Starting phenix.real_space_refine on Thu Jan 23 02:44:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xop_38537/01_2025/8xop_38537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xop_38537/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xop_38537/01_2025/8xop_38537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xop_38537/01_2025/8xop_38537.map" model { file = "/net/cci-nas-00/data/ceres_data/8xop_38537/01_2025/8xop_38537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xop_38537/01_2025/8xop_38537.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 12474 2.51 5 N 3304 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19740 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "B" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "E" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "H" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "N" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 11.56, per 1000 atoms: 0.59 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: 7.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 42 sheets defined 51.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 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: 7.62 Time building geometry restraints manager: 6.14 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 46.010 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20041 Z= 0.303 Angle : 0.691 8.958 27111 Z= 0.356 Chirality : 0.045 0.200 3150 Planarity : 0.006 0.074 3556 Dihedral : 12.473 89.713 7399 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2464 helix: 1.54 (0.15), residues: 1358 sheet: 1.74 (0.34), residues: 245 loop : -0.21 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.002 0.000 HIS G 138 PHE 0.022 0.001 PHE I 104 TYR 0.020 0.001 TYR H 51 ARG 0.009 0.001 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8779 (mm-40) REVERT: B 50 GLN cc_start: 0.9261 (pt0) cc_final: 0.9036 (pt0) REVERT: C 43 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8965 (mm-30) REVERT: C 73 LYS cc_start: 0.9319 (mttm) cc_final: 0.9090 (mtpp) REVERT: C 97 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8778 (mm-40) REVERT: D 43 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8917 (mm-30) REVERT: D 100 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8722 (mptt) REVERT: E 43 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8983 (mm-30) REVERT: E 97 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8855 (mm-40) REVERT: E 114 MET cc_start: 0.9055 (tpp) cc_final: 0.8804 (mmm) REVERT: F 43 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9036 (mm-30) REVERT: F 50 GLN cc_start: 0.9307 (pt0) cc_final: 0.9070 (pt0) REVERT: F 73 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9220 (mtpp) REVERT: G 50 GLN cc_start: 0.9253 (pt0) cc_final: 0.9035 (pt0) REVERT: G 97 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8988 (mm110) REVERT: H 166 GLN cc_start: 0.7993 (pt0) cc_final: 0.7516 (pt0) REVERT: H 222 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8689 (tp-100) REVERT: I 85 GLU cc_start: 0.8169 (pp20) cc_final: 0.7940 (pp20) REVERT: I 91 ARG cc_start: 0.9309 (mtp85) cc_final: 0.9107 (mtp-110) REVERT: I 203 ILE cc_start: 0.9556 (tp) cc_final: 0.9349 (tp) REVERT: I 222 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8749 (tp-100) REVERT: J 60 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8877 (mm-30) REVERT: K 91 ARG cc_start: 0.9271 (ttm110) cc_final: 0.8793 (ttm110) REVERT: K 197 GLU cc_start: 0.9012 (pm20) cc_final: 0.8761 (pm20) REVERT: K 201 GLU cc_start: 0.9059 (mp0) cc_final: 0.8501 (mp0) REVERT: K 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7962 (tm-30) REVERT: L 185 GLU cc_start: 0.8351 (pt0) cc_final: 0.8097 (pt0) REVERT: L 200 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8560 (ttm110) REVERT: M 60 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8894 (mm-30) REVERT: M 185 GLU cc_start: 0.8531 (pt0) cc_final: 0.8244 (pt0) REVERT: N 91 ARG cc_start: 0.9068 (ptp90) cc_final: 0.8712 (pmm-80) REVERT: N 122 GLN cc_start: 0.7402 (mt0) cc_final: 0.7059 (mt0) REVERT: N 204 GLU cc_start: 0.8697 (tp30) cc_final: 0.8024 (tp30) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 2.0391 time to fit residues: 1191.7678 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 : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 50 GLN D 58 ASN D 63 GLN E 50 GLN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 122 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 80 GLN L 122 GLN N 175 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.055126 restraints weight = 54905.736| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.92 r_work: 0.2655 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20041 Z= 0.289 Angle : 0.646 8.001 27111 Z= 0.334 Chirality : 0.043 0.171 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.281 34.174 2800 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.85 % Allowed : 14.72 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2464 helix: 1.91 (0.14), residues: 1358 sheet: 1.69 (0.34), residues: 245 loop : -0.21 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.026 0.001 PHE L 58 TYR 0.018 0.001 TYR H 51 ARG 0.009 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 487 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8808 (mm-40) REVERT: A 171 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8963 (tm-30) REVERT: B 50 GLN cc_start: 0.9330 (pt0) cc_final: 0.9064 (pt0) REVERT: B 97 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: B 100 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8628 (mmtt) REVERT: B 194 GLU cc_start: 0.8851 (pt0) cc_final: 0.8494 (pt0) REVERT: B 205 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8155 (mtp) REVERT: C 43 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9101 (mm-30) REVERT: C 97 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8845 (mm-40) REVERT: C 134 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8680 (mt-10) REVERT: D 43 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9093 (mm-30) REVERT: D 100 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8834 (mptt) REVERT: D 134 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8644 (mt-10) REVERT: D 194 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8585 (mt-10) REVERT: E 43 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9065 (mm-30) REVERT: E 97 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9013 (mm-40) REVERT: E 134 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8742 (mt-10) REVERT: F 43 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9151 (mm-30) REVERT: F 50 GLN cc_start: 0.9343 (pt0) cc_final: 0.9085 (pt0) REVERT: F 100 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8655 (mmtt) REVERT: F 108 MET cc_start: 0.8717 (ptp) cc_final: 0.8261 (ptp) REVERT: F 194 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8579 (mt-10) REVERT: G 50 GLN cc_start: 0.9281 (pt0) cc_final: 0.9009 (pt0) REVERT: G 97 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8952 (mm-40) REVERT: H 59 GLU cc_start: 0.9000 (mp0) cc_final: 0.8681 (mp0) REVERT: H 204 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8301 (tm-30) REVERT: H 222 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8716 (tp-100) REVERT: I 85 GLU cc_start: 0.8497 (pp20) cc_final: 0.8234 (pp20) REVERT: I 91 ARG cc_start: 0.9488 (mtp85) cc_final: 0.9246 (mtp85) REVERT: I 157 GLN cc_start: 0.9362 (pt0) cc_final: 0.9015 (pt0) REVERT: I 181 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8617 (ttm-80) REVERT: I 222 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8777 (tp-100) REVERT: J 200 ARG cc_start: 0.8939 (mpp80) cc_final: 0.8719 (mpp80) REVERT: J 203 ILE cc_start: 0.9356 (tp) cc_final: 0.9128 (tp) REVERT: J 204 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8183 (tm-30) REVERT: K 87 MET cc_start: 0.6799 (mtt) cc_final: 0.6526 (mtm) REVERT: K 91 ARG cc_start: 0.9243 (ttm110) cc_final: 0.8641 (ttm110) REVERT: K 166 GLN cc_start: 0.8362 (tt0) cc_final: 0.8008 (tt0) REVERT: K 197 GLU cc_start: 0.9220 (pm20) cc_final: 0.8880 (pm20) REVERT: K 200 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8563 (mmm160) REVERT: K 201 GLU cc_start: 0.8978 (mp0) cc_final: 0.8659 (mp0) REVERT: K 203 ILE cc_start: 0.9530 (tp) cc_final: 0.9188 (tp) REVERT: K 204 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8298 (tm-30) REVERT: L 91 ARG cc_start: 0.9462 (mtp-110) cc_final: 0.9251 (mtp85) REVERT: L 166 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: L 198 LYS cc_start: 0.9380 (tppp) cc_final: 0.9067 (tppp) REVERT: L 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8177 (tm-30) REVERT: M 51 TYR cc_start: 0.8017 (t80) cc_final: 0.7788 (t80) REVERT: M 60 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9050 (mm-30) REVERT: M 185 GLU cc_start: 0.8811 (pt0) cc_final: 0.8531 (pt0) REVERT: M 204 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8303 (tm-30) REVERT: N 122 GLN cc_start: 0.7638 (mt0) cc_final: 0.7224 (mt0) REVERT: N 198 LYS cc_start: 0.9473 (mmmm) cc_final: 0.9048 (tptp) REVERT: N 204 GLU cc_start: 0.9116 (tp30) cc_final: 0.8338 (tp30) outliers start: 59 outliers final: 10 residues processed: 500 average time/residue: 1.9753 time to fit residues: 1070.9424 Evaluate side-chains 460 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 446 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 66 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 202 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 G 35 GLN H 157 GLN I 122 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 122 GLN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056411 restraints weight = 54287.296| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.89 r_work: 0.2706 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20041 Z= 0.200 Angle : 0.612 8.705 27111 Z= 0.314 Chirality : 0.042 0.155 3150 Planarity : 0.005 0.045 3556 Dihedral : 4.237 56.855 2800 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 18.34 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2464 helix: 2.01 (0.14), residues: 1379 sheet: 2.06 (0.31), residues: 224 loop : -0.14 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 189 HIS 0.003 0.000 HIS G 138 PHE 0.020 0.001 PHE M 58 TYR 0.015 0.001 TYR H 51 ARG 0.013 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 489 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8890 (mm-40) REVERT: B 39 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.8931 (mtp-110) REVERT: B 50 GLN cc_start: 0.9396 (pt0) cc_final: 0.9168 (pt0) REVERT: B 100 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8650 (mmtt) REVERT: B 163 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9144 (tmmm) REVERT: C 43 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9121 (mm-30) REVERT: C 97 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8936 (mm-40) REVERT: C 134 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8695 (mt-10) REVERT: C 163 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8872 (tmmm) REVERT: D 42 ASN cc_start: 0.9590 (m-40) cc_final: 0.9151 (m110) REVERT: D 43 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9097 (mm-30) REVERT: D 100 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8847 (mptt) REVERT: D 134 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8638 (mt-10) REVERT: E 43 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9096 (mm-30) REVERT: E 97 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8997 (mm-40) REVERT: E 134 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8751 (mt-10) REVERT: F 39 ARG cc_start: 0.9209 (ttp80) cc_final: 0.8842 (mtp-110) REVERT: F 43 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9168 (mm-30) REVERT: F 100 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8754 (mmtt) REVERT: F 108 MET cc_start: 0.8727 (ptp) cc_final: 0.8360 (ptp) REVERT: F 194 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8891 (mt-10) REVERT: G 50 GLN cc_start: 0.9369 (pt0) cc_final: 0.9135 (pt0) REVERT: G 97 GLN cc_start: 0.9334 (mm-40) cc_final: 0.9045 (mm-40) REVERT: G 163 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8753 (tmmm) REVERT: H 59 GLU cc_start: 0.9128 (mp0) cc_final: 0.8603 (mp0) REVERT: H 84 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8742 (mm) REVERT: H 91 ARG cc_start: 0.9443 (ptm160) cc_final: 0.8672 (ptp90) REVERT: H 203 ILE cc_start: 0.9555 (tp) cc_final: 0.9296 (tp) REVERT: H 204 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8348 (tm-30) REVERT: H 222 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8820 (tp-100) REVERT: I 85 GLU cc_start: 0.8433 (pp20) cc_final: 0.8195 (pp20) REVERT: I 91 ARG cc_start: 0.9509 (mtp85) cc_final: 0.9276 (mtp85) REVERT: I 150 ASN cc_start: 0.9484 (m-40) cc_final: 0.9155 (m110) REVERT: J 60 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9043 (mm-30) REVERT: J 144 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8358 (ptpp) REVERT: J 203 ILE cc_start: 0.9499 (tp) cc_final: 0.9215 (tp) REVERT: J 204 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8216 (tm-30) REVERT: K 91 ARG cc_start: 0.9263 (ttm110) cc_final: 0.8626 (ttm110) REVERT: K 152 ARG cc_start: 0.7307 (tmt170) cc_final: 0.7026 (tmt170) REVERT: K 166 GLN cc_start: 0.8453 (tt0) cc_final: 0.8070 (tt0) REVERT: K 185 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7865 (mt-10) REVERT: K 198 LYS cc_start: 0.9209 (tppp) cc_final: 0.8966 (tppp) REVERT: K 203 ILE cc_start: 0.9607 (tp) cc_final: 0.9385 (tp) REVERT: K 204 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 91 ARG cc_start: 0.9498 (mtp-110) cc_final: 0.9203 (mtp85) REVERT: L 118 LYS cc_start: 0.8520 (mptt) cc_final: 0.8270 (mptt) REVERT: L 122 GLN cc_start: 0.8174 (pt0) cc_final: 0.7543 (pm20) REVERT: L 166 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: L 198 LYS cc_start: 0.9452 (tppp) cc_final: 0.9088 (tppp) REVERT: L 200 ARG cc_start: 0.9263 (ttm110) cc_final: 0.8906 (mtm110) REVERT: L 204 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8278 (tm-30) REVERT: M 51 TYR cc_start: 0.8191 (t80) cc_final: 0.7937 (t80) REVERT: M 60 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9006 (mm-30) REVERT: M 185 GLU cc_start: 0.8872 (pt0) cc_final: 0.8551 (pt0) REVERT: M 198 LYS cc_start: 0.9320 (tppp) cc_final: 0.9062 (tppp) REVERT: M 204 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8324 (tm-30) REVERT: N 122 GLN cc_start: 0.7644 (mt0) cc_final: 0.7323 (mt0) REVERT: N 166 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8098 (mm-40) REVERT: N 197 GLU cc_start: 0.9347 (mp0) cc_final: 0.9053 (pm20) REVERT: N 198 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9202 (tptp) REVERT: N 203 ILE cc_start: 0.9367 (tp) cc_final: 0.9121 (tp) REVERT: N 204 GLU cc_start: 0.9139 (tp30) cc_final: 0.8395 (tp30) outliers start: 47 outliers final: 12 residues processed: 501 average time/residue: 1.9540 time to fit residues: 1061.7082 Evaluate side-chains 478 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 460 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 164 ARG 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 F residue 85 SER Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 84 