Starting phenix.real_space_refine on Sun Aug 24 11:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_38537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_38537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_38537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_38537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xop_38537/08_2025/8xop_38537.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8: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: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.06, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 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: 1.94 Conformation dependent library (CDL) restraints added in 856.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.90 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: 4.09 Time building geometry restraints manager: 2.48 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: 0.00 - 1.79: 26358 1.79 - 3.58: 545 3.58 - 5.38: 169 5.38 - 7.17: 32 7.17 - 8.96: 7 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: 0.01 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.230 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- 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 0.079 20069 Z= 0.319 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG H 200 TYR 0.020 0.001 TYR H 51 PHE 0.022 0.001 PHE I 104 TRP 0.005 0.001 TRP B 189 HIS 0.002 0.000 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00459 (20041) covalent geometry : angle 0.69119 (27111) hydrogen bonds : bond 0.13034 ( 1054) hydrogen bonds : angle 5.00377 ( 3255) Misc. bond : bond 0.06281 ( 28) *********************** 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 to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 0.825 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: 0.9218 (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: 0.7515 (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: 0.8812 (ptm160) REVERT: K 197 GLU cc_start: 0.9012 (pm20) cc_final: 0.8756 (pm20) REVERT: K 201 GLU cc_start: 0.9059 (mp0) cc_final: 0.8500 (mp0) REVERT: K 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7961 (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: 1.0483 time to fit residues: 610.2771 Evaluate side-chains 427 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN G 35 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054426 restraints weight = 55328.547| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.90 r_work: 0.2650 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20069 Z= 0.191 Angle : 0.649 8.163 27111 Z= 0.335 Chirality : 0.043 0.169 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.301 34.117 2800 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.75 % Allowed : 14.77 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.17), residues: 2464 helix: 1.92 (0.14), residues: 1365 sheet: 1.69 (0.34), residues: 245 loop : -0.24 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 200 TYR 0.019 0.001 TYR H 51 PHE 0.026 0.001 PHE L 58 TRP 0.005 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00451 (20041) covalent geometry : angle 0.64925 (27111) hydrogen bonds : bond 0.03994 ( 1054) hydrogen bonds : angle 4.02062 ( 3255) Misc. bond : bond 0.00057 ( 28) *********************** 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 543 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 486 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8808 (mm-40) REVERT: A 171 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8965 (tm-30) REVERT: B 50 GLN cc_start: 0.9339 (pt0) cc_final: 0.9071 (pt0) REVERT: B 97 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: B 100 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8620 (mmtt) REVERT: B 194 GLU cc_start: 0.8850 (pt0) cc_final: 0.8452 (pt0) REVERT: B 205 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: C 43 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9122 (mm-30) REVERT: C 97 GLN cc_start: 0.9283 (mm-40) cc_final: 0.9006 (mm110) REVERT: C 134 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8685 (mt-10) REVERT: D 42 ASN cc_start: 0.9600 (m-40) cc_final: 0.9116 (m110) REVERT: D 43 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9095 (mm-30) REVERT: D 100 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8827 (mptt) REVERT: D 134 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8654 (mt-10) REVERT: D 194 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8602 (mt-10) REVERT: E 43 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9064 (mm-30) REVERT: E 97 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9023 (mm-40) REVERT: E 134 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8738 (mt-10) REVERT: F 43 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9148 (mm-30) REVERT: F 50 GLN cc_start: 0.9343 (pt0) cc_final: 0.9080 (pt0) REVERT: F 100 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8649 (mmtt) REVERT: F 108 MET cc_start: 0.8723 (ptp) cc_final: 0.8265 (ptp) REVERT: F 194 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8820 (mt-10) REVERT: G 50 GLN cc_start: 0.9291 (pt0) cc_final: 0.9018 (pt0) REVERT: H 59 GLU cc_start: 0.8993 (mp0) cc_final: 0.8766 (mp0) REVERT: H 204 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8299 (tm-30) REVERT: I 85 GLU cc_start: 0.8494 (pp20) cc_final: 0.8218 (pp20) REVERT: I 91 ARG cc_start: 0.9488 (mtp85) cc_final: 0.9247 (mtp85) REVERT: I 157 GLN cc_start: 0.9354 (pt0) cc_final: 0.9031 (pt0) REVERT: I 181 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8626 (ttm-80) REVERT: I 222 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8774 (tp-100) REVERT: J 200 ARG cc_start: 0.8968 (mpp80) cc_final: 0.8746 (mpp80) REVERT: J 203 ILE cc_start: 0.9359 (tp) cc_final: 0.9130 (tp) REVERT: J 204 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8185 (tm-30) REVERT: K 87 MET cc_start: 0.6767 (mtt) cc_final: 0.6485 (mtm) REVERT: K 91 ARG cc_start: 0.9250 (ttm110) cc_final: 0.8646 (ttm110) REVERT: K 152 ARG cc_start: 0.7211 (tmt170) cc_final: 0.6945 (tmt170) REVERT: K 166 GLN cc_start: 0.8328 (tt0) cc_final: 0.8055 (tt0) REVERT: K 197 GLU cc_start: 0.9233 (pm20) cc_final: 0.8934 (pm20) REVERT: K 200 ARG cc_start: 0.8861 (mmm160) cc_final: 0.8376 (mmm160) REVERT: K 201 GLU cc_start: 0.8932 (mp0) cc_final: 0.8620 (mp0) REVERT: K 203 ILE cc_start: 0.9505 (tp) cc_final: 0.9169 (tp) REVERT: K 204 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8296 (tm-30) REVERT: L 91 ARG cc_start: 0.9472 (mtp-110) cc_final: 0.9270 (mtp85) REVERT: L 166 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: L 198 LYS cc_start: 0.9389 (tppp) cc_final: 0.9077 (tppp) REVERT: L 204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8185 (tm-30) REVERT: M 51 TYR cc_start: 0.8023 (t80) cc_final: 0.7795 (t80) REVERT: M 60 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9045 (mm-30) REVERT: M 185 GLU cc_start: 0.8813 (pt0) cc_final: 0.8534 (pt0) REVERT: M 204 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8303 (tm-30) REVERT: N 60 GLU cc_start: 0.8665 (mp0) cc_final: 0.8315 (mp0) REVERT: N 122 GLN cc_start: 0.7660 (mt0) cc_final: 0.7241 (mt0) REVERT: N 198 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9038 (tptp) REVERT: N 204 GLU cc_start: 0.9112 (tp30) cc_final: 0.8309 (tp30) outliers