Starting phenix.real_space_refine on Tue Jun 17 05:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xop_38537/06_2025/8xop_38537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xop_38537/06_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_38537/06_2025/8xop_38537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xop_38537/06_2025/8xop_38537.map" model { file = "/net/cci-nas-00/data/ceres_data/8xop_38537/06_2025/8xop_38537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xop_38537/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.86, per 1000 atoms: 0.60 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: 5.33 Conformation dependent library (CDL) restraints added in 2.5 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: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 removed outlier: 4.020A pdb=" N ILE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 148 through 174 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.509A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 removed outlier: 3.743A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 149 through 174 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.944A pdb=" N ILE D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.720A pdb=" N GLY E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 removed outlier: 4.175A pdb=" N ILE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.797A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 52 through 59 Processing helix chain 'H' and resid 70 through 87 removed outlier: 3.628A pdb=" N MET H 87 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'H' and resid 130 through 139 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.641A pdb=" N GLU H 204 " --> pdb=" O ARG H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 52 through 59 removed outlier: 3.749A pdb=" N GLU I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 104 through 117 Processing helix chain 'I' and resid 131 through 139 removed outlier: 3.506A pdb=" N VAL I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 191 Processing helix chain 'I' and resid 195 through 204 removed outlier: 4.042A pdb=" N GLU I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 52 through 59 Processing helix chain 'J' and resid 70 through 87 removed outlier: 3.906A pdb=" N MET J 87 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 117 removed outlier: 3.727A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 167 through 192 Processing helix chain 'J' and resid 195 through 204 removed outlier: 3.669A pdb=" N GLU J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.795A pdb=" N GLU K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'K' and resid 104 through 117 Processing helix chain 'K' and resid 131 through 139 Processing helix chain 'K' and resid 167 through 191 removed outlier: 3.548A pdb=" N HIS K 191 " --> pdb=" O MET K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.752A pdb=" N GLU K 204 " --> pdb=" O ARG K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 52 through 59 Processing helix chain 'L' and resid 70 through 87 removed outlier: 3.895A pdb=" N MET L 87 " --> pdb=" O CYS L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 117 removed outlier: 3.664A pdb=" N LEU L 107 " --> pdb=" O SER L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 167 through 191 Processing helix chain 'L' and resid 195 through 204 removed outlier: 3.713A pdb=" N GLU L 204 " --> pdb=" O ARG L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 52 through 59 Processing helix chain 'M' and resid 70 through 87 removed outlier: 3.697A pdb=" N MET M 87 " --> pdb=" O CYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.560A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 167 through 191 Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 52 through 59 Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.699A pdb=" N MET N 87 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 117 removed outlier: 3.593A pdb=" N LEU N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 139 Processing helix chain 'N' and resid 167 through 192 Processing helix chain 'N' and resid 195 through 203 Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.849A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 81 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 110 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.849A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 81 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 110 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG A 127 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.558A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.558A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG B 127 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.521A pdb=" N ALA B 142 " --> pdb=" O GLY J 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.739A pdb=" N GLY B 146 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER J 160 " --> pdb=" O GLY B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.449A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER C 81 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 110 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 134 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 109 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU C 136 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA C 111 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.449A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER C 81 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 110 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 127 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.015A pdb=" N GLY C 146 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER K 160 " --> pdb=" O GLY C 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.521A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.521A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG D 127 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.682A pdb=" N GLY D 146 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER L 160 " --> pdb=" O GLY D 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.383A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.383A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG E 127 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.630A pdb=" N ILE F 46 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN F 80 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 48 " --> pdb=" O ASN F 80 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER F 81 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU F 110 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 134 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY F 109 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU F 136 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA F 111 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.630A pdb=" N ILE F 46 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN F 80 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 48 " --> pdb=" O ASN F 80 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER F 81 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU F 110 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG F 127 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC6, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.415A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU G 134 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY G 109 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU G 136 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA G 111 " --> pdb=" O LEU G 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.415A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG G 127 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AD1, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AD2, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.260A pdb=" N ILE H 63 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN H 98 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU H 65 " --> pdb=" O ASN H 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 124 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 97 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER H 99 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN H 128 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG H 145 " --> pdb=" O GLN H 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'I' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE I 63 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN I 98 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 65 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU I 154 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA I 129 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE I 63 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN I 98 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 65 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG I 145 " --> pdb=" O GLN I 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.583A pdb=" N ILE J 63 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN J 98 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 65 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER J 99 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN J 128 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG J 152 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY J 127 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU J 154 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA J 129 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.583A pdb=" N ILE J 63 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN J 98 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 65 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER J 99 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN J 128 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N MET J 146 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR J 123 " --> pdb=" O MET J 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.639A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU K 154 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA K 129 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.639A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG K 145 " --> pdb=" O GLN K 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.406A pdb=" N ILE L 63 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN L 98 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU L 65 " --> pdb=" O ASN L 98 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N MET L 146 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR L 123 " --> pdb=" O MET L 146 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG L 145 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 153 through 155 Processing sheet with id=AE3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.383A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER M 99 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN M 128 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG M 152 " --> pdb=" O CYS M 125 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY M 127 " --> pdb=" O ARG M 152 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU M 154 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA M 129 " --> pdb=" O LEU M 154 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.383A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER M 99 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN M 128 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG M 145 " --> pdb=" O GLN M 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.362A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ARG N 152 " --> pdb=" O CYS N 125 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY N 127 " --> pdb=" O ARG N 152 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU N 154 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA N 129 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.362A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N MET N 146 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR N 123 " --> pdb=" O MET N 146 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG N 145 " --> pdb=" O GLN N 222 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 6.09 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.420 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20069 Z= 0.319 Angle : 0.691 8.958 27111 Z= 0.356 Chirality : 0.045 0.200 3150 Planarity : 0.006 0.074 3556 Dihedral : 12.473 89.713 7399 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.13034 ( 1054) hydrogen bonds : angle 5.00377 ( 3255) covalent geometry : bond 0.00459 (20041) covalent geometry : angle 0.69119 (27111) Misc. bond : bond 0.06281 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8779 (mm-40) REVERT: B 50 GLN cc_start: 0.9261 (pt0) cc_final: 0.9036 (pt0) REVERT: C 43 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8965 (mm-30) REVERT: C 73 LYS cc_start: 0.9319 (mttm) cc_final: 0.9090 (mtpp) REVERT: C 97 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8778 (mm-40) REVERT: D 43 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8917 (mm-30) REVERT: D 100 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8722 (mptt) REVERT: E 43 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8983 (mm-30) REVERT: E 97 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8855 (mm-40) REVERT: E 114 MET cc_start: 0.9055 (tpp) cc_final: 0.8804 (mmm) REVERT: F 43 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9036 (mm-30) REVERT: F 50 GLN cc_start: 0.9307 (pt0) cc_final: 0.9070 (pt0) REVERT: F 73 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9220 (mtpp) REVERT: G 50 GLN cc_start: 0.9253 (pt0) cc_final: 0.9035 (pt0) REVERT: G 97 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8988 (mm110) REVERT: H 166 GLN cc_start: 0.7993 (pt0) cc_final: 0.7516 (pt0) REVERT: H 222 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8689 (tp-100) REVERT: I 85 GLU cc_start: 0.8169 (pp20) cc_final: 0.7940 (pp20) REVERT: I 91 ARG cc_start: 0.9309 (mtp85) cc_final: 0.9107 (mtp-110) REVERT: I 203 ILE cc_start: 0.9556 (tp) cc_final: 0.9349 (tp) REVERT: I 222 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8749 (tp-100) REVERT: J 60 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8877 (mm-30) REVERT: K 91 ARG cc_start: 0.9271 (ttm110) cc_final: 0.8793 (ttm110) REVERT: K 197 GLU cc_start: 0.9012 (pm20) cc_final: 0.8761 (pm20) REVERT: K 201 GLU cc_start: 0.9059 (mp0) cc_final: 0.8501 (mp0) REVERT: K 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7962 (tm-30) REVERT: L 185 GLU cc_start: 0.8351 (pt0) cc_final: 0.8097 (pt0) REVERT: L 200 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8560 (ttm110) REVERT: M 60 