLN cc_start: 0.9205 (pt0) cc_final: 0.8486 (pt0) REVERT: I 166 GLN cc_start: 0.8533 (pt0) cc_final: 0.8286 (pt0) REVERT: I 181 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8314 (ttm-80) REVERT: I 222 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8746 (tp-100) REVERT: J 58 PHE cc_start: 0.9199 (t80) cc_final: 0.8762 (t80) REVERT: J 144 LYS cc_start: 0.8720 (ptpp) cc_final: 0.8417 (ptpp) REVERT: J 166 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7090 (tm-30) REVERT: J 203 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9197 (tp) REVERT: J 204 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7944 (tm-30) REVERT: K 58 PHE cc_start: 0.9082 (t80) cc_final: 0.8826 (t80) REVERT: K 87 MET cc_start: 0.6970 (mtt) cc_final: 0.6679 (mtm) REVERT: K 91 ARG cc_start: 0.9155 (ttm110) cc_final: 0.8648 (ttm110) REVERT: K 166 GLN cc_start: 0.8173 (tt0) cc_final: 0.7437 (tt0) REVERT: K 185 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7332 (pt0) REVERT: K 197 GLU cc_start: 0.9069 (pm20) cc_final: 0.8847 (pm20) REVERT: K 201 GLU cc_start: 0.8871 (mp0) cc_final: 0.8601 (mp0) REVERT: K 204 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8239 (tm-30) REVERT: L 59 GLU cc_start: 0.9048 (mp0) cc_final: 0.8483 (mp0) REVERT: L 91 ARG cc_start: 0.9343 (mtp-110) cc_final: 0.9058 (mtp85) REVERT: L 122 GLN cc_start: 0.8055 (pt0) cc_final: 0.7383 (pm20) REVERT: L 166 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: L 198 LYS cc_start: 0.9460 (tppp) cc_final: 0.9198 (tppp) REVERT: L 200 ARG cc_start: 0.9002 (ttm110) cc_final: 0.8709 (ttm110) REVERT: L 204 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8106 (tm-30) REVERT: M 51 TYR cc_start: 0.8290 (t80) cc_final: 0.8081 (t80) REVERT: M 59 GLU cc_start: 0.9192 (mp0) cc_final: 0.8855 (mp0) REVERT: M 60 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8843 (mm-30) REVERT: M 122 GLN cc_start: 0.7889 (pt0) cc_final: 0.7307 (pm20) REVERT: M 185 GLU cc_start: 0.8637 (pt0) cc_final: 0.8307 (pt0) REVERT: M 203 ILE cc_start: 0.9402 (tp) cc_final: 0.9133 (tp) REVERT: M 204 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8114 (tm-30) REVERT: N 91 ARG cc_start: 0.8950 (pmm-80) cc_final: 0.8601 (pmm-80) REVERT: N 122 GLN cc_start: 0.7233 (mt0) cc_final: 0.6961 (mt0) REVERT: N 166 GLN cc_start: 0.8239 (mm-40) cc_final: 0.8001 (mt0) REVERT: N 198 LYS cc_start: 0.9435 (tppp) cc_final: 0.9081 (tptp) REVERT: N 203 ILE cc_start: 0.9431 (tp) cc_final: 0.9216 (tp) REVERT: N 204 GLU cc_start: 0.8909 (tp30) cc_final: 0.8113 (tp30) outliers start: 57 outliers final: 11 residues processed: 515 average time/residue: 1.8418 time to fit residues: 1031.1897 Evaluate side-chains 495 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 469 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 59 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN D 58 ASN E 35 GLN E 139 GLN F 35 GLN F 97 GLN G 35 GLN H 150 ASN K 150 ASN N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.005 0.055 20041 Z= 0.306 Angle : 0.656 9.615 27111 Z= 0.338 Chirality : 0.043 0.220 3150 Planarity : 0.005 0.056 3556 Dihedral : 4.283 52.603 2800 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.33 % Allowed : 21.24 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2464 helix: 2.10 (0.15), residues: 1372 sheet: 2.09 (0.32), residues: 224 loop : -0.19 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.024 0.001 PHE J 58 TYR 0.015 0.001 TYR F 93 ARG 0.011 0.001 ARG N 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 463 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8728 (mm-40) REVERT: A 156 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: A 176 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8849 (t) REVERT: A 178 GLU cc_start: 0.9238 (pm20) cc_final: 0.8896 (pm20) REVERT: B 39 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8854 (mtp-110) REVERT: B 50 GLN cc_start: 0.9248 (pt0) cc_final: 0.9034 (pt0) REVERT: B 100 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8430 (mmtt) REVERT: B 163 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8829 (tmmm) REVERT: C 39 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8645 (mtp-110) REVERT: C 43 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8964 (mm-30) REVERT: C 73 LYS cc_start: 0.9162 (mttm) cc_final: 0.8883 (mtpp) REVERT: C 134 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 156 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: D 39 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8563 (mtp-110) REVERT: D 42 ASN cc_start: 0.9561 (m-40) cc_final: 0.9120 (m110) REVERT: D 43 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8979 (mm-30) REVERT: D 100 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8714 (mptt) REVERT: D 156 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: D 194 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8395 (mt-10) REVERT: E 39 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8807 (mtp-110) REVERT: E 43 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8973 (mm-30) REVERT: E 50 GLN cc_start: 0.9339 (pt0) cc_final: 0.9061 (pt0) REVERT: E 134 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8502 (mt-10) REVERT: E 156 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: E 163 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8691 (tmmm) REVERT: F 39 ARG cc_start: 0.9178 (ttp80) cc_final: 0.8792 (mtp-110) REVERT: F 50 GLN cc_start: 0.9238 (pt0) cc_final: 0.8971 (pt0) REVERT: F 100 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8582 (mmtt) REVERT: F 156 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: F 194 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8661 (mt-10) REVERT: G 50 GLN cc_start: 0.9254 (pt0) cc_final: 0.8999 (pt0) REVERT: G 100 LYS cc_start: 0.8707 (mptt) cc_final: 0.8465 (mptt) REVERT: H 85 GLU cc_start: 0.8960 (pm20) cc_final: 0.8682 (pm20) REVERT: H 91 ARG cc_start: 0.9311 (ptm160) cc_final: 0.9096 (ptm-80) REVERT: H 144 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8727 (ttmm) REVERT: H 203 ILE cc_start: 0.9504 (tp) cc_final: 0.9266 (tp) REVERT: H 204 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8284 (tp30) REVERT: H 222 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8749 (tp-100) REVERT: I 122 GLN cc_start: 0.7957 (pt0) cc_final: 0.7321 (pm20) REVERT: I 222 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8744 (tp-100) REVERT: J 144 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8413 (ptpp) REVERT: J 166 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7025 (mm-40) REVERT: J 170 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8846 (mp) REVERT: J 187 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: J 203 ILE cc_start: 0.9462 (tp) cc_final: 0.9205 (tp) REVERT: J 204 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7970 (tm-30) REVERT: K 58 PHE cc_start: 0.9146 (t80) cc_final: 0.8861 (t80) REVERT: K 91 ARG cc_start: 0.9134 (ttm110) cc_final: 0.8801 (ttm-80) REVERT: K 166 GLN cc_start: 0.8267 (tt0) cc_final: 0.7600 (tt0) REVERT: K 198 LYS cc_start: 0.9251 (tppp) cc_final: 0.8995 (tppp) REVERT: K 204 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8225 (tm-30) REVERT: L 91 ARG cc_start: 0.9328 (mtp-110) cc_final: 0.9002 (mtp85) REVERT: L 122 GLN cc_start: 0.8081 (pt0) cc_final: 0.7343 (pm20) REVERT: L 166 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: L 170 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8667 (mp) REVERT: L 204 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8099 (tm-30) REVERT: M 51 TYR cc_start: 0.8297 (t80) cc_final: 0.8055 (t80) REVERT: M 59 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: M 60 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8884 (mm-30) REVERT: M 122 GLN cc_start: 0.7961 (pt0) cc_final: 0.7325 (pm20) REVERT: M 166 GLN cc_start: 0.8819 (mt0) cc_final: 0.8265 (pt0) REVERT: M 185 GLU cc_start: 0.8640 (pt0) cc_final: 0.8325 (pt0) REVERT: M 203 ILE cc_start: 0.9422 (tp) cc_final: 0.9202 (tp) REVERT: M 204 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 91 ARG cc_start: 0.8989 (pmm-80) cc_final: 0.8586 (pmm-80) REVERT: N 122 GLN cc_start: 0.7313 (mt0) cc_final: 0.7029 (mt0) REVERT: N 198 LYS cc_start: 0.9477 (tppp) cc_final: 0.9088 (tptp) REVERT: N 204 GLU cc_start: 0.8928 (tp30) cc_final: 0.8150 (tp30) outliers start: 69 outliers final: 16 residues processed: 489 average time/residue: 1.8692 time to fit residues: 992.6107 Evaluate side-chains 484 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 451 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 59 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 230 optimal weight: 0.3980 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN M 80 GLN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20041 Z= 0.258 Angle : 0.663 10.564 27111 Z= 0.339 Chirality : 0.043 0.180 3150 Planarity : 0.005 0.060 3556 Dihedral : 4.132 28.660 2800 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.14 % Allowed : 23.02 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.18), residues: 2464 helix: 2.08 (0.15), residues: 1379 sheet: 2.09 (0.31), residues: 224 loop : -0.24 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.023 0.001 PHE L 58 TYR 0.020 0.001 TYR H 159 ARG 0.010 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 472 time to evaluate : 2.394 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: A 97 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8723 (mm-40) REVERT: A 156 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: A 163 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8749 (tmmm) REVERT: A 176 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8793 (t) REVERT: A 178 GLU cc_start: 0.9228 (pm20) cc_final: 0.8884 (pm20) REVERT: B 39 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8844 (mtp-110) REVERT: B 50 GLN cc_start: 0.9252 (pt0) cc_final: 0.9030 (pt0) REVERT: B 58 ASN cc_start: 0.9501 (m-40) cc_final: 0.9192 (m110) REVERT: B 100 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8443 (mmtt) REVERT: B 156 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: B 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8803 (tmmm) REVERT: C 43 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8980 (mm-30) REVERT: C 73 LYS cc_start: 0.9159 (mttm) cc_final: 0.8878 (mtpp) REVERT: C 97 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8733 (mm-40) REVERT: C 134 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8396 (mt-10) REVERT: C 156 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: C 163 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8707 (tmmm) REVERT: D 42 ASN cc_start: 0.9561 (m-40) cc_final: 0.9112 (m110) REVERT: D 43 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8980 (mm-30) REVERT: D 156 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: D 194 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 