start: 57 outliers final: 8 residues processed: 499 average time/residue: 0.9577 time to fit residues: 516.4600 Evaluate side-chains 454 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 442 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN 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** J 175 ASN M 122 GLN N 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.052760 restraints weight = 56089.618| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.83 r_work: 0.2607 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20069 Z= 0.247 Angle : 0.669 9.321 27111 Z= 0.346 Chirality : 0.044 0.165 3150 Planarity : 0.005 0.049 3556 Dihedral : 4.494 52.843 2800 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.65 % Allowed : 18.53 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2464 helix: 1.95 (0.14), residues: 1358 sheet: 1.80 (0.32), residues: 259 loop : -0.37 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 200 TYR 0.017 0.001 TYR H 51 PHE 0.021 0.001 PHE M 58 TRP 0.006 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00576 (20041) covalent geometry : angle 0.66946 (27111) hydrogen bonds : bond 0.04246 ( 1054) hydrogen bonds : angle 4.01830 ( 3255) Misc. bond : bond 0.00079 ( 28) *********************** 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 526 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 471 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8874 (mm-40) REVERT: B 39 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8923 (mtp-110) REVERT: B 50 GLN cc_start: 0.9330 (pt0) cc_final: 0.9065 (pt0) REVERT: B 100 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8616 (mmtt) REVERT: B 163 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8796 (tmmm) REVERT: B 205 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: C 39 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8705 (mtp-110) REVERT: C 43 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9100 (mm-30) REVERT: C 97 GLN cc_start: 0.9301 (mm-40) cc_final: 0.9100 (mm-40) REVERT: C 134 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8653 (mt-10) REVERT: C 163 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8854 (tmmm) REVERT: D 39 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8656 (mtp-110) REVERT: D 43 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9093 (mm-30) REVERT: D 134 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8683 (mt-10) REVERT: E 43 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9084 (mm-30) REVERT: E 50 GLN cc_start: 0.9449 (pt0) cc_final: 0.9224 (pt0) REVERT: E 97 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9175 (mm110) REVERT: E 134 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8738 (mt-10) REVERT: E 156 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: F 39 ARG cc_start: 0.9191 (ttp80) cc_final: 0.8863 (mtp-110) REVERT: F 50 GLN cc_start: 0.9283 (pt0) cc_final: 0.8965 (pt0) REVERT: F 194 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8796 (mt-10) REVERT: G 50 GLN cc_start: 0.9349 (pt0) cc_final: 0.9096 (pt0) REVERT: G 163 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8727 (tmmm) REVERT: H 91 ARG cc_start: 0.9367 (ptm160) cc_final: 0.9109 (ptp90) REVERT: H 203 ILE cc_start: 0.9502 (tp) cc_final: 0.9264 (tp) REVERT: H 222 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8678 (tp40) REVERT: I 85 GLU cc_start: 0.8589 (pp20) cc_final: 0.8305 (pp20) REVERT: I 91 ARG cc_start: 0.9458 (mtp85) cc_final: 0.9200 (mtp85) REVERT: I 185 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7851 (mp0) REVERT: J 59 GLU cc_start: 0.9069 (mp0) cc_final: 0.8695 (mp0) REVERT: J 144 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8299 (ptpp) REVERT: J 166 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7561 (mm-40) REVERT: J 203 ILE cc_start: 0.9442 (tp) cc_final: 0.9164 (tp) REVERT: J 204 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8147 (tm-30) REVERT: K 87 MET cc_start: 0.6877 (mtt) cc_final: 0.6547 (mtm) REVERT: K 91 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8539 (ttm110) REVERT: K 152 ARG cc_start: 0.7376 (tmt170) cc_final: 0.6926 (tmt170) REVERT: K 166 GLN cc_start: 0.8360 (tt0) cc_final: 0.7936 (tt0) REVERT: K 198 LYS cc_start: 0.9167 (tppp) cc_final: 0.8951 (tppp) REVERT: K 203 ILE cc_start: 0.9545 (tp) cc_final: 0.9272 (tp) REVERT: K 204 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8324 (tm-30) REVERT: L 59 GLU cc_start: 0.9151 (mp0) cc_final: 0.8884 (mp0) REVERT: L 91 ARG cc_start: 0.9416 (mtp-110) cc_final: 0.9100 (mtp85) REVERT: L 122 GLN cc_start: 0.8292 (pt0) cc_final: 0.7557 (pm20) REVERT: L 166 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: L 200 ARG cc_start: 0.9246 (ttm110) cc_final: 0.8798 (mtm110) REVERT: L 204 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8373 (tm-30) REVERT: M 51 TYR cc_start: 0.8118 (t80) cc_final: 0.7831 (t80) REVERT: M 60 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9050 (mm-30) REVERT: M 167 VAL cc_start: 0.9281 (t) cc_final: 0.9051 (m) REVERT: M 185 GLU cc_start: 0.8850 (pt0) cc_final: 0.8545 (pt0) REVERT: M 197 GLU cc_start: 0.9313 (mp0) cc_final: 0.9087 (pm20) REVERT: M 204 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8283 (tm-30) REVERT: N 60 GLU cc_start: 0.8743 (mp0) cc_final: 0.8169 (mp0) REVERT: N 122 GLN cc_start: 0.7717 (mt0) cc_final: 0.7373 (mt0) REVERT: N 166 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8192 (mm-40) REVERT: N 197 GLU cc_start: 0.9362 (mp0) cc_final: 0.9129 (pm20) REVERT: N 204 GLU cc_start: 0.9149 (tp30) cc_final: 0.8340 (tp30) outliers start: 55 outliers final: 13 residues processed: 485 average time/residue: 0.9978 time to fit residues: 522.6796 Evaluate side-chains 468 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 446 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER 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 B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG 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 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 180 MET 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 42 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 80 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN N 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055492 restraints weight = 55532.759| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.87 r_work: 0.2679 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20069 Z= 0.131 Angle : 0.624 9.027 27111 Z= 0.320 Chirality : 0.042 0.163 3150 Planarity : 0.005 0.050 3556 Dihedral : 4.317 54.973 2800 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.65 % Allowed : 20.42 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.18), residues: 2464 helix: 2.06 (0.15), residues: 1365 sheet: 2.02 (0.31), residues: 224 loop : -0.20 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 200 TYR 0.020 0.001 TYR I 159 PHE 0.025 0.001 PHE L 58 TRP 0.002 0.000 TRP D 189 HIS 0.003 0.000 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00313 (20041) covalent geometry : angle 0.62434 (27111) hydrogen bonds : bond 0.03421 ( 1054) hydrogen bonds : angle 3.73702 ( 3255) Misc. bond : bond 0.00028 ( 28) *********************** 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 538 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 483 