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8894 (mm-30) REVERT: M 185 GLU cc_start: 0.8531 (pt0) cc_final: 0.8244 (pt0) REVERT: N 91 ARG cc_start: 0.9068 (ptp90) cc_final: 0.8712 (pmm-80) REVERT: N 122 GLN cc_start: 0.7402 (mt0) cc_final: 0.7059 (mt0) REVERT: N 204 GLU cc_start: 0.8697 (tp30) cc_final: 0.8024 (tp30) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 1.9568 time to fit residues: 1144.8259 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 : 2.353 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.068821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056272 restraints weight = 54807.293| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.92 r_work: 0.2700 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20069 Z= 0.149 Angle : 0.629 7.892 27111 Z= 0.324 Chirality : 0.042 0.165 3150 Planarity : 0.005 0.046 3556 Dihedral : 4.214 32.615 2800 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 2.70 % Allowed : 14.91 % Favored : 82.38 % 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: 1.77 (0.17), residues: 2464 helix: 1.94 (0.14), residues: 1358 sheet: 1.69 (0.34), residues: 245 loop : -0.20 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 189 HIS 0.003 0.001 HIS G 138 PHE 0.024 0.001 PHE L 58 TYR 0.018 0.001 TYR H 51 ARG 0.010 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1054) hydrogen bonds : angle 3.97000 ( 3255) covalent geometry : bond 0.00352 (20041) covalent geometry : angle 0.62919 (27111) Misc. bond : bond 0.00049 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 492 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8840 (mm-40) REVERT: A 171 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8992 (tm-30) REVERT: B 50 GLN cc_start: 0.9401 (pt0) cc_final: 0.9171 (pt0) REVERT: B 97 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: B 205 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: C 43 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9138 (mm-30) REVERT: C 73 LYS cc_start: 0.9295 (mttm) cc_final: 0.9090 (mtpp) REVERT: C 97 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8997 (mm-40) REVERT: C 134 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8717 (mt-10) REVERT: D 42 ASN cc_start: 0.9597 (m-40) cc_final: 0.9115 (m110) REVERT: D 43 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9128 (mm-30) REVERT: D 100 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8898 (mptt) REVERT: D 134 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 194 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8741 (mt-10) REVERT: E 43 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9093 (mm-30) REVERT: E 97 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9057 (mm-40) REVERT: E 114 MET cc_start: 0.9119 (tpp) cc_final: 0.8915 (mmm) REVERT: E 134 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8770 (mt-10) REVERT: F 43 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9193 (mm-30) REVERT: F 50 GLN cc_start: 0.9415 (pt0) cc_final: 0.9177 (pt0) REVERT: F 100 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8743 (mmtt) REVERT: F 108 MET cc_start: 0.8800 (ptp) cc_final: 0.8446 (ptp) REVERT: F 194 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8617 (mt-10) REVERT: G 50 GLN cc_start: 0.9378 (pt0) cc_final: 0.9142 (pt0) REVERT: G 97 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9003 (mm-40) REVERT: G 100 LYS cc_start: 0.8887 (mptp) cc_final: 0.8623 (mptt) REVERT: H 59 GLU cc_start: 0.8997 (mp0) cc_final: 0.8553 (mp0) REVERT: H 144 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8829 (ttmm) REVERT: H 204 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8361 (tm-30) REVERT: H 222 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8832 (tp-100) REVERT: I 85 GLU cc_start: 0.8436 (pp20) cc_final: 0.8212 (pp20) REVERT: I 91 ARG cc_start: 0.9511 (mtp85) cc_final: 0.9299 (mtp85) REVERT: I 157 GLN cc_start: 0.9342 (pt0) cc_final: 0.9032 (pt0) REVERT: I 181 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8668 (ttm-80) REVERT: I 222 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8858 (tp-100) REVERT: J 200 ARG cc_start: 0.9022 (mpp80) cc_final: 0.8787 (mpp80) REVERT: J 203 ILE cc_start: 0.9450 (tp) cc_final: 0.9200 (tp) REVERT: J 204 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8282 (tm-30) REVERT: K 87 MET cc_start: 0.6793 (mtt) cc_final: 0.6513 (mtm) REVERT: K 91 ARG cc_start: 0.9317 (ttm110) cc_final: 0.8699 (ttm110) REVERT: K 152 ARG cc_start: 0.7391 (tmt170) cc_final: 0.7127 (tmt170) REVERT: K 166 GLN cc_start: 0.8503 (tt0) cc_final: 0.8202 (tt0) REVERT: K 197 GLU cc_start: 0.9206 (pm20) cc_final: 0.8847 (pm20) REVERT: K 200 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8576 (mmm160) REVERT: K 201 GLU cc_start: 0.8998 (mp0) cc_final: 0.8661 (mp0) REVERT: K 203 ILE cc_start: 0.9618 (tp) cc_final: 0.9320 (tp) REVERT: K 204 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8313 (tm-30) REVERT: L 91 ARG cc_start: 0.9522 (mtp-110) cc_final: 0.9307 (mtp85) REVERT: L 126 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7492 (pmm) REVERT: L 166 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: L 203 ILE cc_start: 0.9512 (tp) cc_final: 0.9306 (tp) REVERT: L 204 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8272 (tm-30) REVERT: M 51 TYR cc_start: 0.8164 (t80) cc_final: 0.7944 (t80) REVERT: M 60 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9036 (mm-30) REVERT: M 185 GLU cc_start: 0.8852 (pt0) cc_final: 0.8555 (pt0) REVERT: M 204 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8301 (tm-30) REVERT: N 59 GLU cc_start: 0.9484 (OUTLIER) cc_final: 0.9180 (mm-30) REVERT: N 60 GLU cc_start: 0.8707 (mp0) cc_final: 0.8378 (mp0) REVERT: N 122 GLN cc_start: 0.7700 (mt0) cc_final: 0.7322 (mt0) REVERT: N 166 GLN cc_start: 0.8440 (mm110) cc_final: 0.8218 (mm-40) REVERT: N 198 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9131 (tptp) REVERT: N 204 GLU cc_start: 0.9150 (tp30) cc_final: 0.8404 (tp30) outliers start: 56 outliers final: 8 residues processed: 504 average time/residue: 1.9064 time to fit residues: 1043.1384 Evaluate side-chains 472 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 458 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 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 126 MET Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 66 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN D 97 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN H 157 GLN I 122 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053939 restraints weight = 55113.494| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.87 r_work: 0.2641 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20069 Z= 0.212 Angle : 0.647 10.005 27111 Z= 0.332 Chirality : 0.043 0.163 3150 Planarity : 0.005 0.048 3556 Dihedral : 4.384 54.710 2800 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 18.00 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.17), residues: 2464 helix: 2.03 (0.14), residues: 1358 sheet: 1.86 (0.32), residues: 259 loop : -0.37 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.022 0.001 PHE M 58 TYR 0.017 0.001 TYR H 51 ARG 0.012 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1054) hydrogen bonds : angle 3.91932 ( 3255) covalent geometry : bond 0.00496 (20041) covalent geometry : angle 0.64680 (27111) Misc. bond : bond 0.00072 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 470 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8915 (mm-40) REVERT: B 39 ARG cc_start: 0.9330 (ttp80) cc_final: 0.8963 (mtp-110) REVERT: B 50 GLN cc_start: 0.9395 (pt0) cc_final: 0.9179 (pt0) REVERT: B 163 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9151 (tmmm) REVERT: B 205 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: C 43 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9145 (mm-30) REVERT: C 73 LYS cc_start: 0.9258 (mttm) cc_final: 0.9008 (mtpp) REVERT: C 97 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8969 (mm-40) REVERT: C 156 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8911 (mp0) REVERT: C 163 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8887 (tmmm) REVERT: D 39 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8631 (mtp-110) REVERT: D 42 ASN cc_start: 0.9587 (m-40) cc_final: 0.9115 (m110) REVERT: D 43 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9116 (mm-30) REVERT: D 100 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8854 (mptt) REVERT: D 156 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8868 (mp0) REVERT: E 43 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9127 (mm-30) REVERT: E 50 GLN cc_start: 0.9496 (pt0) cc_final: 0.9280 (pt0) REVERT: E 134 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8766 (mt-10) REVERT: E 156 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: F 39 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8878 (mtp-110) REVERT: F 43 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9190 (mm-30) REVERT: F 50 GLN cc_start: 0.9369 (pt0) cc_final: 0.9145 (pt0) REVERT: F 156 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8881 (mp0) REVERT: F 194 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8891 (mt-10) REVERT: G 50 GLN cc_start: 0.9418 (pt0) cc_final: 0.9193 (pt0) REVERT: G 100 LYS cc_start: 0.8939 (mptp) cc_final: 0.8617 (mptt) REVERT: G 163 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8786 (tmmm) REVERT: H 91 ARG cc_start: 0.9432 (ptp-110) cc_final: 0.9048 (ptp90) REVERT: H 144 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8891 (ttpt) REVERT: H 203 ILE cc_start: 0.9553 (tp) cc_final: 0.9296 (tp) REVERT: H 222 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8791 (tp-100) REVERT: I 85 GLU cc_start: 0.8548 (pp20) cc_final: 0.8310 (pp20) REVERT: I 91 ARG cc_start: 0.9506 (mtp85) cc_final: 0.9276 (mtp85) REVERT: I 222 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8834 (tp-100) REVERT: J 59 GLU cc_start: 0.9042 (mp0) cc_final: 0.8814 (mp0) REVERT: J 60 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9113 (mm-30) REVERT: J 144 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8345 (ptpp) REVERT: J 166 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7676 (mm-40) REVERT: J 203 ILE cc_start: 0.9515 (tp) cc_final: 0.9232 (tp) REVERT: J 204 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8214 (tm-30) REVERT: K 91 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8596 (ttm110) REVERT: K 166 GLN cc_start: 0.8504 (tt0) cc_final: 0.8041 (tt0) REVERT: K 203 ILE cc_start: 0.9611 (tp) cc_final: 0.9400 (tp) REVERT: K 204 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8383 (tm-30) REVERT: L 59 GLU cc_start: 0.9158 (mp0) cc_final: 0.8912 (mp0) REVERT: L 91 ARG cc_start: 0.9473 (mtp-110) cc_final: 0.9163 (mtp85) REVERT: L 122 GLN cc_start: 0.8354 (pt0) cc_final: 0.7631 (pm20) REVERT: L 166 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: L 200 ARG cc_start: 0.9269 (ttm110) cc_final: 0.8831 (mtm110) REVERT: L 204 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8316 (tm-30) REVERT: M 51 TYR cc_start: 0.8230 (t80) cc_final: 0.7961 (t80) REVERT: M 60 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9010 (mm-30) REVERT: M 185 GLU cc_start: 0.8923 (pt0) cc_final: 0.8659 (pt0) REVERT: M 204 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8261 (tm-30) REVERT: N 60 GLU cc_start: 0.8820 (mp0) cc_final: 0.8526 (mp0) REVERT: N 122 GLN cc_start: 0.7750 (mt0) cc_final: 0.7424 (mt0) REVERT: N 197 GLU cc_start: 0.9343 (mp0) cc_final: 0.9066 (pm20) REVERT: N 198 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9170 (tptp) REVERT: N 204 GLU cc_start: 0.9162 (tp30) cc_final: 0.8386 (tp30) outliers start: 56 outliers final: 14 residues processed: 485 average time/residue: 1.9231 time to fit residues: 1011.6623 Evaluate side-chains 473 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 449 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 180 MET 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 N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 97 GLN E 35 GLN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN N 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054000 restraints weight = 55971.798| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.87 r_work: 0.2647 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20069 Z= 0.179 Angle : 0.637 9.358 27111 Z= 0.327 Chirality : 0.043 0.164 3150 Planarity : 0.005 0.078 3556 Dihedral : 4.402 55.160 2800 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.09 % Allowed : 19.69 % Favored : 77.22 % 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: 1.86 (0.17), residues: 2464 helix: 1.99 (0.14), residues: 1372 sheet: 2.07 (0.32), residues: 224 loop : -0.21 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.025 0.001 PHE J 58 TYR 0.019 0.001 TYR I 159 ARG 0.010 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1054) hydrogen bonds : angle 3.78799 ( 3255) covalent geometry : bond 0.00425 (20041) covalent geometry : angle 0.63735 (27111) Misc. bond : bond 0.00057 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 473 time to evaluate : 2.195 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: 0.9184 (mm-40) cc_final: 0.8892 (mm-40) REVERT: A 176 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8839 (t) REVERT: A 178 GLU cc_start: 0.9391 (pm20) cc_final: 0.9070 (pm20) REVERT: B 39 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8962 (mtp-110) REVERT: B 50 GLN cc_start: 0.9399 (pt0) cc_final: 0.9178 (pt0) REVERT: C 39 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8657 (mtp-110) REVERT: C 43 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9126 (mm-30) REVERT: C 73 LYS cc_start: 0.9186 (mttm) cc_final: 0.8934 (mtpp) REVERT: C 97 GLN cc_start: 0.9304 (mm-40) cc_final: 0.8933 (mm-40) REVERT: C 163 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.8909 (tmmm) REVERT: D 39 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8619 (mtp-110) REVERT: D 42 ASN cc_start: 0.9584 (m-40) cc_final: 0.9100 (m110) REVERT: D 43 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9106 (mm-30) REVERT: D 194 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8658 (mt-10) REVERT: E 39 ARG cc_start: 0.9213 (ttp80) cc_final: 0.8786 (mtp-110) REVERT: E 43 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9115 (mm-30) REVERT: E 50 GLN cc_start: 0.9465 (pt0) cc_final: 0.9224 (pt0) REVERT: E 97 GLN cc_start: 0.9337 (mm110) cc_final: 0.9057 (mm-40) REVERT: E 134 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8637 (mt-10) REVERT: E 163 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.8885 (tmmm) REVERT: F 35 GLN cc_start: 0.8957 (tt0) cc_final: 0.8748 (tt0) REVERT: F 39 ARG cc_start: 0.9240 (ttp80) cc_final: 0.8852 (mtp-110) REVERT: F 50 GLN cc_start: 0.9371 (pt0) cc_final: 0.9153 (pt0) REVERT: F 108 MET cc_start: 0.8839 (ptp) cc_final: 0.8588 (ptp) REVERT: F 194 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8877 (mt-10) REVERT: G 50 GLN cc_start: 0.9415 (pt0) cc_final: 0.9188 (pt0) REVERT: G 97 GLN cc_start: 0.9387 (mm-40) cc_final: 0.9083 (mm-40) REVERT: G 163 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8784 (tmmm) REVERT: H 91 ARG cc_start: 0.9385 (ptp-110) cc_final: 0.8573 (ptp90) REVERT: H 203 ILE cc_start: 0.9581 (tp) cc_final: 0.9320 (tp) REVERT: H 222 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8788 (tp-100) REVERT: I 85 GLU cc_start: 0.8551 (pp20) cc_final: 0.8276 (pp20) REVERT: I 91 ARG cc_start: 0.9502 (mtp85) cc_final: 0.9299 (mtp85) REVERT: I 122 GLN cc_start: 0.8339 (pt0) cc_final: 0.7732 (pm20) REVERT: I 157 GLN cc_start: 0.9321 (pt0) cc_final: 0.8583 (pt0) REVERT: I 181 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8569 (ttm-80) REVERT: I 222 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8840 (tp-100) REVERT: J 144 LYS cc_start: 0.8802 (ptpp) cc_final: 0.8452 (ptpp) REVERT: J 187 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: J 203 ILE cc_start: 0.9530 (tp) cc_final: 0.9255 (tp) REVERT: J 204 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8174 (tm-30) REVERT: K 58 PHE cc_start: 0.9252 (t80) cc_final: 0.8995 (t80) REVERT: K 91 ARG cc_start: 0.9238 (ttm110) cc_final: 0.8894 (ttm-80) REVERT: K 126 MET cc_start: 0.8553 (mtp) cc_final: 0.8315 (mtp) REVERT: K 166 GLN cc_start: 0.8484 (tt0) cc_final: 0.7996 (tt0) REVERT: K 185 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7927 (pt0) REVERT: K 201 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8799 (mp0) REVERT: K 203 ILE cc_start: 0.9590 (tp) cc_final: 0.9290 (tt) REVERT: K 204 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8324 (tm-30) REVERT: L 59 GLU cc_start: 0.9159 (mp0) cc_final: 0.8678 (mp0) REVERT: L 91 ARG cc_start: 0.9493 (mtp-110) cc_final: 0.9186 (mtp85) REVERT: L 122 GLN cc_start: 0.8367 (pt0) cc_final: 0.7630 (pm20) REVERT: L 166 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: L 170 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8837 (mp) REVERT: L 204 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8384 (tm-30) REVERT: M 51 TYR cc_start: 0.8277 (t80) cc_final: 0.8060 (t80) REVERT: M 60 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9032 (mm-30) REVERT: M 122 GLN cc_start: 0.8268 (pt0) cc_final: 0.7707 (pm20) REVERT: M 185 GLU cc_start: 0.8927 (pt0) cc_final: 0.8659 (pt0) REVERT: M 190 LYS cc_start: 0.9375 (tppt) cc_final: 0.9111 (ttpp) REVERT: M 197 GLU cc_start: 0.9216 (pm20) cc_final: 0.8995 (pm20) REVERT: M 204 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8304 (tm-30) REVERT: N 122 GLN cc_start: 0.7794 (mt0) cc_final: 0.7427 (mt0) REVERT: N 197 GLU cc_start: 0.9352 (mp0) cc_final: 0.9067 (pm20) REVERT: N 198 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9201 (tptp) REVERT: N 204 GLU cc_start: 0.9173 (tp30) cc_final: 0.8414 (tp30) outliers start: 64 outliers final: 15 residues processed: 495 average time/residue: 1.9177 time to fit residues: 1029.2712 Evaluate side-chains 483 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 456 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 107 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 58 ASN E 35 GLN F 97 GLN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 175 ASN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.065818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053422 restraints weight = 56092.331| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.85 r_work: 0.2627 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20069 Z= 0.213 Angle : 0.668 9.702 27111 Z= 0.344 Chirality : 0.043 0.199 3150 Planarity : 0.005 0.076 3556 Dihedral : 4.401 50.060 2800 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.72 % Allowed : 20.61 % Favored : 75.68 % 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: 1.80 (0.17), residues: 2464 helix: 1.96 (0.14), residues: 1379 sheet: 2.06 (0.32), residues: 224 loop : -0.30 (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 0.013 0.001 PHE I 104 TYR 0.018 0.001 TYR B 93 ARG 0.014 0.001 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1054) hydrogen bonds : angle 3.83298 ( 3255) covalent geometry : bond 0.00501 (20041) covalent geometry : angle 0.66823 (27111) Misc. bond : bond 0.00063 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 464 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8904 (mm-40) REVERT: A 176 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8860 (t) REVERT: A 178 GLU cc_start: 0.9375 (pm20) cc_final: 0.9040 (pm20) REVERT: B 39 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8947 (mtp-110) REVERT: B 50 GLN cc_start: 0.9392 (pt0) cc_final: 0.9161 (pt0) REVERT: B 156 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: B 163 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9013 (tmmm) REVERT: C 39 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8692 (mtp-110) REVERT: C 43 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9135 (mm-30) REVERT: D 39 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8632 (mtp-110) REVERT: D 42 ASN cc_start: 0.9592 (m-40) cc_final: 0.9112 (m110) REVERT: D 43 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9120 (mm-30) REVERT: D 100 LYS cc_start: 0.9018 (mptt) cc_final: 0.8596 (mptt) REVERT: D 194 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8709 (mt-10) REVERT: E 39 ARG cc_start: 0.9237 (tpp80) cc_final: 0.8831 (mtp-110) REVERT: E 43 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9137 (mm-30) REVERT: E 50 GLN cc_start: 0.9458 (pt0) cc_final: 0.9192 (pt0) REVERT: E 97 GLN cc_start: 0.9352 (mm110) cc_final: 0.9032 (mm-40) REVERT: E 134 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8703 (mt-10) REVERT: F 39 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8821 (mtp-110) REVERT: F 50 GLN cc_start: 0.9370 (pt0) cc_final: 0.9147 (pt0) REVERT: F 100 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8741 (mmtt) REVERT: F 108 MET cc_start: 0.8882 (ptp) cc_final: 0.8613 (ptp) REVERT: F 194 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8814 (mt-10) REVERT: G 50 GLN cc_start: 0.9407 (pt0) cc_final: 0.9179 (pt0) REVERT: G 156 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8837 (mp0) REVERT: H 84 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8764 (mm) REVERT: H 91 ARG cc_start: 0.9336 (ptp-110) cc_final: 0.9128 (ptp90) REVERT: H 203 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9317 (tp) REVERT: H 222 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8792 (tp-100) REVERT: I 85 GLU cc_start: 0.8573 (pp20) cc_final: 0.8328 (pp20) REVERT: I 91 ARG cc_start: 0.9485 (mtp85) cc_final: 0.9284 (mtp85) REVERT: I 122 GLN cc_start: 0.8406 (pt0) cc_final: 0.7780 (pm20) REVERT: I 204 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8463 (tm-30) REVERT: I 222 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8819 (tp-100) REVERT: J 144 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8462 (ptpp) REVERT: J 187 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: J 203 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9246 (tp) REVERT: J 204 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8216 (tm-30) REVERT: K 58 PHE cc_start: 0.9261 (t80) cc_final: 0.8996 (t80) REVERT: K 85 GLU cc_start: 0.8544 (pp20) cc_final: 0.8336 (pp20) REVERT: K 91 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8864 (ttm-80) REVERT: K 166 GLN cc_start: 0.8532 (tt0) cc_final: 0.7922 (tt0) REVERT: K 185 