39 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8779 (mtp-110) REVERT: E 43 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8964 (mm-30) REVERT: E 50 GLN cc_start: 0.9339 (pt0) cc_final: 0.9070 (pt0) REVERT: E 134 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8431 (mt-10) REVERT: E 156 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: E 163 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8692 (tmmm) REVERT: F 39 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8770 (mtp-110) REVERT: F 100 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8548 (mmtt) REVERT: F 156 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: F 163 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8775 (tmmm) REVERT: F 194 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8603 (mt-10) REVERT: G 50 GLN cc_start: 0.9254 (pt0) cc_final: 0.8997 (pt0) REVERT: G 100 LYS cc_start: 0.8779 (mptt) cc_final: 0.8571 (mptt) REVERT: G 156 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: G 163 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8675 (tmmm) REVERT: H 84 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8749 (mm) REVERT: H 91 ARG cc_start: 0.9319 (ptm160) cc_final: 0.8558 (ptp90) REVERT: H 144 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8893 (tttp) REVERT: H 203 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9288 (tp) REVERT: H 204 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8291 (tp30) REVERT: H 222 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8741 (tp-100) REVERT: I 122 GLN cc_start: 0.7967 (pt0) cc_final: 0.7360 (pm20) REVERT: I 222 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8742 (tp-100) REVERT: J 144 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8451 (ptpp) REVERT: J 166 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7096 (mm-40) REVERT: J 170 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8855 (mp) REVERT: J 187 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: J 203 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9202 (tp) REVERT: J 204 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7990 (tm-30) REVERT: K 58 PHE cc_start: 0.9152 (t80) cc_final: 0.8850 (t80) REVERT: K 91 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8790 (ttm-80) REVERT: K 152 ARG cc_start: 0.7205 (tmt170) cc_final: 0.6955 (tmt170) REVERT: K 197 GLU cc_start: 0.9043 (pm20) cc_final: 0.8809 (pm20) REVERT: K 201 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: K 204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8237 (tm-30) REVERT: L 91 ARG cc_start: 0.9334 (mtp-110) cc_final: 0.9020 (mtp85) REVERT: L 122 GLN cc_start: 0.8101 (pt0) cc_final: 0.7458 (pm20) REVERT: L 152 ARG cc_start: 0.7265 (tmt170) cc_final: 0.6786 (tmt170) REVERT: L 166 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: L 170 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8628 (mp) REVERT: L 198 LYS cc_start: 0.9482 (tppp) cc_final: 0.9252 (tppp) REVERT: L 204 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8191 (tm-30) REVERT: M 51 TYR cc_start: 0.8318 (t80) cc_final: 0.8092 (t80) REVERT: M 122 GLN cc_start: 0.7941 (pt0) cc_final: 0.7308 (pm20) REVERT: M 166 GLN cc_start: 0.8818 (mt0) cc_final: 0.8291 (pt0) REVERT: M 185 GLU cc_start: 0.8626 (pt0) cc_final: 0.8286 (pt0) REVERT: M 197 GLU cc_start: 0.9093 (pm20) cc_final: 0.8706 (pm20) REVERT: M 203 ILE cc_start: 0.9428 (tp) cc_final: 0.9218 (tp) REVERT: M 204 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8179 (tm-30) REVERT: N 91 ARG cc_start: 0.9010 (pmm-80) cc_final: 0.8569 (pmm-80) REVERT: N 122 GLN cc_start: 0.7289 (mt0) cc_final: 0.7016 (mt0) REVERT: N 166 GLN cc_start: 0.8481 (mt0) cc_final: 0.8008 (tt0) REVERT: N 204 GLU cc_start: 0.8963 (tp30) cc_final: 0.8185 (tp30) outliers start: 65 outliers final: 19 residues processed: 498 average time/residue: 1.8755 time to fit residues: 1015.3952 Evaluate side-chains 494 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 451 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 193 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN H 150 ASN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 150 ASN K 157 GLN N 175 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20041 Z= 0.252 Angle : 0.692 11.211 27111 Z= 0.352 Chirality : 0.043 0.190 3150 Planarity : 0.005 0.070 3556 Dihedral : 4.075 28.830 2800 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.43 % Allowed : 23.94 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.18), residues: 2464 helix: 2.09 (0.15), residues: 1379 sheet: 2.14 (0.31), residues: 224 loop : -0.22 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.014 0.001 PHE M 58 TYR 0.020 0.001 TYR N 159 ARG 0.013 0.001 ARG L 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 464 time to evaluate : 2.367 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 97 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8708 (mm-40) REVERT: A 100 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8356 (mmtt) REVERT: A 108 MET cc_start: 0.8595 (ptp) cc_final: 0.8092 (ptp) REVERT: A 156 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: A 163 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8748 (tmmm) REVERT: A 176 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8800 (t) REVERT: A 178 GLU cc_start: 0.9227 (pm20) cc_final: 0.8895 (pm20) REVERT: B 39 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8846 (mtp-110) REVERT: B 50 GLN cc_start: 0.9255 (pt0) cc_final: 0.9035 (pt0) REVERT: B 58 ASN cc_start: 0.9493 (m-40) cc_final: 0.9171 (m110) REVERT: B 100 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8406 (mmtt) REVERT: B 156 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: B 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8732 (tmmm) REVERT: B 205 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7845 (mtp) REVERT: C 43 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8971 (mm-30) REVERT: C 73 LYS cc_start: 0.9171 (mttm) cc_final: 0.8882 (mtpp) REVERT: C 97 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8728 (mm-40) REVERT: C 134 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8400 (mt-10) REVERT: C 139 GLN cc_start: 0.8083 (tt0) cc_final: 0.6850 (tt0) REVERT: C 156 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 163 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8691 (tmmm) REVERT: D 39 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8569 (mtp-110) REVERT: D 42 ASN cc_start: 0.9558 (m-40) cc_final: 0.9111 (m110) REVERT: D 43 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8984 (mm-30) REVERT: D 100 LYS cc_start: 0.8837 (mptt) cc_final: 0.8342 (mptt) REVERT: D 156 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: D 194 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8338 (mt-10) REVERT: E 39 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8775 (mtp-110) REVERT: E 43 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8959 (mm-30) REVERT: E 50 GLN cc_start: 0.9329 (pt0) cc_final: 0.9064 (pt0) REVERT: E 134 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8393 (mt-10) REVERT: E 156 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: E 163 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8689 (tmmm) REVERT: F 39 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8770 (mtp-110) REVERT: F 100 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8648 (mmtt) REVERT: F 156 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: F 194 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8598 (mt-10) REVERT: G 50 GLN cc_start: 0.9244 (pt0) cc_final: 0.8984 (pt0) REVERT: G 156 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: G 163 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8684 (tmmm) REVERT: H 84 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8741 (mm) REVERT: H 91 ARG cc_start: 0.9324 (ptm160) cc_final: 0.9092 (ptm-80) REVERT: H 144 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8867 (ttmp) REVERT: H 203 ILE cc_start: 0.9488 (tp) cc_final: 0.9265 (tp) REVERT: H 204 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8315 (tp30) REVERT: H 222 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8740 (tp-100) REVERT: I 104 PHE cc_start: 0.7863 (t80) cc_final: 0.7659 (t80) REVERT: I 122 GLN cc_start: 0.7961 (pt0) cc_final: 0.7343 (pm20) REVERT: I 184 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8826 (mp) REVERT: I 222 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8736 (tp-100) REVERT: J 144 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8448 (ptpp) REVERT: J 187 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7891 (mtp) REVERT: J 203 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9192 (tp) REVERT: J 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7990 (tm-30) REVERT: K 58 PHE cc_start: 0.9132 (t80) cc_final: 0.8810 (t80) REVERT: K 91 ARG cc_start: 0.9152 (ttm110) cc_final: 0.8867 (ttp-110) REVERT: K 152 ARG cc_start: 0.7243 (tmt170) cc_final: 0.6898 (tmt170) REVERT: K 166 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: K 204 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8162 (tm-30) REVERT: L 91 ARG cc_start: 0.9328 (mtp-110) cc_final: 0.9017 (mtp85) REVERT: L 122 GLN cc_start: 0.8073 (pt0) cc_final: 0.7452 (pm20) REVERT: L 166 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: L 170 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8619 (mp) REVERT: L 198 LYS cc_start: 0.9509 (tppp) cc_final: 0.9251 (tppp) REVERT: L 200 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8745 (mtm-85) REVERT: L 204 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8182 (tm-30) REVERT: M 51 TYR cc_start: 0.8333 (t80) cc_final: 0.7921 (t80) REVERT: M 122 GLN cc_start: 0.7911 (pt0) cc_final: 0.7267 (pm20) REVERT: M 166 GLN cc_start: 0.8814 (mt0) cc_final: 0.8289 (pt0) REVERT: M 185 GLU cc_start: 0.8651 (pt0) cc_final: 0.8310 (pt0) REVERT: M 203 ILE cc_start: 0.9463 (tp) cc_final: 0.9237 (tp) REVERT: M 204 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8217 (tm-30) REVERT: N 91 ARG cc_start: 0.9035 (pmm-80) cc_final: 0.8570 (pmm-80) REVERT: N 122 GLN cc_start: 0.7267 (mt0) cc_final: 0.6988 (mt0) REVERT: N 166 GLN cc_start: 0.8501 (mt0) cc_final: 0.8197 (mt0) REVERT: N 198 LYS cc_start: 0.9403 (tppp) cc_final: 0.8988 (tptp) REVERT: N 204 GLU cc_start: 0.8984 (tp30) cc_final: 0.8234 (tp30) outliers start: 71 outliers final: 23 residues processed: 492 average time/residue: 1.8700 time to fit residues: 999.0586 Evaluate side-chains 501 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 454 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN D 97 GLN E 35 GLN G 35 GLN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN K 157 GLN L 157 GLN N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20041 Z= 0.252 Angle : 0.730 11.730 27111 Z= 0.370 