time to evaluate : 0.798 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: A 97 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8840 (mm-40) REVERT: A 176 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8810 (t) REVERT: A 178 GLU cc_start: 0.9367 (pm20) cc_final: 0.9047 (pm20) REVERT: B 39 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.8938 (mtp-110) REVERT: B 50 GLN cc_start: 0.9419 (pt0) cc_final: 0.9206 (pt0) REVERT: C 43 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9123 (mm-30) REVERT: C 97 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9062 (mm110) REVERT: C 134 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8676 (mt-10) REVERT: C 139 GLN cc_start: 0.8359 (tt0) cc_final: 0.7451 (tt0) REVERT: C 163 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8925 (tmmm) REVERT: D 42 ASN cc_start: 0.9593 (m-40) cc_final: 0.9130 (m110) REVERT: D 43 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9111 (mm-30) REVERT: D 100 LYS cc_start: 0.9145 (mptt) cc_final: 0.8742 (mptt) REVERT: D 156 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8845 (mp0) REVERT: D 194 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8696 (mt-10) REVERT: E 39 ARG cc_start: 0.9246 (ttp80) cc_final: 0.8814 (mtp-110) REVERT: E 43 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9113 (mm-30) REVERT: E 50 GLN cc_start: 0.9477 (pt0) cc_final: 0.9224 (pt0) REVERT: E 97 GLN cc_start: 0.9406 (mm-40) cc_final: 0.9164 (mm110) REVERT: E 134 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8653 (mt-10) REVERT: E 163 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8871 (tmmm) REVERT: F 35 GLN cc_start: 0.8939 (tt0) cc_final: 0.8726 (tt0) REVERT: F 39 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8845 (mtp-110) REVERT: F 50 GLN cc_start: 0.9385 (pt0) cc_final: 0.9117 (pt0) REVERT: F 100 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8715 (mmtt) REVERT: F 108 MET cc_start: 0.8850 (ptp) cc_final: 0.8624 (ptp) REVERT: F 194 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8755 (mt-10) REVERT: G 50 GLN cc_start: 0.9431 (pt0) cc_final: 0.9182 (pt0) REVERT: G 163 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8784 (tmmm) REVERT: H 91 ARG cc_start: 0.9403 (ptm160) cc_final: 0.9129 (ptp90) REVERT: H 197 GLU cc_start: 0.9325 (pm20) cc_final: 0.8959 (pm20) REVERT: H 203 ILE cc_start: 0.9575 (tp) cc_final: 0.9291 (tp) REVERT: I 85 GLU cc_start: 0.8487 (pp20) cc_final: 0.8220 (pp20) REVERT: I 122 GLN cc_start: 0.8131 (pt0) cc_final: 0.7611 (pm20) REVERT: J 144 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8515 (ptpp) REVERT: J 203 ILE cc_start: 0.9520 (tp) cc_final: 0.9246 (tp) REVERT: J 204 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8211 (tm-30) REVERT: K 58 PHE cc_start: 0.9254 (t80) cc_final: 0.9041 (t80) REVERT: K 87 MET cc_start: 0.6900 (mtt) cc_final: 0.6567 (mtm) REVERT: K 91 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8566 (ttm110) REVERT: K 166 GLN cc_start: 0.8516 (tt0) cc_final: 0.7827 (tt0) REVERT: K 185 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6695 (mt-10) REVERT: K 197 GLU cc_start: 0.9202 (pm20) cc_final: 0.8971 (pm20) REVERT: K 198 LYS cc_start: 0.9260 (tppp) cc_final: 0.9056 (tppp) REVERT: K 204 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8422 (tm-30) REVERT: L 59 GLU cc_start: 0.9190 (mp0) cc_final: 0.8703 (mp0) REVERT: L 91 ARG cc_start: 0.9480 (mtp-110) cc_final: 0.9176 (mtp85) REVERT: L 122 GLN cc_start: 0.8366 (pt0) cc_final: 0.7650 (pm20) REVERT: L 166 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: L 198 LYS cc_start: 0.9509 (tppp) cc_final: 0.9224 (tppp) REVERT: L 204 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8393 (tm-30) REVERT: M 51 TYR cc_start: 0.8233 (t80) cc_final: 0.7996 (t80) REVERT: M 60 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8985 (mm-30) REVERT: M 122 GLN cc_start: 0.8255 (pt0) cc_final: 0.7645 (pm20) REVERT: M 167 VAL cc_start: 0.9325 (t) cc_final: 0.9104 (m) REVERT: M 185 GLU cc_start: 0.8896 (pt0) cc_final: 0.8610 (pt0) REVERT: M 190 LYS cc_start: 0.9370 (tppt) cc_final: 0.9129 (ttpp) REVERT: M 204 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8347 (tm-30) REVERT: N 91 ARG cc_start: 0.9058 (pmm-80) cc_final: 0.8715 (pmm-80) REVERT: N 122 GLN cc_start: 0.7716 (mt0) cc_final: 0.7340 (mt0) REVERT: N 166 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8396 (mt0) REVERT: N 198 LYS cc_start: 0.9476 (tppp) cc_final: 0.9131 (tptp) REVERT: N 204 GLU cc_start: 0.9173 (tp30) cc_final: 0.8418 (tp30) outliers start: 55 outliers final: 13 residues processed: 502 average time/residue: 0.9836 time to fit residues: 534.2865 Evaluate side-chains 474 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 454 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER 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 C residue 163 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER 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 I residue 193 THR Chi-restraints excluded: chain J residue 87 MET 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 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 119 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 58 ASN D 97 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 97 GLN G 35 GLN ** G 139 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 N 175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052110 restraints weight = 56252.598| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.78 r_work: 0.2584 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 20069 Z= 0.328 Angle : 0.738 9.814 27111 Z= 0.382 Chirality : 0.046 0.305 3150 Planarity : 0.005 0.049 3556 Dihedral : 4.651 51.616 2800 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 3.72 % Allowed : 21.19 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.17), residues: 2464 helix: 1.84 (0.14), residues: 1372 sheet: 1.74 (0.32), residues: 259 loop : -0.48 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 200 TYR 0.016 0.001 TYR F 93 PHE 0.013 0.001 PHE I 104 TRP 0.007 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00754 (20041) covalent geometry : angle 0.73780 (27111) hydrogen bonds : bond 0.04591 ( 1054) hydrogen bonds : angle 4.17977 ( 3255) Misc. bond : bond 0.00102 ( 28) *********************** 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 533 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 456 time to evaluate : 0.795 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: A 176 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8846 (t) REVERT: A 178 GLU cc_start: 0.9350 (pm20) cc_final: 0.8948 (pm20) REVERT: B 39 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8967 (mtp-110) REVERT: B 50 GLN cc_start: 0.9398 (pt0) cc_final: 0.9161 (pt0) REVERT: B 100 LYS cc_start: 0.8973 (mptt) cc_final: 0.8650 (mmtt) REVERT: B 163 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8925 (tmmm) REVERT: C 39 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8719 (mtp-110) REVERT: C 134 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8728 (mt-10) REVERT: D 39 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8694 (mtp-110) REVERT: D 42 ASN cc_start: 0.9599 (m-40) cc_final: 0.9153 (m110) REVERT: D 194 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8729 (mt-10) REVERT: E 39 ARG