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 J residue 86 SER Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 180 MET Chi-restraints excluded: chain N residue 59 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 0.0270 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- 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 ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 50 GLN E 58 ASN F 50 GLN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 122 GLN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 80 GLN K 150 ASN N 175 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.052454 restraints weight = 56458.743| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.86 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: 0.8809 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20041 Z= 0.415 Angle : 0.688 9.361 27111 Z= 0.356 Chirality : 0.045 0.171 3150 Planarity : 0.005 0.091 3556 Dihedral : 4.574 55.390 2800 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 3.43 % Allowed : 18.82 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2464 helix: 1.96 (0.14), residues: 1365 sheet: 1.81 (0.32), residues: 259 loop : -0.37 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.022 0.002 PHE L 58 TYR 0.020 0.001 TYR I 159 ARG 0.008 0.001 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 468 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8957 (mm-40) REVERT: A 176 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8859 (t) REVERT: A 178 GLU cc_start: 0.9394 (pm20) cc_final: 0.9069 (pm20) REVERT: B 39 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8976 (mtp-110) REVERT: B 50 GLN cc_start: 0.9384 (pt0) cc_final: 0.9135 (pt0) REVERT: B 100 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8665 (mmtt) REVERT: B 205 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8129 (mtp) REVERT: C 43 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9139 (mm-30) REVERT: C 134 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8680 (mt-10) REVERT: C 156 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8906 (mp0) REVERT: C 163 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.8931 (tmmm) REVERT: D 39 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8675 (mtp-110) REVERT: D 42 ASN cc_start: 0.9590 (m-40) cc_final: 0.9117 (m110) REVERT: D 43 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9114 (mm-30) REVERT: D 100 LYS cc_start: 0.9163 (mmtm) cc_final: 0.8841 (mptt) REVERT: D 156 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (mp0) REVERT: D 194 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 39 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8846 (mtp-110) REVERT: E 134 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8625 (mt-10) REVERT: F 39 ARG cc_start: 0.9222 (ttp80) cc_final: 0.8852 (mtp-110) REVERT: F 156 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: F 194 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8835 (mt-10) REVERT: G 50 GLN cc_start: 0.9411 (pt0) cc_final: 0.9175 (pt0) REVERT: H 91 ARG cc_start: 0.9377 (ptm160) cc_final: 0.9094 (ptp90) REVERT: H 144 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8747 (ttmt) REVERT: H 197 GLU cc_start: 0.9353 (pm20) cc_final: 0.8914 (pm20) REVERT: H 203 ILE cc_start: 0.9575 (tp) cc_final: 0.9302 (tp) REVERT: H 204 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8556 (tp30) REVERT: H 222 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8802 (tp-100) REVERT: I 85 GLU cc_start: 0.8601 (pp20) cc_final: 0.8324 (pp20) REVERT: I 91 ARG cc_start: 0.9501 (mtp85) cc_final: 0.9290 (mtp85) REVERT: I 122 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: I 157 GLN cc_start: 0.9249 (pt0) cc_final: 0.7950 (pt0) REVERT: I 181 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8337 (ttm-80) REVERT: J 144 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8432 (ptpp) REVERT: J 166 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7301 (tm-30) REVERT: J 203 ILE cc_start: 0.9532 (tp) cc_final: 0.9254 (tp) REVERT: J 204 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8248 (tm-30) REVERT: K 58 PHE cc_start: 0.9258 (t80) cc_final: 0.8966 (t80) REVERT: K 91 ARG cc_start: 0.9233 (ttm110) cc_final: 0.8890 (ttm-80) REVERT: K 166 GLN cc_start: 0.8528 (tt0) cc_final: 0.7974 (tt0) REVERT: K 197 GLU cc_start: 0.9280 (pm20) cc_final: 0.9071 (pm20) REVERT: K 203 ILE cc_start: 0.9617 (tp) cc_final: 0.9410 (tp) REVERT: K 204 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8412 (tm-30) REVERT: L 91 ARG cc_start: 0.9465 (mtp-110) cc_final: 0.9138 (mtp85) REVERT: L 122 GLN cc_start: 0.8396 (pt0) cc_final: 0.7645 (pm20) REVERT: L 166 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: L 170 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8911 (mp) REVERT: L 204 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8414 (tm-30) REVERT: M 51 TYR cc_start: 0.8274 (t80) cc_final: 0.8030 (t80) REVERT: M 60 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9001 (mm-30) REVERT: M 104 PHE cc_start: 0.8263 (t80) cc_final: 0.7996 (t80) REVERT: M 122 GLN cc_start: 0.8381 (pt0) cc_final: 0.7791 (pm20) REVERT: M 185 GLU cc_start: 0.8944 (pt0) cc_final: 0.8705 (pt0) REVERT: M 203 ILE cc_start: 0.9497 (tp) cc_final: 0.9256 (tp) REVERT: M 204 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8274 (tm-30) REVERT: N 122 GLN cc_start: 0.7866 (mt0) cc_final: 0.7490 (mt0) REVERT: N 197 GLU cc_start: 0.9341 (mp0) cc_final: 0.9093 (pm20) REVERT: N 204 GLU cc_start: 0.9154 (tp30) cc_final: 0.8379 (tp30) outliers start: 71 outliers final: 14 residues processed: 489 average time/residue: 1.9968 time to fit residues: 1057.6688 Evaluate side-chains 472 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 446 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain H residue 76 ASP 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 122 GLN Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 86 SER 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 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 107 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 C 50 GLN C 58 ASN D 58 ASN D 97 GLN E 35 GLN F 97 GLN G 35 GLN H 157 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN N 175 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054003 restraints weight = 56026.156| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.86 r_work: 0.2645 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20041 Z= 0.267 Angle : 0.653 9.647 27111 Z= 0.336 Chirality : 0.043 0.203 3150 Planarity : 0.005 0.051 3556 Dihedral : 4.368 49.972 2800 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.91 % Allowed : 20.13 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2464 helix: 2.01 (0.14), residues: 1379 sheet: 1.97 (0.32), residues: 224 loop : -0.18 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.013 0.001 PHE I 104 TYR 0.021 0.001 TYR F 93 ARG 0.015 0.001 ARG L 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 472 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8813 (mm-40) REVERT: A 163 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8875 (tmmm) REVERT: A 176 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8855 (t) REVERT: A 178 GLU cc_start: 0.9374 (pm20) cc_final: 0.9043 (pm20) REVERT: B 39 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8957 (mtp-110) REVERT: B 50 GLN cc_start: 0.9395 (pt0) cc_final: 0.9193 (pt0) REVERT: B 100 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8627 (mmtt) REVERT: B 156 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8786 (mp0) REVERT: B 163 