Chirality : 0.043 0.212 3150 Planarity : 0.005 0.089 3556 Dihedral : 4.055 28.933 2800 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.52 % Allowed : 24.32 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.18), residues: 2464 helix: 2.09 (0.15), residues: 1379 sheet: 2.18 (0.31), residues: 224 loop : -0.23 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.021 0.001 PHE L 58 TYR 0.027 0.001 TYR B 93 ARG 0.011 0.001 ARG L 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 468 time to evaluate : 2.488 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: A 97 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8708 (mm-40) REVERT: A 108 MET cc_start: 0.8573 (ptp) cc_final: 0.8052 (ptp) REVERT: A 156 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: A 163 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8754 (tmmm) REVERT: A 176 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8730 (t) REVERT: A 178 GLU cc_start: 0.9223 (pm20) cc_final: 0.8887 (pm20) REVERT: A 197 GLU cc_start: 0.8160 (pp20) cc_final: 0.7952 (pp20) REVERT: A 198 TYR cc_start: 0.8812 (t80) cc_final: 0.8546 (t80) REVERT: B 39 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8842 (mtp-110) REVERT: B 50 GLN cc_start: 0.9255 (pt0) cc_final: 0.8981 (pt0) REVERT: B 58 ASN cc_start: 0.9491 (m-40) cc_final: 0.9170 (m110) REVERT: B 156 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8725 (tmmm) REVERT: B 205 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: C 39 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8613 (mtp-110) REVERT: C 43 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8967 (mm-30) REVERT: C 73 LYS cc_start: 0.9165 (mttm) cc_final: 0.8880 (mtpp) REVERT: C 97 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8922 (mm110) REVERT: C 100 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8409 (mmtt) REVERT: C 134 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8387 (mt-10) REVERT: C 139 GLN cc_start: 0.8052 (tt0) cc_final: 0.7004 (tt0) REVERT: C 156 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: C 163 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8710 (tmmm) REVERT: D 39 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8564 (mtp-110) REVERT: D 42 ASN cc_start: 0.9553 (m-40) cc_final: 0.9127 (m110) REVERT: D 43 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8983 (mm-30) REVERT: D 156 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: D 194 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8310 (mt-10) REVERT: E 39 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8790 (mtp-110) REVERT: E 43 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8954 (mm-30) REVERT: E 50 GLN cc_start: 0.9326 (pt0) cc_final: 0.9120 (pt0) REVERT: E 134 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8487 (mt-10) REVERT: E 156 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: E 163 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8684 (tmmm) REVERT: F 39 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8752 (mtp-110) REVERT: F 96 MET cc_start: 0.8796 (ttm) cc_final: 0.8579 (mtp) REVERT: F 156 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: F 194 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8589 (mt-10) REVERT: G 50 GLN cc_start: 0.9248 (pt0) cc_final: 0.8942 (pt0) REVERT: G 156 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: G 163 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8670 (tmmm) REVERT: H 84 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8750 (mm) REVERT: H 91 ARG cc_start: 0.9319 (ptm160) cc_final: 0.8807 (ptp90) REVERT: H 203 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9256 (tp) REVERT: H 204 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8292 (tp30) REVERT: H 222 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8741 (tp-100) REVERT: I 122 GLN cc_start: 0.7949 (pt0) cc_final: 0.7326 (pm20) REVERT: I 184 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8762 (mp) REVERT: I 222 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8740 (tp-100) REVERT: J 144 LYS cc_start: 0.8804 (ptpp) cc_final: 0.8474 (ptpp) REVERT: J 187 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: J 203 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9183 (tp) REVERT: J 204 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8008 (tm-30) REVERT: K 58 PHE cc_start: 0.9132 (t80) cc_final: 0.8849 (t80) REVERT: K 59 GLU cc_start: 0.9120 (mp0) cc_final: 0.8681 (mp0) REVERT: K 91 ARG cc_start: 0.9105 (ttm110) cc_final: 0.8811 (ttp-110) REVERT: K 166 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: K 204 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8206 (tm-30) REVERT: K 222 GLN cc_start: 0.8962 (tp40) cc_final: 0.8733 (tp40) REVERT: L 91 ARG cc_start: 0.9320 (mtp-110) cc_final: 0.9010 (mtp85) REVERT: L 122 GLN cc_start: 0.8110 (pt0) cc_final: 0.7451 (pm20) REVERT: L 166 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: L 170 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8612 (mp) REVERT: L 198 LYS cc_start: 0.9506 (tppp) cc_final: 0.9274 (tppp) REVERT: L 200 ARG cc_start: 0.9158 (ttm110) cc_final: 0.8721 (mtm-85) REVERT: L 204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8192 (tm-30) REVERT: M 51 TYR cc_start: 0.8333 (t80) cc_final: 0.7907 (t80) REVERT: M 122 GLN cc_start: 0.7910 (pt0) cc_final: 0.7248 (pm20) REVERT: M 166 GLN cc_start: 0.8808 (mt0) cc_final: 0.8270 (pt0) REVERT: M 185 GLU