cc_start: 0.9299 (tpp80) cc_final: 0.8879 (mtp-110) REVERT: E 50 GLN cc_start: 0.9473 (pt0) cc_final: 0.9203 (pt0) REVERT: E 134 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8746 (mt-10) REVERT: E 163 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.8931 (tmmm) REVERT: F 39 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8859 (mtp-110) REVERT: F 50 GLN cc_start: 0.9375 (pt0) cc_final: 0.9138 (pt0) REVERT: F 108 MET cc_start: 0.8929 (ptp) cc_final: 0.8661 (ptp) REVERT: F 194 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8748 (mt-10) REVERT: G 156 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8853 (mp0) REVERT: H 84 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8776 (mm) REVERT: H 91 ARG cc_start: 0.9375 (ptm160) cc_final: 0.9172 (ptm-80) REVERT: H 144 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8962 (ttmt) REVERT: H 203 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9329 (tp) REVERT: H 204 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8433 (tm-30) REVERT: I 85 GLU cc_start: 0.8592 (pp20) cc_final: 0.8313 (pp20) REVERT: I 122 GLN cc_start: 0.8431 (pt0) cc_final: 0.7753 (pm20) REVERT: I 181 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8378 (ttm-80) REVERT: I 184 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9103 (mt) REVERT: I 203 ILE cc_start: 0.9564 (tp) cc_final: 0.9356 (tp) REVERT: J 144 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8368 (ptpp) REVERT: J 203 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9269 (tp) REVERT: J 204 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8310 (tm-30) REVERT: K 91 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8831 (ttm-80) REVERT: K 185 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7239 (mp0) REVERT: K 198 LYS cc_start: 0.9351 (tppp) cc_final: 0.9125 (tppp) REVERT: K 201 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: K 204 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8346 (tm-30) REVERT: L 59 GLU cc_start: 0.9284 (mp0) cc_final: 0.8770 (mp0) REVERT: L 91 ARG cc_start: 0.9458 (mtp-110) cc_final: 0.9135 (mtp85) REVERT: L 122 GLN cc_start: 0.8433 (pt0) cc_final: 0.7750 (pm20) REVERT: L 152 ARG cc_start: 0.7889 (tmt170) cc_final: 0.7079 (tmt170) REVERT: L 166 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: L 170 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8888 (mp) REVERT: L 200 ARG cc_start: 0.9361 (ttm110) cc_final: 0.9006 (mtm-85) REVERT: L 204 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8484 (tm-30) REVERT: M 60 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8993 (mm-30) REVERT: M 104 PHE cc_start: 0.8319 (t80) cc_final: 0.8090 (t80) REVERT: M 122 GLN cc_start: 0.8439 (pt0) cc_final: 0.7825 (pm20) REVERT: M 166 GLN cc_start: 0.9144 (mt0) cc_final: 0.8693 (pt0) REVERT: M 167 VAL cc_start: 0.9371 (t) cc_final: 0.9159 (m) REVERT: M 185 GLU cc_start: 0.8962 (pt0) cc_final: 0.8703 (pt0) REVERT: M 204 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8397 (tm-30) REVERT: N 91 ARG cc_start: 0.9123 (pmm-80) cc_final: 0.8685 (pmm-80) REVERT: N 122 GLN cc_start: 0.7897 (mt0) cc_final: 0.7509 (mt0) REVERT: N 203 ILE cc_start: 0.9595 (tp) cc_final: 0.9353 (tp) REVERT: N 204 GLU cc_start: 0.9195 (tp30) cc_final: 0.8409 (tp30) outliers start: 77 outliers final: 25 residues processed: 486 average time/residue: 0.9493 time to fit residues: 499.6103 Evaluate side-chains 477 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 437 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 MET 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 D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G 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 84 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 136 LEU Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 203 ILE 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 L residue 170 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 163 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 B 97 GLN D 97 GLN E 35 GLN F 35 GLN G 35 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN K 157 GLN N 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.053186 restraints weight = 55925.463| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.81 r_work: 0.2614 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20069 Z= 0.222 Angle : 0.706 10.521 27111 Z= 0.364 Chirality : 0.044 0.178 3150 Planarity : 0.005 0.066 3556 Dihedral : 4.537 54.441 2800 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 4.15 % Allowed : 22.39 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.17), residues: 2464 helix: 1.85 (0.14), residues: 1386 sheet: 1.87 (0.31), residues: 224 loop : -0.31 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 200 TYR 0.020 0.001 TYR H 159 PHE 0.025 0.001 PHE L 58 TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00520 (20041) covalent geometry : angle 0.70577 (27111) hydrogen bonds : bond 0.04131 ( 1054) hydrogen bonds : angle 3.97357 ( 3255) Misc. bond : bond 0.00068 ( 28) *********************** 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 548 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 462 time to evaluate : 0.823 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: 0.9187 (mm-40) cc_final: 0.8848 (mm-40) REVERT: A 176 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8861 (t) REVERT: A 178 GLU cc_start: 0.9344 (pm20) cc_final: 0.8986 (pm20) REVERT: B 39 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8958 (mtp-110) REVERT: B 50 GLN cc_start: 0.9410 (pt0) cc_final: 0.9177 (pt0) REVERT: B 58 ASN cc_start: 0.9542 (m-40) cc_final: 0.9279 (m110) REVERT: B 100 LYS cc_start: 0.8970 (mptt) cc_final: 0.8644 (mmtt) REVERT: B 163 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8916 (tmmm) REVERT: C 39 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8753 (mtp-110) REVERT: C 100 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8668 (mmtt) REVERT: C 134 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8698 (mt-10) REVERT: C 163 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8893 (tmmm) REVERT: D 39 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8688 (mtp-110) REVERT: D 42 ASN cc_start: 0.9610 (m-40) cc_final: 0.9163 (m110) REVERT: D 100 LYS cc_start: 0.9150 (mptt) cc_final: 0.8889 (mptt) REVERT: D 194 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8694 (mt-10) REVERT: E 39 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8875 (mtp-110) REVERT: E 50 GLN cc_start: 0.9454 (pt0) cc_final: 0.9192 (pt0) REVERT: E 134 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8717 (mt-10) REVERT: E 163 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8945 (tmmm) REVERT: F 39 ARG cc_start: 0.9222 (ttp80) cc_final: 0.8837 (mtp-110) REVERT: F 50 GLN cc_start: 0.9387 (pt0) cc_final: 0.9115 (pt0) REVERT: F 108 MET cc_start: 0.8938 (ptp) cc_final: 0.8707 (ptp) REVERT: F 194 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8735 (mt-10) REVERT: H 84 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8762 (mm) REVERT: H 91 ARG cc_start: 0.9374 (ptm160) cc_final: 0.9168 (ptm-80) REVERT: H 203 ILE cc_start: 0.9605 (tp) cc_final: 0.9340 (tp) REVERT: H 204 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8469 (tm-30) REVERT: I 85 GLU cc_start: 0.8579 (pp20) cc_final: 0.8323 (pp20) REVERT: I 122 GLN cc_start: 0.8409 (pt0) cc_final: 0.7763 (pm20) REVERT: I 181 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8367 (ttm-80) REVERT: I 184 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9057 (mt) REVERT: J 91 ARG cc_start: 0.9416 (mtp85) cc_final: 0.8813 (ptp-110) REVERT: J 144 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8504 (ptpp) REVERT: J 203 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9278 (tp) REVERT: J 204 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8323 (tm-30) REVERT: K 91 ARG cc_start: 0.9138 (ttm110) cc_final: 0.8565 (ttm110) REVERT: K 197 GLU cc_start: 0.9286 (pm20) cc_final: 0.9016 (pm20) REVERT: K 201 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: K 204 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8303 (tm-30) REVERT: L 91 ARG cc_start: 0.9470 (mtp-110) cc_final: 0.9158 (mtp85) REVERT: L 122 GLN cc_start: 0.8428 (pt0) cc_final: 0.7745 (pm20) REVERT: L 152 ARG cc_start: 0.7876 (tmt170) cc_final: 0.7664 (tmt170) REVERT: L 166 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: L 170 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8878 (mp) REVERT: L 198 LYS cc_start: 0.9560 (tppp) cc_final: 0.9317 (tppp) REVERT: L 204 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8448 (tm-30) REVERT: M 122 GLN cc_start: 0.8402 (pt0) cc_final: 0.7791 (pm20) REVERT: M 166 GLN cc_start: 0.9159 (mt0) cc_final: 0.8687 (pt0) REVERT: M 167 VAL cc_start: 0.9360 (t) cc_final: 0.9155 (m) REVERT: M 185 GLU cc_start: 0.8961 (pt0) cc_final: 0.8683 (pt0) REVERT: M 190 LYS cc_start: 0.9387 (tppt) cc_final: 0.9128 (ttpp) REVERT: M 204 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8402 (tm-30) REVERT: N 91 ARG cc_start: 0.9151 (pmm-80) cc_final: 0.8903 (pmm-80) REVERT: N 122 GLN cc_start: 0.7847 (mt0) cc_final: 0.7455 (mt0) REVERT: N 166 GLN cc_start: 0.8854 (mt0) cc_final: 0.8458 (mt0) REVERT: N 198 LYS cc_start: 0.9470 (tppp) cc_final: 0.9116 (tptp) REVERT: N 203 ILE cc_start: 0.9583 (tp) cc_final: 0.9306 (tp) REVERT: N 204 GLU cc_start: 0.9210 (tp30) cc_final: 0.8456 (tp30) outliers start: 86 outliers final: 26 residues processed: 498 average time/residue: 0.9889 time to fit residues: 533.0376 Evaluate side-chains 482 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 442 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER 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 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 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 180 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 223 VAL 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 N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 E 35 GLN F 35 GLN G 35 GLN H 157 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053363 restraints weight = 56025.339| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.84 r_work: 0.2627 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20069 Z= 0.194 Angle : 0.731 11.067 27111 Z= 0.374 Chirality : 0.044 0.199 3150 Planarity : 0.005 0.059 3556 Dihedral : 4.332 28.807 2800 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.91 % Allowed : 23.79 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2464 helix: 1.88 (0.14), residues: 1386 sheet: 1.88 (0.31), residues: 224 loop : -0.27 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 200 TYR 0.012 0.001 TYR F 93 PHE 0.016 0.001 PHE I 104 TRP 0.003 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00460 (20041) covalent geometry : angle 0.73052 (27111) hydrogen bonds : bond 0.03936 ( 1054) hydrogen bonds : angle 3.90616 ( 3255) Misc. bond : bond 0.00056 ( 28) *********************** 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 539 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 458 time to evaluate : 0.844 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: 0.9186 (mm-40) cc_final: 0.8855 (mm-40) REVERT: A 108 MET cc_start: 0.8957 (ptp) cc_final: 0.8511 (ptp) REVERT: A 163 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8933 (tmmm) REVERT: A 176 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 178 GLU cc_start: 0.9358 (pm20) cc_final: 0.9013 (pm20) REVERT: B 39 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8944 (mtp-110) REVERT: B 50 GLN cc_start: 0.9406 (pt0) cc_final: 0.9192 (pt0) REVERT: B 54 ASP cc_start: 0.9204 (m-30) cc_final: 0.8982 (m-30) REVERT: B 58 ASN cc_start: 0.9537 (m-40) cc_final: 0.9165 (m110) REVERT: B 100 LYS cc_start: 0.8958 (mptt) cc_final: 0.8617 (mmtt) REVERT: B 163 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8925 (tmmm) REVERT: C 39 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8759 (mtp-110) REVERT: C 134 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8690 (mt-10) REVERT: C 163 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8911 (tmmm) REVERT: D 39 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (mtp-110) REVERT: D 42 ASN cc_start: 0.9597 (m-40) cc_final: 0.9143 (m110) REVERT: D 100 LYS cc_start: 0.9166 (mptt) cc_final: 0.8764 (mptt) REVERT: D 194 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8655 (mt-10) REVERT: E 39 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8854 (mtp-110) REVERT: E 50 GLN cc_start: 0.9442 (pt0) cc_final: 0.9187 (pt0) REVERT: E 134 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8689 (mt-10) REVERT: F 39 ARG cc_start: 0.9216 (ttp80) cc_final: 0.8824 (mtp-110) REVERT: F 50 GLN cc_start: 0.9388 (pt0) cc_final: 0.9180 (pt0) REVERT: F 108 MET cc_start: 0.8929 (ptp) cc_final: 0.8665 (ptp) REVERT: F 194 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8726 (mt-10) REVERT: H 84 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8778 (mm) REVERT: H 91 ARG cc_start: 0.9381 (ptm160) cc_final: 0.8803 (ptp90) REVERT: H 144 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8952 (ttmt) REVERT: H 203 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9337 (tp) REVERT: H 204 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8428 (tm-30) REVERT: H 222 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8745 (tp40) REVERT: I 85 GLU cc_start: 0.8557 (pp20) cc_final: 0.8269 (pp20) REVERT: I 122 GLN cc_start: 0.8301 (pt0) cc_final: 0.7697 (pm20) REVERT: J 91 ARG cc_start: 0.9442 (mtp85) cc_final: 0.8847 (ptp-110) REVERT: J 146 MET cc_start: 0.8735 (mmm) cc_final: 0.8421 (mmt) REVERT: J 187 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8127 (mtp) REVERT: J 203 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9269 (tp) REVERT: J 204 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8349 (tm-30) REVERT: K 91 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8837 (ttp-110) REVERT: K 185 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7278 (mp0) REVERT: K 198 LYS cc_start: 0.9268 (tppp) cc_final: 0.9033 (tppp) REVERT: K 201 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: K 204 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8357 (tm-30) REVERT: L 91 ARG cc_start: 0.9487 (mtp-110) cc_final: 0.9178 (mtp85) REVERT: L 122 GLN cc_start: 0.8418 (pt0) cc_final: 0.7742 (pm20) REVERT: L 166 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: L 198 LYS cc_start: 0.9562 (tppp) cc_final: 0.9279 (tppp) REVERT: L 200 ARG cc_start: 0.9460 (ttm110) cc_final: 0.9042 (mtm-85) REVERT: L 204 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8445 (tm-30) REVERT: M 122 GLN cc_start: 0.8365 (pt0) cc_final: 0.7681 (pm20) REVERT: M 167 VAL cc_start: 0.9356 (t) cc_final: 0.9142 (m) REVERT: M 185 GLU cc_start: 0.8957 (pt0) cc_final: 0.8628 (pt0) REVERT: M 204 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8420 (tm-30) REVERT: N 91 ARG cc_start: 0.9147 (pmm-80) cc_final: 0.8596 (pmm-80) REVERT: N 122 GLN cc_start: 0.7833 (mt0) cc_final: 0.7441 (mt0) REVERT: N 166 GLN cc_start: 0.8889 (mt0) cc_final: 0.8651 (mt0) REVERT: N 198 LYS cc_start: 0.9511 (tppp) cc_final: 0.9166 (tptp) REVERT: N 203 ILE cc_start: 0.9570 (tp) cc_final: 0.9320 (tp) REVERT: N 204 GLU cc_start: 0.9198 (tp30) cc_final: 0.8455 (tp30) outliers start: 81 outliers final: 30 residues processed: 490 average time/residue: 1.0033 time to fit residues: 531.3040 Evaluate side-chains 487 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 444 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 205 MET 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 180 MET Chi-restraints excluded: chain H residue 193 THR 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 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 201 GLU Chi-restraints excluded: chain K residue 223 VAL 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 87 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 Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 203 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 97 GLN G 35 GLN H 150 ASN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN K 150 ASN K 157 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.053192 restraints weight = 56035.712| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.82 r_work: 0.2624 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20069 Z= 0.210 Angle : 0.758 11.839 27111 Z= 0.389 Chirality : 0.044 0.198 3150 Planarity : 0.005 0.061 3556 Dihedral : 4.416 29.995 2800 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.81 % Allowed : 24.71 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.17), residues: 2464 helix: 1.83 (0.15), residues: 1379 sheet: 1.92 (0.31), residues: 224 loop : -0.28 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 200 TYR 0.021 0.001 TYR J 159 PHE 0.024 0.001 PHE L 58 TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00498 (20041) covalent geometry : angle 0.75815 (27111) hydrogen bonds : bond 0.04034 ( 1054) hydrogen bonds : angle 3.96078 ( 3255) Misc. bond : bond 0.00062 ( 28) *********************** 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 531 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 452 time to evaluate : 0.823 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: 0.9196 (mm-40) cc_final: 0.8864 (mm-40) REVERT: A 108 MET cc_start: 0.8965 (ptp) cc_final: 0.8503 (ptp) REVERT: A 163 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8912 (tmmm) REVERT: A 176 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 178 GLU cc_start: 0.9366 (pm20) cc_final: 0.9034 (pm20) REVERT: B 39 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8954 (mtp-110) REVERT: B 50 GLN cc_start: 0.9408 (pt0) cc_final: 0.9188 (pt0) REVERT: B 54 ASP cc_start: 0.9214 (m-30) cc_final: 0.8997 (m-30) REVERT: B 58 ASN cc_start: 0.9533 (m-40) cc_final: 0.9174 (m110) REVERT: B 163 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8915 (tmmm) REVERT: C 39 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8712 (mtp-110) REVERT: C 134 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8691 (mt-10) REVERT: C 163 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8915 (tmmm) REVERT: D 39 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8750 (mtp-110) REVERT: D 100 LYS cc_start: 0.9169 (mptt) cc_final: 0.8766 (mptt) REVERT: D 194 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8633 (mt-10) REVERT: E 39 ARG cc_start: 0.9237 (tpp80) cc_final: 0.8874 (mtp-110) REVERT: E 50 GLN cc_start: 0.9453 (pt0) cc_final: 0.9202 (pt0) REVERT: E 72 GLU cc_start: 0.8565 (pm20) cc_final: 0.8338 (pm20) REVERT: E 73 LYS cc_start: 0.9291 (mtpp) cc_final: 0.8782 (mtmm) REVERT: E 134 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8768 (mt-10) REVERT: F 39 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8812 (mtp-110) REVERT: F 50 GLN cc_start: 0.9391 (pt0) cc_final: 0.9181 (pt0) REVERT: F 108 MET cc_start: 0.8936 (ptp) cc_final: 0.8660 (ptp) REVERT: F 194 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8718 (mt-10) REVERT: G 97 GLN cc_start: 0.9149 (mm110) cc_final: 0.8912 (mp10) REVERT: G 163 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8839 (tmmm) REVERT: H 84 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (mm) REVERT: H 91 ARG cc_start: 0.9374 (ptm160) cc_final: 0.9116 (ptp90) REVERT: H 144 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8926 (ttmp) REVERT: H 152 ARG cc_start: 0.7726 (tmt170) cc_final: 0.7517 (tmt170) REVERT: H 203 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9356 (tp) REVERT: H 204 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8415 (tm-30) REVERT: I 85 GLU cc_start: 0.8562 (pp20) cc_final: 0.8265 (pp20) REVERT: I 122 GLN cc_start: 0.8296 (pt0) cc_final: 0.7677 (pm20) REVERT: J 91 ARG cc_start: 0.9443 (mtp85) cc_final: 0.8856 (ptp-110) REVERT: J 187 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8138 (mtp) REVERT: J 203 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9271 (tp) REVERT: J 204 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8328 (tm-30) REVERT: K 91 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8827 (ttp-110) REVERT: K 197 GLU cc_start: 0.9303 (pm20) cc_final: 0.9058 (pm20) REVERT: K 201 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: K 204 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8369 (tm-30) REVERT: L 91 ARG cc_start: 0.9477 (mtp-110) cc_final: 0.9155 (mtp85) REVERT: L 122 GLN cc_start: 0.8413 (pt0) cc_final: 0.7726 (pm20) REVERT: L 166 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: L 170 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8890 (mp) REVERT: L 198 LYS cc_start: 0.9570 (tppp) cc_final: 0.9280 (tppp) REVERT: L 204 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8494 (tm-30) REVERT: M 122 GLN cc_start: 0.8374 (pt0) cc_final: 0.7727 (pm20) REVERT: M 166 GLN cc_start: 0.9144 (mt0) cc_final: 0.8724 (pt0) REVERT: M 167 VAL cc_start: 0.9348 (t) cc_final: 0.9140 (m) REVERT: M 185 GLU cc_start: 0.8969 (pt0) cc_final: 0.8634 (pt0) REVERT: M 204 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8409 (tm-30) REVERT: N 91 ARG cc_start: 0.9166 (pmm-80) cc_final: 0.8592 (pmm-80) REVERT: N 122 GLN cc_start: 0.7814 (mt0) cc_final: 0.7418 (mt0) REVERT: N 166 GLN cc_start: 0.8925 (mt0) cc_final: 0.8717 (mt0) REVERT: N 203 ILE cc_start: 0.9580 (tp) cc_final: 0.9351 (tp) REVERT: N 204 GLU cc_start: 0.9231 (tp30) cc_final: 0.8468 (tp30) outliers start: 79 outliers final: 31 residues processed: 483 average time/residue: 1.0093 time to fit residues: 526.5293 Evaluate side-chains 485 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 439 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 205 MET 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 180 MET Chi-restraints excluded: chain H residue 193 THR 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 193 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 193 THR 