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9007 (tmmm) REVERT: C 43 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9132 (mm-30) REVERT: C 97 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8885 (mm-40) REVERT: C 134 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8640 (mt-10) REVERT: D 39 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8635 (mtp-110) REVERT: D 42 ASN cc_start: 0.9593 (m-40) cc_final: 0.9117 (m110) REVERT: D 43 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9114 (mm-30) REVERT: D 100 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8892 (mptt) REVERT: D 194 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8694 (mt-10) REVERT: E 39 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8894 (mtp-110) REVERT: E 134 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8694 (mt-10) REVERT: E 163 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.8867 (tmmm) REVERT: F 39 ARG cc_start: 0.9199 (ttp80) cc_final: 0.8804 (mtp-110) REVERT: F 108 MET cc_start: 0.8872 (ptp) cc_final: 0.8617 (ptp) REVERT: F 194 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8827 (mt-10) REVERT: G 50 GLN cc_start: 0.9415 (pt0) cc_final: 0.9183 (pt0) REVERT: G 156 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: G 163 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8791 (tmmm) REVERT: H 78 MET cc_start: 0.8864 (mtp) cc_final: 0.8138 (mtp) REVERT: H 84 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8810 (mm) REVERT: H 91 ARG cc_start: 0.9377 (ptm160) cc_final: 0.8608 (ptp90) REVERT: H 203 ILE cc_start: 0.9573 (tp) cc_final: 0.9289 (tp) REVERT: H 204 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8499 (tp30) REVERT: H 222 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8795 (tp-100) REVERT: I 85 GLU cc_start: 0.8559 (pp20) cc_final: 0.8285 (pp20) REVERT: I 91 ARG cc_start: 0.9486 (mtp85) cc_final: 0.9263 (mtp85) REVERT: I 122 GLN cc_start: 0.8351 (pt0) cc_final: 0.7896 (pp30) REVERT: I 157 GLN cc_start: 0.9245 (pt0) cc_final: 0.8032 (pt0) REVERT: I 181 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8377 (ttm-80) REVERT: J 144 LYS cc_start: 0.8811 (ptpp) cc_final: 0.8460 (ptpp) REVERT: J 166 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7424 (mm-40) REVERT: J 187 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8114 (mtp) REVERT: J 203 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9239 (tp) REVERT: J 204 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8228 (tm-30) REVERT: K 58 PHE cc_start: 0.9253 (t80) cc_final: 0.8993 (t80) REVERT: K 91 ARG cc_start: 0.9205 (ttm110) cc_final: 0.8869 (ttm-80) REVERT: K 203 ILE cc_start: 0.9599 (tp) cc_final: 0.9381 (tp) REVERT: K 204 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8316 (tm-30) REVERT: L 91 ARG cc_start: 0.9481 (mtp-110) cc_final: 0.9169 (mtp85) REVERT: L 122 GLN cc_start: 0.8389 (pt0) cc_final: 0.7726 (pm20) REVERT: L 166 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: L 170 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8846 (mp) REVERT: L 198 LYS cc_start: 0.9490 (tppp) cc_final: 0.9219 (tppp) REVERT: L 200 ARG cc_start: 0.9338 (ttm110) cc_final: 0.8874 (mtm110) REVERT: L 204 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8417 (tm-30) REVERT: M 51 TYR cc_start: 0.8210 (t80) cc_final: 0.7990 (t80) REVERT: M 60 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8956 (mm-30) REVERT: M 122 GLN cc_start: 0.8329 (pt0) cc_final: 0.7722 (pm20) REVERT: M 166 GLN cc_start: 0.9156 (mt0) cc_final: 0.8656 (pt0) REVERT: M 185 GLU cc_start: 0.8939 (pt0) cc_final: 0.8671 (pt0) REVERT: M 204 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8312 (tm-30) REVERT: N 91 ARG cc_start: 0.9047 (pmm-80) cc_final: 0.8673 (pmm-80) REVERT: N 122 GLN cc_start: 0.7756 (mt0) cc_final: 0.7387 (mt0) REVERT: N 152 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7129 (tmt170) REVERT: N 166 GLN cc_start: 0.8720 (mt0) cc_final: 0.8364 (mt0) REVERT: N 190 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8757 (tmmt) REVERT: N 198 LYS cc_start: 0.9479 (tppp) cc_final: 0.9050 (tptp) REVERT: N 204 GLU cc_start: 0.9166 (tp30) cc_final: 0.8424 (tp30) outliers start: 81 outliers final: 22 residues processed: 503 average time/residue: 1.9795 time to fit residues: 1085.3037 Evaluate side-chains 488 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 451 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain 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 32 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 180 MET 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 J residue 86 SER Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE 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 85 GLU Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 187 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN K 150 ASN K 157 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 = 0.3086 r_free = 0.3086 target = 0.066397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.054006 restraints weight = 55787.813| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.87 r_work: 0.2642 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20041 Z= 0.277 Angle : 0.670 10.049 27111 Z= 0.344 Chirality : 0.043 0.173 3150 Planarity : 0.005 0.054 3556 Dihedral : 4.301 50.885 2800 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 22.35 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2464 helix: 1.97 (0.15), residues: 1379 sheet: 2.01 (0.32), residues: 224 loop : -0.22 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.025 0.001 PHE L 58 TYR 0.019 0.001 TYR M 159 ARG 0.011 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 469 time to evaluate : 2.809 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: 0.9162 (mm-40) cc_final: 0.8842 (mm-40) REVERT: A 163 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8877 (tmmm) REVERT: A 176 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 178 GLU cc_start: 0.9368 (pm20) cc_final: 0.9009 (pm20) REVERT: B 39 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8946 (mtp-110) REVERT: B 50 GLN cc_start: 0.9393 (pt0) cc_final: 0.9164 (pt0) REVERT: B 54 ASP cc_start: 0.9234 (m-30) cc_final: 0.9030 (m-30) REVERT: B 58 ASN cc_start: 0.9542 (m-40) cc_final: 0.9166 (m110) REVERT: B 100 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8625 (mmtt) REVERT: B 156 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: B 163 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8971 (tmmm) REVERT: C 43 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9125 (mm-30) REVERT: C 97 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8887 (mm-40) REVERT: C 134 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8648 (mt-10) REVERT: C 163 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8892 (tmmm) REVERT: D 39 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8633 (mtp-110) REVERT: D 42 ASN cc_start: 0.9602 (m-40) cc_final: 0.9153 (m110) REVERT: D 43 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9134 (mm-30) REVERT: D 194 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8662 (mt-10) REVERT: E 39 ARG cc_start: 0.9204 (tpp80) cc_final: 0.8886 (mtp-110) REVERT: E 134 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8678 (mt-10) REVERT: E 163 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8863 (tmmm) REVERT: F 39 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8831 (mtp-110) REVERT: F 100 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8712 (mmtt) REVERT: F 108 MET cc_start: 0.8854 (ptp) cc_final: 0.8605 (ptp) REVERT: F 194 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8789 (mt-10) REVERT: G 50 GLN cc_start: 0.9412 (pt0) cc_final: 0.9184 (pt0) REVERT: G 156 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8884 (mp0) REVERT: G 163 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8788 (tmmm) REVERT: H 84 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8781 (mm) REVERT: H 91 ARG cc_start: 0.9378 (ptm160) cc_final: 0.9171 (ptm-80) REVERT: H 144 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8869 (ttmp) REVERT: H 203 ILE cc_start: 0.9571 (OUTLIER) cc_final: 0.9319 (tp) REVERT: H 204 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8573 (tp30) REVERT: H 222 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8803 (tp-100) REVERT: I 85 GLU cc_start: 0.8561 (pp20) cc_final: 0.8276 (pp20) REVERT: I 91 ARG cc_start: 0.9485 (mtp85) cc_final: 0.9251 (mtp85) REVERT: J 144 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8509 (ptpp) REVERT: J 146 MET cc_start: 0.8637 (mmm) cc_final: 0.8353 (mmt) REVERT: J 187 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: J 203 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9227 (tp) REVERT: J 204 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8233 (tm-30) REVERT: K 58 PHE cc_start: 0.9260 (t80) cc_final: 0.8985 (t80) REVERT: K 91 ARG cc_start: 0.9205 (ttm110) cc_final: 0.8886 (ttm-80) REVERT: K 197 GLU cc_start: 0.9305 (pm20) cc_final: 0.8985 (pm20) REVERT: K 201 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: K 204 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8360 (tm-30) REVERT: L 91 ARG cc_start: 0.9483 (mtp-110) cc_final: 0.9163 (mtp85) REVERT: L 122 GLN cc_start: 0.8413 (pt0) cc_final: 0.7731 (pm20) REVERT: L 152 ARG cc_start: 0.7623 (tmt170) cc_final: 0.7002 (tmt170) REVERT: L 166 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: L 170 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8852 (mp) REVERT: L 198 LYS cc_start: 0.9509 (tppp) cc_final: 0.9223 (tppp) REVERT: L 200 ARG cc_start: 0.9336 (ttm110) cc_final: 0.8970 (mtm-85) REVERT: L 204 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8401 (tm-30) REVERT: M 51 TYR cc_start: 0.8326 (t80) cc_final: 0.8110 (t80) REVERT: M 59 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: M 122 GLN cc_start: 0.8329 (pt0) cc_final: 0.7710 (pm20) REVERT: M 166 GLN cc_start: 0.9127 (mt0) cc_final: 0.8677 (pt0) REVERT: M 185 GLU cc_start: 0.8910 (pt0) cc_final: 0.8628 (pt0) REVERT: M 204 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8407 (tm-30) REVERT: N 91 ARG cc_start: 0.9076 (pmm-80) cc_final: 0.8665 (pmm-80) REVERT: N 122 GLN cc_start: 0.7786 (mt0) cc_final: 0.7414 (mt0) REVERT: N 166 GLN cc_start: 0.8778 (mt0) cc_final: 0.8410 (mt0) REVERT: N 198 LYS cc_start: 0.9479 (tppp) cc_final: 0.9155 (tptp) REVERT: N 204 GLU cc_start: 0.9186 (tp30) cc_final: 0.8435 (tp30) outliers start: 70 outliers final: 26 residues processed: 497 average time/residue: 1.9615 time to fit residues: 1056.9810 Evaluate side-chains 493 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 449 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 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 163 LYS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 200 ARG 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 87 MET Chi-restraints excluded: chain J residue 180 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 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain N residue 59 GLU 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 195 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 112 optimal weight: 0.0270 chunk 1 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- 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 50 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 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 = 0.3100 r_free = 0.3100 target = 0.067047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054753 restraints weight = 55368.911| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.86 r_work: 0.2660 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20041 Z= 0.255 Angle : 0.699 11.157 27111 Z= 0.355 Chirality : 0.043 0.179 3150 Planarity : 0.005 0.061 3556 Dihedral : 4.261 48.357 2800 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.91 % Allowed : 23.12 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2464 helix: 2.01 (0.15), residues: 1386 sheet: 2.07 (0.31), residues: 224 loop : -0.23 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.006 0.001 PHE B 193 TYR 0.020 0.001 TYR H 159 ARG 0.014 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 472 time to evaluate : 2.307 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: 0.9183 (mm-40) cc_final: 0.8870 (mm-40) REVERT: A 108 MET cc_start: 0.8876 (ptp) cc_final: 0.8429 (ptp) REVERT: A 163 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8881 (tmmm) REVERT: A 176 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 178 GLU cc_start: 0.9370 (pm20) cc_final: 0.9038 (pm20) REVERT: B 39 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8956 (mtp-110) REVERT: B 50 GLN cc_start: 0.9391 (pt0) cc_final: 0.9186 (pt0) REVERT: B 54 ASP cc_start: 0.9226 (m-30) cc_final: 0.9004 (m-30) REVERT: B 58 ASN cc_start: 0.9531 (m-40) cc_final: 0.9133 (m110) REVERT: B 156 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: B 163 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8889 (tmmm) REVERT: B 205 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7926 (mtp) REVERT: C 43 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9135 (mm-30) REVERT: C 97 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8882 (mm-40) REVERT: C 134 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8623 (mt-10) REVERT: C 139 GLN cc_start: 0.8265 (tt0) cc_final: 0.7089 (tt0) REVERT: C 163 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8887 (tmmm) REVERT: D 39 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8638 (mtp-110) REVERT: D 42 ASN cc_start: 0.9602 (m-40) cc_final: 0.9178 (m110) REVERT: D 43 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9126 (mm-30) REVERT: D 100 LYS cc_start: 0.9076 (mptt) cc_final: 0.8867 (mptt) REVERT: D 194 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8632 (mt-10) REVERT: E 39 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8872 (mtp-110) REVERT: E 134 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8653 (mt-10) REVERT: E 163 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8847 (tmmm) REVERT: F 39 ARG cc_start: 0.9203 (ttp80) cc_final: 0.8812 (mtp-110) REVERT: F 100 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8626 (mmtt) REVERT: F 108 MET cc_start: 0.8839 (ptp) cc_final: 0.8578 (ptp) REVERT: F 194 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8779 (mt-10) REVERT: G 50 GLN cc_start: 0.9422 (pt0) cc_final: 0.9202 (pt0) REVERT: G 163 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8795 (tmmm) REVERT: H 84 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (mm) REVERT: H 91 ARG cc_start: 0.9384 (ptm160) cc_final: 0.8817 (ptp90) REVERT: H 144 LYS cc_start: 0.9101 (ttmt) cc_final: 0.8687 (ttmt) REVERT: H 152 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6497 (tmt170) REVERT: H 203 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9306 (tp) REVERT: H 204 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8572 (tp30) REVERT: H 222 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8831 (tp-100) REVERT: I 85 GLU cc_start: 0.8540 (pp20) cc_final: 0.8254 (pp20) REVERT: I 91 ARG cc_start: 0.9481 (mtp85) cc_final: 0.9252 (mtp85) REVERT: I 122 GLN cc_start: 0.8283 (pt0) cc_final: 0.7748 (pp30) REVERT: J 