cc_start: 0.8625 (pt0) cc_final: 0.8305 (pt0) REVERT: M 203 ILE cc_start: 0.9452 (tp) cc_final: 0.9218 (tp) REVERT: M 204 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8215 (tm-30) REVERT: N 91 ARG cc_start: 0.9029 (pmm-80) cc_final: 0.8526 (pmm-80) REVERT: N 122 GLN cc_start: 0.7346 (mt0) cc_final: 0.7033 (mt0) REVERT: N 152 ARG cc_start: 0.7456 (tmt170) cc_final: 0.6950 (tmt170) REVERT: N 166 GLN cc_start: 0.8552 (mt0) cc_final: 0.8258 (mt0) REVERT: N 198 LYS cc_start: 0.9448 (tppp) cc_final: 0.9074 (tptp) REVERT: N 204 GLU cc_start: 0.8992 (tp30) cc_final: 0.8237 (tp30) outliers start: 73 outliers final: 24 residues processed: 499 average time/residue: 1.8622 time to fit residues: 1008.9982 Evaluate side-chains 505 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 456 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.0670 chunk 219 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.0770 chunk 128 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.1278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20041 Z= 0.226 Angle : 0.751 12.575 27111 Z= 0.381 Chirality : 0.043 0.207 3150 Planarity : 0.005 0.106 3556 Dihedral : 3.987 28.878 2800 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.75 % Allowed : 25.19 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2464 helix: 2.06 (0.15), residues: 1372 sheet: 2.20 (0.31), residues: 224 loop : -0.21 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 189 HIS 0.003 0.000 HIS G 138 PHE 0.016 0.001 PHE I 104 TYR 0.038 0.001 TYR D 93 ARG 0.009 0.001 ARG L 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 475 time to evaluate : 2.542 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 97 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8715 (mm-40) REVERT: A 100 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8241 (mmtt) REVERT: A 108 MET cc_start: 0.8522 (ptp) cc_final: 0.8022 (ptp) REVERT: A 152 LYS cc_start: 0.8425 (tttt) cc_final: 0.8223 (tttt) REVERT: A 163 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8748 (tmmm) REVERT: A 176 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8762 (t) REVERT: A 178 GLU cc_start: 0.9225 (pm20) cc_final: 0.8910 (pm20) REVERT: A 197 GLU cc_start: 0.8199 (pp20) cc_final: 0.7977 (pp20) REVERT: A 198 TYR cc_start: 0.8806 (t80) cc_final: 0.8509 (t80) REVERT: B 39 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8850 (mtp-110) REVERT: B 50 GLN cc_start: 0.9240 (pt0) cc_final: 0.8990 (pt0) REVERT: B 54 ASP cc_start: 0.9014 (m-30) cc_final: 0.8689 (m-30) REVERT: B 58 ASN cc_start: 0.9485 (m-40) cc_final: 0.9012 (m110) REVERT: B 156 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: B 163 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8735 (tmmm) REVERT: C 43 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8948 (mm-30) REVERT: C 73 LYS cc_start: 0.9154 (mttm) cc_final: 0.8871 (mtpp) REVERT: C 97 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8801 (mm-40) REVERT: C 100 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8373 (mmtt) REVERT: C 134 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8356 (mt-10) REVERT: C 139 GLN cc_start: 0.7974 (tt0) cc_final: 0.7133 (tt0) REVERT: C 156 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: C 163 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8696 (tmmm) REVERT: D 39 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8544 (mtp-110) REVERT: D 42 ASN cc_start: 0.9553 (m-40) cc_final: 0.9132 (m110) REVERT: D 43 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8990 (mm-30) REVERT: D 100 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8569 (mmtt) REVERT: D 156 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: D 194 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 39 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8784 (mtp-110) REVERT: E 43 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8940 (mm-30) REVERT: E 134 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8467 (mt-10) REVERT: E 156 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: E 163 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8655 (tmmm) REVERT: F 39 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8738 (mtp-110) REVERT: F 96 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: F 100 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8443 (mmtt) REVERT: F 156 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: F 194 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8599 (mt-10) REVERT: F 205 MET cc_start: 0.8633 (mmp) cc_final: 0.8365 (mtp) REVERT: G 50 GLN cc_start: 0.9240 (pt0) cc_final: 0.8937 (pt0) REVERT: G 108 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8298 (ptp) REVERT: G 156 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: G 163 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8654 (tmmm) REVERT: H 84 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8712 (mm) REVERT: H 91 ARG cc_start: 0.9312 (ptm160) cc_final: 0.8802 (ptp90) REVERT: H 144 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8640 (ttmt) REVERT: H 200 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8462 (mmp-170) REVERT: H 203 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9187 (tp) REVERT: H 204 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8317 (tp30) REVERT: H 222 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8742 (tp-100) REVERT: I 122 GLN cc_start: 0.7900 (pt0) cc_final: 