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7646 (mt-10) REVERT: K 197 GLU cc_start: 0.9197 (pm20) cc_final: 0.8977 (pm20) REVERT: K 203 ILE cc_start: 0.9601 (tp) cc_final: 0.9401 (tp) REVERT: K 204 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8318 (tm-30) REVERT: L 59 GLU cc_start: 0.9176 (mp0) cc_final: 0.8753 (mp0) REVERT: L 91 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9148 (mtp85) REVERT: L 122 GLN cc_start: 0.8378 (pt0) cc_final: 0.7705 (pm20) REVERT: L 166 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: L 170 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8841 (mp) REVERT: L 200 ARG cc_start: 0.9338 (ttm110) cc_final: 0.8989 (mtm-85) REVERT: L 203 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9350 (tp) REVERT: L 204 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8412 (tm-30) REVERT: M 51 TYR cc_start: 0.8228 (t80) cc_final: 0.8015 (t80) REVERT: M 59 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: M 122 GLN cc_start: 0.8388 (pt0) cc_final: 0.7723 (pm20) REVERT: M 166 GLN cc_start: 0.9151 (mt0) cc_final: 0.8699 (pt0) REVERT: M 185 GLU cc_start: 0.8929 (pt0) cc_final: 0.8647 (pt0) REVERT: M 197 GLU cc_start: 0.9274 (pm20) cc_final: 0.8784 (pm20) REVERT: M 200 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8869 (ppt170) REVERT: M 201 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8901 (mt-10) REVERT: M 204 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8368 (tm-30) REVERT: N 91 ARG cc_start: 0.9041 (pmm-80) cc_final: 0.8671 (pmm-80) REVERT: N 122 GLN cc_start: 0.7799 (mt0) cc_final: 0.7423 (mt0) REVERT: N 125 CYS cc_start: 0.9389 (t) cc_final: 0.9116 (t) REVERT: N 166 GLN cc_start: 0.8704 (mt0) cc_final: 0.8345 (tt0) REVERT: N 198 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9099 (tptp) REVERT: N 204 GLU cc_start: 0.9178 (tp30) cc_final: 0.8419 (tp30) outliers start: 77 outliers final: 24 residues processed: 495 average time/residue: 1.9163 time to fit residues: 1029.8919 Evaluate side-chains 492 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 452 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 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 39 ARG Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain 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 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 157 GLN 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 L residue 203 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 200 ARG 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: 0.8980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 155 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 97 GLN D 58 ASN E 35 GLN F 35 GLN G 35 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054744 restraints weight = 55500.477| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.87 r_work: 0.2658 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20069 Z= 0.155 Angle : 0.674 10.356 27111 Z= 0.343 Chirality : 0.043 0.173 3150 Planarity : 0.005 0.056 3556 Dihedral : 4.279 50.123 2800 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.28 % Allowed : 22.25 % Favored : 74.47 % 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: 2.04 (0.15), residues: 1372 sheet: 2.04 (0.31), residues: 224 loop : -0.25 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.024 0.001 PHE L 58 TYR 0.019 0.001 TYR N 159 ARG 0.012 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1054) hydrogen bonds : angle 3.70579 ( 3255) covalent geometry : bond 0.00372 (20041) covalent geometry : angle 0.67406 (27111) Misc. bond : bond 0.00038 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 485 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8867 (mm-40) REVERT: A 100 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8730 (mmtt) REVERT: A 163 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8881 (tmmm) REVERT: A 176 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8789 (t) REVERT: A 178 GLU cc_start: 0.9368 (pm20) cc_final: 0.9012 (pm20) REVERT: B 39 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8927 (mtp-110) REVERT: B 50 GLN cc_start: 0.9378 (pt0) cc_final: 0.9169 (pt0) REVERT: B 58 ASN cc_start: 0.9538 (m-40) cc_final: 0.9215 (m110) REVERT: B 156 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: B 163 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8958 (tmmm) REVERT: C 39 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8670 (mtp-110) REVERT: C 43 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9152 (mm-30) REVERT: C 97 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8917 (mm-40) REVERT: C 139 GLN cc_start: 0.8304 (tt0) cc_final: 0.7241 (tt0) REVERT: C 163 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8889 (tmmm) REVERT: D 42 ASN cc_start: 0.9594 (m-40) cc_final: 0.9148 (m110) REVERT: D 43 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9114 (mm-30) REVERT: D 100 LYS cc_start: 0.9029 (mptt) cc_final: 0.8633 (mptt) REVERT: D 194 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8642 (mt-10) REVERT: E 39 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8855 (mtp-110) REVERT: E 43 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9136 (mm-30) REVERT: E 50 GLN cc_start: 0.9456 (pt0) cc_final: 0.9201 (pt0) REVERT: E 97 GLN cc_start: 0.9352 (mm110) cc_final: 0.9019 (mm-40) REVERT: E 134 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8583 (mt-10) REVERT: E 163 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8836 (tmmm) REVERT: F 39 ARG cc_start: 0.9213 (ttp80) cc_final: 0.8825 (mtp-110) REVERT: F 50 GLN cc_start: 0.9376 (pt0) cc_final: 0.9157 (pt0) REVERT: F 100 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8710 (mmtt) REVERT: F 108 MET cc_start: 0.8836 (ptp) cc_final: 0.8623 (ptp) REVERT: F 194 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8793 (mt-10) REVERT: G 50 GLN cc_start: 0.9420 (pt0) cc_final: 0.9184 (pt0) REVERT: G 163 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8788 (tmmm) REVERT: H 84 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8731 (mm) REVERT: H 128 GLN cc_start: 0.9031 (tp40) cc_final: 0.8809 (tp40) REVERT: H 197 GLU cc_start: 0.9330 (pm20) cc_final: 0.9010 (pm20) REVERT: H 198 LYS cc_start: 0.9515 (tppp) cc_final: 0.9291 (tppp) REVERT: H 203 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9317 (tp) REVERT: H 222 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8772 (tp-100) REVERT: I 85 GLU cc_start: 0.8526 (pp20) cc_final: 0.8245 (pp20) REVERT: I 91 ARG cc_start: 0.9486 (mtp85) cc_final: 0.9258 (mtp85) REVERT: I 122 GLN cc_start: 0.8298 (pt0) cc_final: 0.7714 (pm20) REVERT: I 204 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8508 (tm-30) REVERT: J 144 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8521 (ptpp) REVERT: J 166 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7723 (tm-30) REVERT: J 187 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: J 203 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9209 (tp) REVERT: J 204 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8252 (tm-30) REVERT: K 58 PHE cc_start: 0.9257 (t80) cc_final: 0.8962 (t80) REVERT: K 85 GLU cc_start: 0.8669 (pp20) cc_final: 0.8427 (pp20) REVERT: K 91 ARG cc_start: 0.9188 (ttm110) cc_final: 0.8865 (ttm-80) REVERT: K 166 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: K 201 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8940 (mp0) REVERT: K 203 ILE cc_start: 0.9590 (tp) cc_final: 