144 LYS cc_start: 0.8795 (ptpp) cc_final: 0.8493 (ptpp) REVERT: J 187 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: J 203 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9212 (tp) REVERT: J 204 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8244 (tm-30) REVERT: K 58 PHE cc_start: 0.9257 (t80) cc_final: 0.8981 (t80) REVERT: K 91 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8883 (ttp-110) REVERT: K 152 ARG cc_start: 0.7304 (tmt170) cc_final: 0.7100 (tmt170) REVERT: K 166 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: K 185 GLU cc_start: 0.8586 (pp20) cc_final: 0.8320 (pt0) REVERT: K 198 LYS cc_start: 0.9304 (tppp) cc_final: 0.9045 (tppp) REVERT: K 201 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: K 203 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9296 (tp) REVERT: K 204 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8403 (tm-30) REVERT: L 91 ARG cc_start: 0.9493 (mtp-110) cc_final: 0.9184 (mtp85) REVERT: L 122 GLN cc_start: 0.8411 (pt0) cc_final: 0.7730 (pm20) REVERT: L 152 ARG cc_start: 0.7696 (tmt170) cc_final: 0.7454 (tmt170) REVERT: L 166 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: L 170 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8838 (mp) REVERT: L 198 LYS cc_start: 0.9528 (tppp) cc_final: 0.9261 (tppp) REVERT: L 204 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8401 (tm-30) REVERT: M 51 TYR cc_start: 0.8287 (t80) cc_final: 0.8043 (t80) REVERT: M 122 GLN cc_start: 0.8325 (pt0) cc_final: 0.7676 (pm20) REVERT: M 166 GLN cc_start: 0.9121 (mt0) cc_final: 0.8662 (pt0) REVERT: M 185 GLU cc_start: 0.8913 (pt0) cc_final: 0.8613 (pt0) REVERT: M 204 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 91 ARG cc_start: 0.9135 (pmm-80) cc_final: 0.8701 (pmm-80) REVERT: N 122 GLN cc_start: 0.7758 (mt0) cc_final: 0.7385 (mt0) REVERT: N 166 GLN cc_start: 0.8832 (mt0) cc_final: 0.8600 (mt0) REVERT: N 198 LYS cc_start: 0.9522 (tppp) cc_final: 0.9166 (tptp) REVERT: N 204 GLU cc_start: 0.9212 (tp30) cc_final: 0.8486 (tp30) outliers start: 81 outliers final: 31 residues processed: 506 average time/residue: 1.9206 time to fit residues: 1054.9000 Evaluate side-chains 510 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 459 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET 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 163 LYS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 85 SER 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 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 180 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 203 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 220 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 80 GLN J 175 ASN K 150 ASN K 157 GLN N 175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055925 restraints weight = 55334.941| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.91 r_work: 0.2687 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20041 Z= 0.228 Angle : 0.719 11.926 27111 Z= 0.366 Chirality : 0.043 0.207 3150 Planarity : 0.005 0.085 3556 Dihedral : 4.098 34.877 2800 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.57 % Allowed : 24.28 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2464 helix: 2.06 (0.15), residues: 1386 sheet: 2.08 (0.31), residues: 224 loop : -0.21 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 189 HIS 0.003 0.001 HIS G 138 PHE 0.020 0.001 PHE L 58 TYR 0.013 0.001 TYR B 93 ARG 0.012 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 482 time to evaluate : 2.224 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: 0.9166 (mm-40) cc_final: 0.8832 (mm-40) REVERT: A 163 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8877 (tmmm) REVERT: A 176 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 178 GLU cc_start: 0.9378 (pm20) cc_final: 0.9045 (pm20) REVERT: B 39 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8957 (mtp-110) REVERT: B 50 GLN cc_start: 0.9380 (pt0) cc_final: 0.9129 (pt0) REVERT: B 54 ASP cc_start: 0.9229 (m-30) cc_final: 0.8992 (m-30) REVERT: B 58 ASN cc_start: 0.9528 (m-40) cc_final: 0.9108 (m110) REVERT: B 100 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8751 (mmtt) REVERT: B 163 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8883 (tmmm) REVERT: C 43 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9114 (mm-30) REVERT: C 97 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8966 (mm-40) REVERT: C 134 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 139 GLN cc_start: 0.8145 (tt0) cc_final: 0.7391 (tt0) REVERT: C 163 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8883 (tmmm) REVERT: D 39 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8618 (mtp-110) REVERT: D 42 ASN cc_start: 0.9589 (m-40) cc_final: 0.9165 (m110) REVERT: D 43 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9142 (mm-30) REVERT: D 100 LYS cc_start: 0.9033 (mptt) cc_final: 0.8818 (mptt) REVERT: D 194 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8584 (mt-10) REVERT: E 39 ARG cc_start: 0.9189 (tpp80) cc_final: 0.8853 (mtp-110) REVERT: E 134 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8619 (mt-10) REVERT: E 163 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8830 (tmmm) REVERT: F 39 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8797 (mtp-110) REVERT: F 100 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8702 (mmtt) REVERT: F 108 MET cc_start: 0.8780 (ptp) cc_final: 0.8553 (ptp) REVERT: F 194 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8800 (mt-10) REVERT: G 50 GLN cc_start: 0.9417 (pt0) cc_final: 0.9161 (pt0) REVERT: H 80 GLN cc_start: 0.9219 (mt0) cc_final: 0.8964 (mt0) REVERT: H 84 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8744 (mm) REVERT: H 91 ARG cc_start: 0.9383 (ptm160) cc_final: 0.9136 (ptp90) REVERT: H 144 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8899 (ttmp) REVERT: H 150 ASN cc_start: 0.9384 (m110) cc_final: 0.9133 (m-40) REVERT: H 152 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6543 (tmt170) REVERT: H 203 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9312 (tp) REVERT: H 204 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8588 (tp30) REVERT: H 222 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8834 (tp-100) REVERT: I 85 GLU cc_start: 0.8470 (pp20) cc_final: 0.8190 (pp20) REVERT: I 91 ARG cc_start: 0.9489 (mtp85) cc_final: 0.9249 (mtp85) REVERT: I 122 GLN cc_start: 0.8240 (pt0) cc_final: 0.7656 (pp30) REVERT: I 222 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8735 (tp40) REVERT: J 144 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8551 (ptpp) REVERT: J 187 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: J 203 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9192 (tp) REVERT: J 204 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8293 (tm-30) REVERT: K 58 PHE cc_start: 0.9224 (t80) cc_final: 0.8950 (t80) REVERT: K 59 GLU cc_start: 0.9195 (mp0) cc_final: 0.8766 (mp0) REVERT: K 91 ARG cc_start: 0.9188 (ttm110) cc_final: 0.8907 (ttp-110) REVERT: K 112 ASP cc_start: 0.9184 (m-30) cc_final: 0.8736 (m-30) REVERT: K 152 ARG cc_start: 0.7344 (tmt170) cc_final: 0.6951 (tmt170) REVERT: K 166 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: K 185 GLU cc_start: 0.8578 (pp20) cc_final: 0.8346 (pt0) REVERT: K 197 GLU cc_start: 0.9320 (pm20) cc_final: 0.8925 (pm20) REVERT: K 198 LYS cc_start: 0.9330 (tppp) cc_final: 0.9089 (tppp) REVERT: K 201 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: K 203 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9311 (tp) REVERT: K 204 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8431 (tm-30) REVERT: K 222 GLN cc_start: 0.9073 (tp40) cc_final: 0.8853 (tp40) REVERT: L 91 ARG cc_start: 0.9506 (mtp-110) cc_final: 0.9207 (mtp85) REVERT: L 122 GLN cc_start: 0.8420 (pt0) cc_final: 0.7741 (pm20) REVERT: L 152 ARG cc_start: 0.7657 (tmt170) cc_final: 0.7109 (tmt170) REVERT: L 166 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: L 198 LYS cc_start: 0.9552 (tppp) cc_final: 0.9308 (tppp) REVERT: L 200 ARG cc_start: 0.9296 (ttp-110) cc_final: 0.8961 (mtm-85) REVERT: L 204 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8479 (tm-30) REVERT: M 51 TYR cc_start: 0.8269 (t80) cc_final: 0.7877 (t80) REVERT: M 122 GLN cc_start: 0.8288 (pt0) cc_final: 0.7559 (pm20) REVERT: M 152 ARG cc_start: 0.7460 (tmt170) cc_final: 0.7007 (tmt170) REVERT: M 185 GLU cc_start: 0.8898 (pt0) cc_final: 0.8607 (pt0) REVERT: M 204 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8432 (tm-30) REVERT: N 91 ARG cc_start: 0.9148 (pmm-80) cc_final: 0.8713 (pmm-80) REVERT: N 122 GLN cc_start: 0.7752 (mt0) cc_final: 0.7358 (mt0) REVERT: N 128 GLN cc_start: 0.9065 (tt0) cc_final: 0.8601 (tt0) REVERT: N 166 GLN cc_start: 0.8853 (mt0) cc_final: 0.8624 (mt0) REVERT: N 185 GLU cc_start: 0.8810 (pp20) cc_final: 0.8588 (pp20) REVERT: N 198 LYS cc_start: 0.9522 (tppp) cc_final: 0.9172 (tptp) REVERT: N 200 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8749 (mmm160) REVERT: N 204 GLU cc_start: 0.9229 (tp30) cc_final: 0.8564 (tp30) outliers start: 74 outliers final: 23 residues processed: 509 average time/residue: 1.9375 time to fit residues: 1070.3712 Evaluate side-chains 508 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 469 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 ARG 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 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 152 ARG 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 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 203 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN D 97 GLN E 35 GLN F 50 GLN G 35 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 157 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.055955 restraints weight = 55341.046| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.93 r_work: 0.2696 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20041 Z= 0.240 Angle : 0.749 12.670 27111 Z= 0.381 Chirality : 0.043 0.207 3150 Planarity : 0.005 0.084 3556 Dihedral : 4.077 39.454 2800 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.75 % Allowed : 25.43 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2464 helix: 2.07 (0.15), residues: 1365 sheet: 2.12 (0.31), residues: 224 loop : -0.28 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.003 0.001 HIS H 156 PHE 0.019 0.001 PHE M 104 TYR 0.035 0.001 TYR B 93 ARG 0.012 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 468 time to evaluate : 2.516 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: 0.9166 (mm-40) cc_final: 0.8905 (mm-40) REVERT: A 163 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8884 (tmmm) REVERT: A 176 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 178 GLU cc_start: 0.9388 (pm20) cc_final: 0.9067 (pm20) REVERT: B 39 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8959 (mtp-110) REVERT: B 50 GLN cc_start: 0.9377 (pt0) cc_final: 0.9146 (pt0) REVERT: B 54 ASP cc_start: 0.9227 (m-30) cc_final: 0.8980 (m-30) REVERT: B 58 ASN cc_start: 0.9526 (m-40) cc_final: 0.9091 (m110) REVERT: B 100 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8747 (mmtt) REVERT: B 163 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.8885 (tmmm) REVERT: C 43 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9108 (mm-30) REVERT: C 97 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8886 (mm-40) REVERT: C 134 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 139 GLN cc_start: 0.8144 (tt0) cc_final: 0.7361 (tt0) REVERT: C 163 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8929 (tmmm) REVERT: D 39 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8631 (mtp-110) REVERT: D 42 ASN cc_start: 0.9594 (m-40) cc_final: 0.9173 (m110) REVERT: D 43 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9133 (mm-30) REVERT: D 156 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: D 194 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8577 (mt-10) REVERT: E 39 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8865 (mtp-110) REVERT: E 134 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8695 (mt-10) REVERT: E 163 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8828 (tmmm) REVERT: F 39 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8804 (mtp-110) REVERT: F 108 MET cc_start: 0.8792 (ptp) cc_final: 0.8560 (ptp) REVERT: F 194 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8773 (mt-10) REVERT: F 205 MET cc_start: 0.8695 (mmp) cc_final: 0.8367 (mtp) REVERT: G 50 GLN cc_start: 0.9417 (pt0) cc_final: 0.9159 (pt0) REVERT: H 80 GLN cc_start: 0.9258 (mt0) cc_final: 0.9032 (mt0) REVERT: H 84 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8754 (mm) REVERT: H 91 ARG cc_start: 0.9385 (ptm160) cc_final: 0.9134 (ptp90) REVERT: H 144 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8861 (ttmt) REVERT: H 150 ASN cc_start: 0.9400 (m110) cc_final: 0.9160 (m-40) REVERT: H 152 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6556 (tmt170) REVERT: H 204 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8466 (tm-30) REVERT: H 222 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8869 (tp-100) REVERT: I 85 GLU cc_start: 0.8466 (pp20) cc_final: 0.8197 (pp20) REVERT: I 91 ARG cc_start: 0.9494 (mtp85) cc_final: 0.9263 (mtp85) REVERT: I 122 GLN cc_start: 0.8284 (pt0) cc_final: 0.7709 (pm20) REVERT: I 222 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8737 (tp40) REVERT: J 144 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8580 (ptpp) REVERT: J 187 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: J 203 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9207 (tp) REVERT: J 204 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8273 (tm-30) REVERT: K 58 PHE cc_start: 0.9224 (t80) cc_final: 0.8954 (t80) REVERT: K 59 GLU cc_start: 0.9178 (mp0) cc_final: 0.8752 (mp0) REVERT: K 91 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8901 (ttp-110) REVERT: K 112 ASP cc_start: 0.9200 (m-30) cc_final: 0.8770 (m-30) REVERT: K 152 ARG cc_start: 0.7462 (tmt170) cc_final: 0.7167 (tmt170) REVERT: K 166 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: K 198 LYS cc_start: 0.9345 (tppp) cc_final: 0.9142 (tppp) REVERT: K 203 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.9313 (tp) REVERT: K 204 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8459 (tm-30) REVERT: L 91 ARG cc_start: 0.9488 (mtp-110) cc_final: 0.9192 (mtp85) REVERT: L 122 GLN cc_start: 0.8422 (pt0) cc_final: 0.7746 (pm20) REVERT: L 166 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: L 198 LYS cc_start: 0.9547 (tppp) cc_final: 0.9324 (tppp) REVERT: L 200 ARG cc_start: 0.9272 (ttp-110) cc_final: 0.8965 (mtm-85) REVERT: L 204 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8485 (tm-30) REVERT: M 51 TYR cc_start: 0.8291 (t80) cc_final: 0.7943 (t80) REVERT: M 122 GLN cc_start: 0.8297 (pt0) cc_final: 0.7554 (pm20) REVERT: M 166 GLN cc_start: 0.9144 (mt0) cc_final: 0.8731 (pt0) REVERT: M 185 GLU cc_start: 0.8913 (pt0) cc_final: 0.8608 (pt0) REVERT: M 204 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8484 (tm-30) REVERT: N 91 ARG cc_start: 0.9138 (pmm-80) cc_final: 0.8683 (pmm-80) REVERT: N 122 GLN cc_start: 0.7753 (mt0) cc_final: 