0.7309 (pm20) REVERT: I 184 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8755 (mp) REVERT: I 222 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8750 (tp-100) REVERT: J 144 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8511 (ptpp) REVERT: J 187 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: J 198 LYS cc_start: 0.9405 (tppp) cc_final: 0.9156 (tppp) REVERT: J 203 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9149 (tp) REVERT: J 204 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8006 (tm-30) REVERT: K 58 PHE cc_start: 0.9120 (t80) cc_final: 0.8813 (t80) REVERT: K 59 GLU cc_start: 0.9131 (mp0) cc_final: 0.8633 (mp0) REVERT: K 91 ARG cc_start: 0.9091 (ttm110) cc_final: 0.8807 (ttp-110) REVERT: K 128 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8546 (tm-30) REVERT: K 166 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: K 204 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8215 (tm-30) REVERT: L 91 ARG cc_start: 0.9318 (mtp-110) cc_final: 0.9019 (mtp85) REVERT: L 122 GLN cc_start: 0.8094 (pt0) cc_final: 0.7440 (pm20) REVERT: L 166 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: L 198 LYS cc_start: 0.9498 (tppp) cc_final: 0.9273 (tppp) REVERT: L 200 ARG cc_start: 0.9153 (ttm110) cc_final: 0.8750 (mtm-85) REVERT: L 204 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8203 (tm-30) REVERT: M 51 TYR cc_start: 0.8323 (t80) cc_final: 0.7921 (t80) REVERT: M 86 SER cc_start: 0.9207 (t) cc_final: 0.8871 (p) REVERT: M 122 GLN cc_start: 0.7885 (pt0) cc_final: 0.7218 (pm20) REVERT: M 152 ARG cc_start: 0.7186 (tmt170) cc_final: 0.6866 (tmt170) REVERT: M 166 GLN cc_start: 0.8788 (mt0) cc_final: 0.8258 (pt0) REVERT: M 185 GLU cc_start: 0.8634 (pt0) cc_final: 0.8297 (pt0) REVERT: M 203 ILE cc_start: 0.9425 (tp) cc_final: 0.9163 (tp) REVERT: M 204 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8177 (tm-30) REVERT: N 91 ARG cc_start: 0.9026 (pmm-80) cc_final: 0.8527 (pmm-80) REVERT: N 122 GLN cc_start: 0.7288 (mt0) cc_final: 0.6975 (mt0) REVERT: N 152 ARG cc_start: 0.7418 (tmt170) cc_final: 0.7021 (tmt170) REVERT: N 166 GLN cc_start: 0.8535 (mt0) cc_final: 0.8291 (mt0) REVERT: N 176 GLU cc_start: 0.8853 (tp30) cc_final: 0.8405 (tp30) REVERT: N 185 GLU cc_start: 0.8407 (pp20) cc_final: 0.7969 (pt0) REVERT: N 190 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8744 (tmmt) REVERT: N 198 LYS cc_start: 0.9444 (tppp) cc_final: 0.9067 (tptp) REVERT: N 204 GLU cc_start: 0.8998 (tp30) cc_final: 0.8208 (tp30) outliers start: 57 outliers final: 21 residues processed: 494 average time/residue: 1.8324 time to fit residues: 984.3777 Evaluate side-chains 507 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 463 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 218 optimal weight: 0.0980 chunk 188 optimal weight: 5.9990 chunk 19 optimal weight: 0.0050 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20041 Z= 0.237 Angle : 0.775 12.756 27111 Z= 0.393 Chirality : 0.043 0.214 3150 Planarity : 0.005 0.097 3556 Dihedral : 3.941 28.733 2800 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.70 % Allowed : 25.39 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2464 helix: 2.05 (0.15), residues: 1365 sheet: 2.28 (0.31), residues: 224 loop : -0.23 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.003 0.000 HIS H 156 PHE 0.022 0.001 PHE L 58 TYR 0.030 0.001 TYR B 93 ARG 0.013 0.001 ARG I 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 472 time to evaluate : 2.378 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 97 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8764 (mm-40) REVERT: A 163 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8752 (tmmm) REVERT: A 176 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8766 (t) REVERT: A 178 GLU cc_start: 0.9229 (pm20) cc_final: 0.8925 (pm20) REVERT: A 198 TYR cc_start: 0.8810 (t80) cc_final: 0.8532 (t80) REVERT: B 39 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8851 (mtp-110) REVERT: B 50 GLN cc_start: 0.9238 (pt0) cc_final: 0.8984 (pt0) REVERT: B 54 ASP cc_start: 0.9030 (m-30) cc_final: 0.8715 (m-30) REVERT: B 58 ASN cc_start: 0.9483 (m-40) cc_final: 0.9009 (m110) REVERT: B 100 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8561 (mmtt) REVERT: B 156 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: B 163 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8731 (tmmm) REVERT: C 39 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8609 (mtp-110) REVERT: C 43 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8938 (mm-30) REVERT: C 73 LYS cc_start: 0.9140 (mttm) cc_final: 0.8863 (mtpp) REVERT: C 97 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8718 (mm-40) REVERT: C 134 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8364 (mt-10) REVERT: C 139 GLN cc_start: 0.7976 (tt0) cc_final: 0.7128 (tt0) REVERT: C 156 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: C 163 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8726 (tmmm) REVERT: C 194 GLU cc_start: 0.8700 (pt0) cc_final: 0.8493 (pt0) REVERT: D 39 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8556 (mtp-110) REVERT: D 42 ASN cc_start: 0.9553 (m-40) cc_final: 0.9145 (m110) REVERT: D 43 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8993 (mm-30) REVERT: D 100 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8486 (mmtt) REVERT: D 152 LYS cc_start: 0.8459 (tttt) cc_final: 0.8174 (tttt) REVERT: D 156 