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 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 N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.0060 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 E 35 GLN F 35 GLN F 63 GLN G 35 GLN H 157 GLN I 122 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN N 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053874 restraints weight = 55501.438| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.80 r_work: 0.2644 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 : 0.004 0.050 20069 Z= 0.179 Angle : 0.773 12.501 27111 Z= 0.395 Chirality : 0.044 0.194 3150 Planarity : 0.005 0.050 3556 Dihedral : 4.419 30.948 2800 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.99 % Allowed : 25.92 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.18), residues: 2464 helix: 1.91 (0.15), residues: 1379 sheet: 1.94 (0.31), residues: 224 loop : -0.28 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 200 TYR 0.021 0.001 TYR N 159 PHE 0.020 0.001 PHE I 104 TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00431 (20041) covalent geometry : angle 0.77257 (27111) hydrogen bonds : bond 0.03784 ( 1054) hydrogen bonds : angle 3.89503 ( 3255) Misc. bond : bond 0.00046 ( 28) *********************** 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 515 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 453 time to evaluate : 0.758 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: 0.9176 (mm-40) cc_final: 0.8851 (mm-40) REVERT: A 108 MET cc_start: 0.8928 (ptp) cc_final: 0.8491 (ptp) REVERT: A 163 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8930 (tmmm) REVERT: A 176 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8803 (t) REVERT: A 178 GLU cc_start: 0.9378 (pm20) cc_final: 0.9057 (pm20) REVERT: B 39 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8944 (mtp-110) REVERT: B 50 GLN cc_start: 0.9425 (pt0) cc_final: 0.9224 (pt0) REVERT: B 58 ASN cc_start: 0.9532 (m-40) cc_final: 0.9239 (m110) REVERT: B 100 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8799 (mmtt) REVERT: B 163 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.8922 (tmmm) REVERT: C 134 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 139 GLN cc_start: 0.8233 (tt0) cc_final: 0.8027 (tt0) REVERT: C 163 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8944 (tmmm) REVERT: D 39 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8684 (mtp-110) REVERT: D 42 ASN cc_start: 0.9597 (m-40) cc_final: 0.9126 (m110) REVERT: D 194 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8660 (mt-10) REVERT: E 39 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8864 (mtp-110) REVERT: E 50 GLN cc_start: 0.9450 (pt0) cc_final: 0.9211 (pt0) REVERT: E 73 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8833 (mtmm) REVERT: E 134 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8718 (mt-10) REVERT: F 39 ARG cc_start: 0.9197 (ttp80) cc_final: 0.8808 (mtp-110) REVERT: F 50 GLN cc_start: 0.9404 (pt0) cc_final: 0.9188 (pt0) REVERT: F 58 ASN cc_start: 0.9505 (m-40) cc_final: 0.8863 (m110) REVERT: F 108 MET cc_start: 0.8919 (ptp) cc_final: 0.8654 (ptp) REVERT: F 194 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8735 (mt-10) REVERT: H 84 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8726 (mm) REVERT: H 91 ARG cc_start: 0.9375 (ptm160) cc_final: 0.9131 (ptp90) REVERT: H 144 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8887 (ttmt) REVERT: H 203 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9338 (tp) REVERT: H 204 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8424 (tm-30) REVERT: H 222 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8780 (tp40) REVERT: I 85 GLU cc_start: 0.8516 (pp20) cc_final: 0.8223 (pp20) REVERT: I 122 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: I 185 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8105 (mt-10) REVERT: I 222 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8805 (tp40) REVERT: J 91 ARG cc_start: 0.9464 (mtp85) cc_final: 0.8874 (ptp-110) REVERT: J 146 MET cc_start: 0.8776 (mmt) cc_final: 0.8340 (mmt) REVERT: J 187 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8054 (mtp) REVERT: J 198 LYS cc_start: 0.9489 (tppp) cc_final: 0.9266 (tppp) REVERT: J 203 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9274 (tp) REVERT: J 204 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8199 (tm-30) REVERT: K 91 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8860 (ttp-110) REVERT: K 185 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7285 (mp0) REVERT: K 201 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: K 204 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8345 (tm-30) REVERT: L 91 ARG cc_start: 0.9494 (mtp-110) cc_final: 0.9176 (mtp85) REVERT: L 122 GLN cc_start: 0.8438 (pt0) cc_final: 0.7664 (pm20) REVERT: L 152 ARG cc_start: 0.7836 (tmt170) cc_final: 0.7053 (tmt170) REVERT: L 166 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: L 170 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8880 (mp) REVERT: L 198 LYS cc_start: 0.9581 (tppp) cc_final: 0.9341 (tppp) REVERT: L 204 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8498 (tm-30) REVERT: M 122 GLN cc_start: 0.8360 (pt0) cc_final: 0.7670 (pm20) REVERT: M 166 GLN cc_start: 0.9139 (mt0) cc_final: 0.8714 (pt0) REVERT: M 167 VAL cc_start: 0.9346 (t) cc_final: 0.9145 (m) REVERT: M 185 GLU cc_start: 0.8958 (pt0) cc_final: 0.8641 (pt0) REVERT: M 204 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8155 (tm-30) REVERT: N 91 ARG cc_start: 0.9159 (pmm-80) cc_final: 0.8574 (pmm-80) REVERT: N 122 GLN cc_start: 0.7824 (mt0) cc_final: 0.7431 (mt0) REVERT: N 166 GLN cc_start: 0.8933 (mt0) cc_final: 0.8725 (mt0) REVERT: N 190 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8852 (tmmt) REVERT: N 198 LYS cc_start: 0.9498 (tppp) cc_final: 0.9137 (tptp) REVERT: N 203 ILE cc_start: 0.9574 (tp) cc_final: 0.9358 (tp) REVERT: N 204 GLU cc_start: 0.9241 (tp30) cc_final: 0.8511 (tp30) REVERT: N 222 GLN cc_start: 0.9009 (tp40) cc_final: 0.8734 (tp40) outliers start: 62 outliers final: 27 residues processed: 477 average time/residue: 0.9903 time to fit residues: 510.7184 Evaluate side-chains 484 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 443 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 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 180 MET Chi-restraints excluded: chain H residue 193 THR 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 122 GLN 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 201 GLU Chi-restraints excluded: chain K residue 223 VAL 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 N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 193 THR 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 22 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 G 35 GLN G 97 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN K 150 ASN K 157 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055150 restraints weight = 55348.955| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.83 r_work: 0.2672 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20069 Z= 0.154 Angle : 0.798 12.800 27111 Z= 0.410 Chirality : 0.044 0.226 3150 Planarity : 0.005 0.079 3556 Dihedral : 4.433 31.804 2800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.27 % Allowed : 26.64 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2464 helix: 1.88 (0.15), residues: 1379 sheet: 1.95 (0.31), residues: 224 loop : -0.28 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 200 TYR 0.022 0.001 TYR J 159 PHE 0.023 0.001 PHE L 58 TRP 0.002 0.000 TRP C 189 HIS 0.002 0.000 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00376 (20041) covalent geometry : angle 0.79784 (27111) hydrogen bonds : bond 0.03570 ( 1054) hydrogen bonds : angle 3.93336 ( 3255) Misc. bond : bond 0.00029 ( 28) ********************** 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 504 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 457 time to evaluate : 0.935 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: 0.9143 (mm-40) cc_final: 0.8860 (mm-40) REVERT: A 108 MET cc_start: 0.8899 (ptp) cc_final: 0.8441 (ptp) REVERT: A 163 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.8911 (tmmm) REVERT: A 176 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 39 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8947 (mtp-110) REVERT: B 50 GLN cc_start: 0.9421 (pt0) cc_final: 0.9176 (pt0) REVERT: B 54 ASP cc_start: 0.9192 (m-30) cc_final: 0.8950 (m-30) REVERT: B 58 ASN cc_start: 0.9529 (m-40) cc_final: 0.9145 (m110) REVERT: B 100 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8758 (mmtt) REVERT: B 163 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8910 (tmmm) REVERT: C 97 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9065 (mm-40) REVERT: C 134 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8711 (mt-10) REVERT: C 139 GLN cc_start: 0.8199 (tt0) cc_final: 0.7955 (tt0) REVERT: C 163 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8918 (tmmm) REVERT: D 39 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8655 (mtp-110) REVERT: D 42 ASN cc_start: 0.9598 (m-40) cc_final: 0.9145 (m110) REVERT: D 100 LYS cc_start: 0.9038 (mptt) cc_final: 0.8760 (mptt) REVERT: D 194 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8520 (mt-10) REVERT: E 39 ARG cc_start: 0.9228 (tpp80) cc_final: 0.8874 (mtp-110) REVERT: E 134 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8719 (mt-10) REVERT: F 39 ARG cc_start: 0.9172 (ttp80) cc_final: 0.8782 (mtp-110) REVERT: F 58 ASN cc_start: 0.9502 (m-40) cc_final: 0.8821 (m110) REVERT: F 108 MET cc_start: 0.8877 (ptp) cc_final: 0.8610 (ptp) REVERT: F 194 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8723 (mt-10) REVERT: H 84 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (mm) REVERT: H 91 ARG cc_start: 0.9388 (ptm160) cc_final: 0.9144 (ptp90) REVERT: H 144 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8941 (ttmt) REVERT: H 185 GLU cc_start: 0.8682 (pp20) cc_final: 0.8477 (pp20) REVERT: H 203 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9328 (tp) REVERT: H 204 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8448 (tm-30) REVERT: H 222 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8832 (tp40) REVERT: I 85 GLU cc_start: 0.8435 (pp20) cc_final: 0.8156 (pp20) REVERT: I 122 GLN cc_start: 0.8253 (pt0) cc_final: 0.7685 (pm20) REVERT: I 185 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8146 (mt-10) REVERT: I 197 GLU cc_start: 0.9247 (mp0) cc_final: 0.8817 (mp0) REVERT: I 201 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8517 (mp0) REVERT: I 222 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8782 (tp40) REVERT: J 91 ARG cc_start: 0.9465 (mtp85) cc_final: 0.8869 (ptp-110) REVERT: J 144 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8424 (ptpp) REVERT: J 198 LYS cc_start: 0.9508 (tppp) cc_final: 0.9238 (tppp) REVERT: J 203 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9275 (tp) REVERT: J 204 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8282 (tm-30) REVERT: K 91 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8864 (ttp-110) REVERT: K 197 GLU cc_start: 0.9267 (pm20) cc_final: 0.9030 (pm20) REVERT: K 201 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8722 (mp0) REVERT: K 203 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9229 (tp) REVERT: K 204 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8362 (tm-30) REVERT: L 91 ARG cc_start: 0.9490 (mtp-110) cc_final: 0.9174 (mtp85) REVERT: L 122 GLN cc_start: 0.8445 (pt0) cc_final: 0.7771 (pm20) REVERT: L 150 ASN cc_start: 0.9521 (m110) cc_final: 0.9128 (m110) REVERT: L 152 ARG cc_start: 0.7766 (tmt170) cc_final: 0.7032 (tmt170) REVERT: L 166 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: L 198 LYS cc_start: 0.9584 (tppp) cc_final: 0.9339 (tppp) REVERT: L 200 ARG cc_start: 0.9482 (ttm110) cc_final: 0.9072 (mtm-85) REVERT: L 204 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8524 (tm-30) REVERT: M 122 GLN cc_start: 0.8321 (pt0) cc_final: 0.7623 (pm20) REVERT: M 166 GLN cc_start: 0.9107 (mt0) cc_final: 0.8655 (pt0) REVERT: M 185 GLU cc_start: 0.8947 (pt0) cc_final: 0.8632 (pt0) REVERT: M 204 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8422 (tm-30) REVERT: N 91 ARG cc_start: 0.9165 (pmm-80) cc_final: 0.8595 (pmm-80) REVERT: N 122 GLN cc_start: 0.7737 (mt0) cc_final: 0.7367 (mt0) REVERT: N 166 GLN cc_start: 0.8931 (mt0) cc_final: 0.8688 (mt0) REVERT: N 190 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8824 (tmmt) REVERT: N 198 LYS cc_start: 0.9472 (tppp) cc_final: 0.9112 (tptp) REVERT: N 203 ILE cc_start: 0.9548 (tp) cc_final: 0.9330 (tp) REVERT: N 204 GLU cc_start: 0.9241 (tp30) cc_final: 0.8552 (tp30) REVERT: N 222 GLN cc_start: 0.9034 (tp40) cc_final: 0.8834 (tp40) outliers start: 47 outliers final: 23 residues processed: 481 average time/residue: 0.9983 time to fit residues: 518.7607 Evaluate side-chains 483 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 448 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 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 193 THR 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 193 THR Chi-restraints excluded: chain J residue 59 GLU 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 203 ILE 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 N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR 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 37 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 F 35 GLN F 50 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 K 150 ASN K 157 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.054033 restraints weight = 55691.330| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.87 r_work: 0.2640 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20069 Z= 0.194 Angle : 0.820 12.819 27111 Z= 0.424 Chirality : 0.045 0.229 3150 Planarity : 0.005 0.079 3556 Dihedral : 4.473 32.823 2800 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.27 % Allowed : 27.22 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2464 helix: 1.75 (0.15), residues: 1379 sheet: 2.00 (0.31), residues: 224 loop : -0.29 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 200 TYR 0.022 0.001 TYR N 51 PHE 0.023 0.001 PHE I 104 TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00464 (20041) covalent geometry : angle 0.82036 (27111) hydrogen bonds : bond 0.03907 ( 1054) hydrogen bonds : angle 4.08271 ( 3255) Misc. bond : bond 0.00052 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8453.98 seconds wall clock time: 144 minutes 37.45 seconds (8677.45 seconds total)