0.7368 (mt0) REVERT: N 128 GLN cc_start: 0.9026 (tt0) cc_final: 0.8561 (tt0) REVERT: N 166 GLN cc_start: 0.8880 (mt0) cc_final: 0.8584 (mt0) REVERT: N 190 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8827 (tmmt) REVERT: N 198 LYS cc_start: 0.9528 (tppp) cc_final: 0.9182 (tptp) REVERT: N 204 GLU cc_start: 0.9277 (tp30) cc_final: 0.8538 (tp30) outliers start: 57 outliers final: 23 residues processed: 491 average time/residue: 1.9683 time to fit residues: 1048.6340 Evaluate side-chains 497 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 459 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 ARG 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 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 152 ARG 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 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 35 GLN F 50 GLN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 80 GLN J 175 ASN K 150 ASN K 157 GLN N 157 GLN N 175 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052466 restraints weight = 56498.203| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.88 r_work: 0.2599 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 20041 Z= 0.438 Angle : 0.846 12.937 27111 Z= 0.437 Chirality : 0.046 0.215 3150 Planarity : 0.005 0.065 3556 Dihedral : 4.602 42.137 2800 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 2.65 % Allowed : 26.01 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2464 helix: 1.72 (0.15), residues: 1372 sheet: 2.16 (0.32), residues: 224 loop : -0.30 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 189 HIS 0.004 0.001 HIS G 138 PHE 0.022 0.001 PHE I 104 TYR 0.026 0.001 TYR B 93 ARG 0.020 0.001 ARG N 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 448 time to evaluate : 2.376 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 108 MET cc_start: 0.8950 (ptp) cc_final: 0.8476 (ptp) REVERT: A 163 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.8894 (tmmm) REVERT: A 176 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8841 (t) REVERT: A 178 GLU cc_start: 0.9380 (pm20) cc_final: 0.9036 (pm20) REVERT: B 39 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8987 (mtp-110) REVERT: B 50 GLN cc_start: 0.9388 (pt0) cc_final: 0.9143 (pt0) REVERT: B 58 ASN cc_start: 0.9553 (m-40) cc_final: 0.9298 (m110) REVERT: B 100 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8741 (mmtt) REVERT: B 163 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8904 (tmmm) REVERT: C 39 ARG cc_start: 0.9183 (ttp80) cc_final: 0.8713 (mtp-110) REVERT: C 134 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8703 (mt-10) REVERT: C 163 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8918 (tmmm) REVERT: D 39 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8695 (mtp-110) REVERT: D 42 ASN cc_start: 0.9598 (m-40) cc_final: 0.9160 (m110) REVERT: D 43 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9151 (mm-30) REVERT: D 194 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8637 (mt-10) REVERT: E 39 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8895 (mtp-110) REVERT: E 50 GLN cc_start: 0.9500 (pt0) cc_final: 0.9279 (pt0) REVERT: E 134 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8752 (mt-10) REVERT: E 163 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8879 (tmmm) REVERT: F 39 ARG cc_start: 0.9207 (ttp80) cc_final: 0.8838 (mtp-110) REVERT: F 108 MET cc_start: 0.8879 (ptp) cc_final: 0.8610 (ptp) REVERT: F 194 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8771 (mt-10) REVERT: G 50 GLN cc_start: 0.9433 (pt0) cc_final: 0.9194 (pt0) REVERT: H 84 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8759 (mm) REVERT: H 91 ARG cc_start: 0.9365 (ptm160) cc_final: 0.8758 (ptp90) REVERT: H 144 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8904 (tttp) REVERT: H 152 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6867 (tmt170) REVERT: H 204 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8219 (tm-30) REVERT: H 222 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8842 (tp-100) REVERT: I 85 GLU cc_start: 0.8575 (pp20) cc_final: 0.8273 (pp20) REVERT: I 91 ARG cc_start: 0.9493 (mtp85) cc_final: 0.9282 (mtp85) REVERT: I 104 PHE cc_start: 0.8193 (t80) cc_final: 0.7887 (t80) REVERT: I 122 GLN cc_start: 0.8454 (pt0) cc_final: 0.7803 (pm20) REVERT: I 184 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8741 (mp) REVERT: I 197 GLU cc_start: 0.9206 (mp0) cc_final: 0.8765 (mp0) REVERT: I 201 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8234 (mp0) REVERT: J 91 ARG cc_start: 0.9428 (mtp85) cc_final: 0.8932 (ptp-110) REVERT: J 144 LYS cc_start: 0.8938 (ptpp) cc_final: 0.8417 (ptpp) REVERT: J 187 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: J 198 LYS cc_start: 0.9479 (tppp) cc_final: 0.9240 (tppp) REVERT: J 203 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9275 (tp) REVERT: J 204 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8317 (tm-30) REVERT: K 58 PHE cc_start: 0.9296 (t80) cc_final: 0.9028 (t80) REVERT: K 91 ARG cc_start: 0.9140 (ttm110) cc_final: 0.8842 (ttp-110) REVERT: K 166 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: K 204 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8372 (tm-30) REVERT: L 91 ARG cc_start: 0.9471 (mtp-110) cc_final: 0.9148 (mtp85) REVERT: L 122 GLN cc_start: 0.8470 (pt0) cc_final: 0.7712 (pm20) REVERT: L 150 ASN cc_start: 0.9572 (m-40) cc_final: 0.9231 (m110) REVERT: L 152 ARG cc_start: 0.7821 (tmt170) cc_final: 0.7602 (tmt170) REVERT: L 203 ILE cc_start: 0.9579 (tp) cc_final: 0.9378 (tp) REVERT: L 204 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8473 (tm-30) REVERT: M 122 GLN cc_start: 0.8400 (pt0) cc_final: 0.7773 (pm20) REVERT: M 166 GLN cc_start: 0.9160 (mt0) cc_final: 0.8740 (pt0) REVERT: M 185 GLU cc_start: 0.8962 (pt0) cc_final: 0.8666 (pt0) REVERT: M 204 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8309 (tm-30) REVERT: N 91 ARG cc_start: 0.9131 (pmm-80) cc_final: 0.8633 (pmm-80) REVERT: N 122 GLN cc_start: 0.7874 (mt0) cc_final: 0.7462 (mt0) REVERT: N 166 GLN cc_start: 0.8879 (mt0) cc_final: 0.8651 (mt0) REVERT: N 204 GLU cc_start: 0.9282 (tp30) cc_final: 0.8533 (tp30) outliers start: 55 outliers final: 26 residues processed: 474 average time/residue: 2.0330 time to fit residues: 1042.3533 Evaluate side-chains 465 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 426 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 D residue 205 MET Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 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 180 MET Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 167 VAL 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 140 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 G 97 GLN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055304 restraints weight = 55821.224| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.89 r_work: 0.2682 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20041 Z= 0.250 Angle : 0.812 13.084 27111 Z= 0.415 Chirality : 0.045 0.215 3150 Planarity : 0.005 0.058 3556 Dihedral : 4.357 29.688 2800 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.22 % Allowed : 26.74 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2464 helix: 1.89 (0.15), residues: 1365 sheet: 2.10 (0.31), residues: 224 loop : -0.35 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 189 HIS 0.003 0.000 HIS K 156 PHE 0.022 0.001 PHE L 58 TYR 0.024 0.001 TYR B 93 ARG 0.013 0.001 ARG K 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16564.85 seconds wall clock time: 291 minutes 49.85 seconds (17509.85 seconds total)