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: D 194 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 39 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8777 (mtp-110) REVERT: E 43 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8929 (mm-30) REVERT: E 134 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8393 (mt-10) REVERT: E 156 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: E 163 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8657 (tmmm) REVERT: F 39 ARG cc_start: 0.9129 (ttp80) cc_final: 0.8743 (mtp-110) REVERT: F 96 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: F 100 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8415 (mmtt) REVERT: F 156 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: F 163 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8777 (tmmm) REVERT: F 194 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 205 MET cc_start: 0.8602 (mmp) cc_final: 0.8367 (mtp) REVERT: G 50 GLN cc_start: 0.9219 (pt0) cc_final: 0.8906 (pt0) REVERT: G 156 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: G 163 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8646 (tmmm) REVERT: H 91 ARG cc_start: 0.9313 (ptm160) cc_final: 0.9038 (ptp90) REVERT: H 144 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8765 (ttmt) REVERT: H 185 GLU cc_start: 0.8497 (pp20) cc_final: 0.8280 (pp20) REVERT: H 203 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9234 (tp) REVERT: H 204 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8192 (tm-30) REVERT: H 222 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8749 (tp-100) REVERT: I 122 GLN cc_start: 0.7845 (pt0) cc_final: 0.7274 (pm20) REVERT: I 184 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8737 (mp) REVERT: I 198 LYS cc_start: 0.8992 (tppp) cc_final: 0.8348 (tppt) REVERT: J 144 LYS cc_start: 0.8790 (ptpp) cc_final: 0.8508 (ptpp) REVERT: J 187 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: J 198 LYS cc_start: 0.9416 (tppp) cc_final: 0.9152 (tppp) REVERT: J 203 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9159 (tp) REVERT: J 204 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8006 (tm-30) REVERT: K 58 PHE cc_start: 0.9118 (t80) cc_final: 0.8820 (t80) REVERT: K 59 GLU cc_start: 0.9141 (mp0) cc_final: 0.8643 (mp0) REVERT: K 91 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8777 (ttp-110) REVERT: K 112 ASP cc_start: 0.9024 (m-30) cc_final: 0.8556 (m-30) REVERT: K 166 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: K 204 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8195 (tm-30) REVERT: L 91 ARG cc_start: 0.9311 (mtp-110) cc_final: 0.9006 (mtp85) REVERT: L 122 GLN cc_start: 0.8101 (pt0) cc_final: 0.7439 (pm20) REVERT: L 150 ASN cc_start: 0.9398 (m-40) cc_final: 0.8996 (m110) REVERT: L 166 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: L 170 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8596 (mp) REVERT: L 198 LYS cc_start: 0.9505 (tppp) cc_final: 0.9270 (tppp) REVERT: L 200 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8681 (mtm-85) REVERT: L 204 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8200 (tm-30) REVERT: M 51 TYR cc_start: 0.8332 (t80) cc_final: 0.7936 (t80) REVERT: M 86 SER cc_start: 0.9212 (t) cc_final: 0.8871 (p) REVERT: M 122 GLN cc_start: 0.7878 (pt0) cc_final: 0.7205 (pm20) REVERT: M 152 ARG cc_start: 0.7229 (tmt170) cc_final: 0.6891 (tmt170) REVERT: M 166 GLN cc_start: 0.8783 (mt0) cc_final: 0.8254 (pt0) REVERT: M 185 GLU cc_start: 0.8626 (pt0) cc_final: 0.8300 (pt0) REVERT: M 203 ILE cc_start: 0.9404 (tp) cc_final: 0.9176 (tp) REVERT: M 204 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8180 (tm-30) REVERT: N 91 ARG cc_start: 0.9034 (pmm-80) cc_final: 0.8533 (pmm-80) REVERT: N 122 GLN cc_start: 0.7265 (mt0) cc_final: 0.6960 (mt0) REVERT: N 146 MET cc_start: 0.8536 (mmm) cc_final: 0.8334 (mmm) REVERT: N 152 ARG cc_start: 0.7441 (tmt170) cc_final: 0.7071 (tmt170) REVERT: N 185 GLU cc_start: 0.8402 (pp20) cc_final: 0.7990 (pt0) REVERT: N 190 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8754 (tmmt) REVERT: N 198 LYS cc_start: 0.9436 (tppp) cc_final: 0.9054 (tptp) REVERT: N 204 GLU cc_start: 0.8993 (tp30) cc_final: 0.8252 (tp30) outliers start: 56 outliers final: 23 residues processed: 492 average time/residue: 1.5697 time to fit residues: 839.2308 Evaluate side-chains 509 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 462 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN D 97 GLN E 35 GLN F 35 GLN G 35 GLN H 80 GLN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 150 ASN K 157 GLN N 175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054211 restraints weight = 55907.305| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.88 r_work: 0.2653 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20041 Z= 0.295 Angle : 0.803 12.797 27111 Z= 0.411 Chirality : 0.044 0.210 3150 Planarity : 0.005 0.108 3556 Dihedral : 4.149 28.618 2800 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.90 % Allowed : 25.68 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2464 helix: 1.94 (0.15), residues: 1365 sheet: 2.33 (0.31), residues: 224 loop : -0.26 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.022 0.001 PHE J 58 TYR 0.025 0.001 TYR B 93 ARG 0.011 0.001 ARG K 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12321.67 seconds wall clock time: 213 minutes 14.60 seconds (12794.60 seconds total)