0.9376 (tp) REVERT: K 204 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8376 (tm-30) REVERT: L 91 ARG cc_start: 0.9486 (mtp-110) cc_final: 0.9171 (mtp85) REVERT: L 122 GLN cc_start: 0.8382 (pt0) cc_final: 0.7718 (pm20) REVERT: L 166 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: L 170 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8787 (mp) REVERT: L 200 ARG cc_start: 0.9316 (ttm110) cc_final: 0.8979 (mtm-85) REVERT: L 203 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9336 (tp) REVERT: L 204 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8424 (tm-30) REVERT: M 51 TYR cc_start: 0.8292 (t80) cc_final: 0.8075 (t80) REVERT: M 59 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: M 122 GLN cc_start: 0.8255 (pt0) cc_final: 0.7602 (pm20) REVERT: M 166 GLN cc_start: 0.9156 (mt0) cc_final: 0.8703 (pt0) REVERT: M 185 GLU cc_start: 0.8914 (pt0) cc_final: 0.8620 (pt0) REVERT: M 203 ILE cc_start: 0.9424 (tp) cc_final: 0.9208 (tp) REVERT: M 204 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8441 (tm-30) REVERT: N 91 ARG cc_start: 0.9066 (pmm-80) cc_final: 0.8659 (pmm-80) REVERT: N 122 GLN cc_start: 0.7797 (mt0) cc_final: 0.7418 (mt0) REVERT: N 152 ARG cc_start: 0.7671 (tmt170) cc_final: 0.7467 (ttt-90) REVERT: N 166 GLN cc_start: 0.8742 (mt0) cc_final: 0.8382 (tt0) REVERT: N 197 GLU cc_start: 0.9353 (mp0) cc_final: 0.9087 (pm20) REVERT: N 198 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9149 (tptp) REVERT: N 204 GLU cc_start: 0.9181 (tp30) cc_final: 0.8443 (tp30) outliers start: 68 outliers final: 21 residues processed: 508 average time/residue: 1.8943 time to fit residues: 1044.8057 Evaluate side-chains 499 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 459 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 163 LYS 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 G residue 59 LYS 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 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 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 157 GLN 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 L residue 203 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 195 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 35 GLN G 35 GLN H 157 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 150 ASN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054294 restraints weight = 55573.094| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.84 r_work: 0.2652 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20069 Z= 0.172 Angle : 0.699 10.842 27111 Z= 0.357 Chirality : 0.043 0.194 3150 Planarity : 0.005 0.074 3556 Dihedral : 4.267 47.859 2800 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.76 % Allowed : 23.36 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2464 helix: 2.00 (0.15), residues: 1386 sheet: 2.07 (0.32), residues: 224 loop : -0.19 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.014 0.001 PHE M 58 TYR 0.014 0.001 TYR B 93 ARG 0.009 0.001 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1054) hydrogen bonds : angle 3.74347 ( 3255) covalent geometry : bond 0.00413 (20041) covalent geometry : angle 0.69862 (27111) Misc. bond : bond 0.00044 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 468 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8877 (mm-40) REVERT: A 100 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8679 (mmtt) REVERT: A 176 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8830 (t) REVERT: A 178 GLU cc_start: 0.9381 (pm20) cc_final: 0.9052 (pm20) REVERT: B 39 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8936 (mtp-110) REVERT: B 50 GLN cc_start: 0.9384 (pt0) cc_final: 0.9170 (pt0) REVERT: B 58 ASN cc_start: 0.9528 (m-40) cc_final: 0.9210 (m110) REVERT: B 156 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8819 (mp0) REVERT: B 163 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8912 (tmmm) REVERT: B 205 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: C 39 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8682 (mtp-110) REVERT: C 43 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9140 (mm-30) REVERT: C 139 GLN cc_start: 0.8277 (tt0) cc_final: 0.7248 (tt0) REVERT: C 163 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8886 (tmmm) REVERT: C 205 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: D 39 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8648 (mtp-110) REVERT: D 42 ASN cc_start: 0.9603 (m-40) cc_final: 0.9189 (m110) REVERT: D 43 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9127 (mm-30) REVERT: D 100 LYS cc_start: 0.9024 (mptt) cc_final: 0.8626 (mptt) REVERT: D 194 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8667 (mt-10) REVERT: E 39 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8848 (mtp-110) REVERT: E 43 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9131 (mm-30) REVERT: E 50 GLN cc_start: 0.9453 (pt0) cc_final: 0.9201 (pt0) REVERT: E 134 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8672 (mt-10) REVERT: E 163 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8852 (tmmm) REVERT: F 39 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8816 (mtp-110) REVERT: F 108 MET cc_start: 0.8828 (ptp) cc_final: 0.8589 (ptp) REVERT: F 194 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8782 (mt-10) REVERT: G 50 GLN cc_start: 0.9412 (pt0) cc_final: 0.9195 (pt0) REVERT: G 163 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8808 (tmmm) REVERT: H 152 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6741 (tmt170) REVERT: H 203 ILE cc_start: 0.9585 (tp) cc_final: 0.9328 (tp) REVERT: H 222 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8833 (tp-100) REVERT: I 85 GLU cc_start: 0.8554 (pp20) cc_final: 0.8269 (pp20) REVERT: I 91 ARG cc_start: 0.9486 (mtp85) cc_final: 0.9253 (mtp85) REVERT: I 122 GLN cc_start: 0.8262 (pt0) cc_final: 0.7648 (pm20) REVERT: I 204 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8472 (tm-30) REVERT: J 144 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8666 (ptpp) REVERT: J 166 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7603 (mm-40) REVERT: J 187 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: J 203 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9216 (tp) REVERT: J 204 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8244 (tm-30) REVERT: K 58 PHE cc_start: 0.9249 (t80) cc_final: 0.8959 (t80) REVERT: K 85 GLU cc_start: 0.8738 (pp20) cc_final: 0.8519 (pp20) REVERT: K 91 ARG cc_start: 0.9183 (ttm110) cc_final: 0.8895 (ttp-110) REVERT: K 152 ARG cc_start: 0.7357 (tmt170) cc_final: 0.6967 (tmt170) REVERT: K 166 GLN cc_start: 0.8489 (tt0) cc_final: 0.7684 (tt0) REVERT: K 201 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: K 203 ILE cc_start: 0.9588 (tp) cc_final: 0.9385 (tp) REVERT: K 204 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8342 (tm-30) REVERT: L 91 ARG cc_start: 0.9485 (mtp-110) cc_final: 0.9173 (mtp85) REVERT: L 122 GLN cc_start: 0.8389 (pt0) cc_final: 0.7718 (pm20) REVERT: L 166 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: L 170 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8777 (mp) REVERT: L 203 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9347 (tp) REVERT: L 204 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8412 (tm-30) REVERT: M 51 TYR cc_start: 0.8279 (t80) cc_final: 0.8043 (t80) REVERT: M 122 GLN cc_start: 0.8332 (pt0) cc_final: 0.7640 (pm20) REVERT: M 166 GLN cc_start: 0.9142 (mt0) cc_final: 0.8670 (pt0) REVERT: M 185 GLU cc_start: 0.8924 (pt0) cc_final: 0.8614 (pt0) REVERT: M 200 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8925 (pmt-80) REVERT: M 204 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8391 (tm-30) REVERT: N 91 ARG cc_start: 0.9137 (pmm-80) cc_final: 0.8709 (pmm-80) REVERT: N 122 GLN cc_start: 0.7801 (mt0) cc_final: 0.7414 (mt0) REVERT: N 166 GLN cc_start: 0.8792 (mt0) cc_final: 0.8473 (mt0) REVERT: N 197 GLU cc_start: 0.9342 (mp0) cc_final: 0.9137 (pm20) REVERT: N 204 GLU cc_start: 0.9209 (tp30) cc_final: 0.8468 (tp30) outliers start: 78 outliers final: 27 residues processed: 502 average time/residue: 2.0050 time to fit residues: 1102.6142 Evaluate side-chains 503 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 457 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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 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 39 ARG Chi-restraints excluded: chain C residue 151 ILE 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 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 59 LYS Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 220 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN D 97 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 N 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055516 restraints weight = 55414.355| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.91 r_work: 0.2677 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20069 Z= 0.146 Angle : 0.729 11.968 27111 Z= 0.369 Chirality : 0.043 0.195 3150 Planarity : 0.005 0.084 3556 Dihedral : 4.141 37.999 2800 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.33 % Allowed : 24.57 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.18), residues: 2464 helix: 2.06 (0.15), residues: 1379 sheet: 1.90 (0.32), residues: 210 loop : -0.16 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.022 0.001 PHE L 58 TYR 0.021 0.001 TYR H 159 ARG 0.013 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 1054) hydrogen bonds : angle 3.68714 ( 3255) covalent geometry : bond 0.00359 (20041) covalent geometry : angle 0.72903 (27111) Misc. bond : bond 0.00027 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 475 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8839 (mm-40) REVERT: A 100 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8640 (mmtt) REVERT: A 108 MET cc_start: 0.8863 (ptp) cc_final: 0.8406 (ptp) REVERT: A 176 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 178 GLU cc_start: 0.9388 (pm20) cc_final: 0.9074 (pm20) REVERT: B 39 ARG cc_start: 0.9281 (ttp80) cc_final: 0.8952 (mtp-110) REVERT: B 50 GLN cc_start: 0.9383 (pt0) cc_final: 0.9122 (pt0) REVERT: B 58 ASN cc_start: 0.9529 (m-40) cc_final: 0.9191 (m110) REVERT: B 156 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8858 (mp0) REVERT: B 163 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8968 (tmmm) REVERT: B 205 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: C 39 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8697 (mtp-110) REVERT: C 43 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9123 (mm-30) REVERT: C 97 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8908 (mm-40) REVERT: C 139 GLN cc_start: 0.8187 (tt0) cc_final: 0.7031 (tt0) REVERT: C 163 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.8879 (tmmm) REVERT: D 39 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8625 (mtp-110) REVERT: D 42 ASN cc_start: 0.9584 (m-40) cc_final: 0.9173 (m110) REVERT: D 43 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9135 (mm-30) REVERT: D 100 LYS cc_start: 0.9027 (mptt) cc_final: 0.8642 (mptt) REVERT: D 194 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8633 (mt-10) REVERT: E 39 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8844 (mtp-110) REVERT: E 43 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9122 (mm-30) REVERT: E 50 GLN cc_start: 0.9444 (pt0) cc_final: 0.9208 (pt0) REVERT: E 134 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8645 (mt-10) REVERT: E 163 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8835 (tmmm) REVERT: F 39 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8802 (mtp-110) REVERT: F 108 MET cc_start: 0.8811 (ptp) cc_final: 0.8565 (ptp) REVERT: F 194 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8778 (mt-10) REVERT: F 205 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8507 (mmp) REVERT: G 50 GLN cc_start: 0.9425 (pt0) cc_final: 0.9176 (pt0) REVERT: G 163 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8786 (tmmm) REVERT: H 144 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8849 (ttmt) REVERT: H 150 ASN cc_start: 0.9410 (m110) cc_final: 0.9176 (m-40) REVERT: H 203 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9323 (tp) REVERT: H 222 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8822 (tp-100) REVERT: I 85 GLU cc_start: 0.8479 (pp20) cc_final: 0.8200 (pp20) REVERT: I 91 ARG cc_start: 0.9479 (mtp85) cc_final: 0.9246 (mtp85) REVERT: I 104 PHE cc_start: 0.8168 (t80) cc_final: 0.7949 (t80) REVERT: I 122 GLN cc_start: 0.8223 (pt0) cc_final: 0.7657 (pm20) REVERT: I 184 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8909 (mp) REVERT: I 204 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8527 (tm-30) REVERT: J 86 SER cc_start: 0.9236 (t) cc_final: 0.8999 (p) REVERT: J 144 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8519 (ptpp) REVERT: J 166 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7718 (tm-30) REVERT: J 203 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9205 (tp) REVERT: J 204 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8274 (tm-30) REVERT: K 58 PHE cc_start: 0.9245 (t80) cc_final: 0.8935 (t80) REVERT: K 59 GLU cc_start: 0.9181 (mp0) cc_final: 0.8730 (mp0) REVERT: K 85 GLU cc_start: 0.8777 (pp20) cc_final: 0.8521 (pp20) REVERT: K 91 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8888 (ttp-110) REVERT: K 166 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: K 185 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7457 (mt-10) REVERT: K 201 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (mp0) REVERT: K 203 ILE cc_start: 0.9582 (tp) cc_final: 0.9306 (tt) REVERT: K 204 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8387 (tm-30) REVERT: K 222 GLN cc_start: 0.9058 (tp40) cc_final: 0.8815 (tp40) REVERT: L 91 ARG cc_start: 0.9501 (mtp-110) cc_final: 0.9201 (mtp85) REVERT: L 122 GLN cc_start: 0.8380 (pt0) cc_final: 0.7701 (pm20) REVERT: L 152 ARG cc_start: 0.7567 (tmt170) cc_final: 0.7331 (tmt170) REVERT: L 166 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: L 170 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8772 (mp) REVERT: L 200 ARG cc_start: 0.9422 (ttm110) cc_final: 0.8884 (mtm110) REVERT: L 204 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8491 (tm-30) REVERT: M 51 TYR cc_start: 0.8291 (t80) cc_final: 0.7890 (t80) REVERT: M 122 GLN cc_start: 0.8221 (pt0) cc_final: 0.7551 (pm20) REVERT: M 166 GLN cc_start: 0.9131 (mt0) cc_final: 0.8662 (pt0) REVERT: M 185 GLU cc_start: 0.8895 (pt0) cc_final: 0.8580 (pt0) REVERT: M 204 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8492 (tm-30) REVERT: N 91 ARG cc_start: 0.9143 (pmm-80) cc_final: 0.8698 (pmm-80) REVERT: N 122 GLN cc_start: 0.7796 (mt0) cc_final: 0.7377 (mt0) REVERT: N 166 GLN cc_start: 0.8787 (mt0) cc_final: 0.8493 (mt0) REVERT: N 190 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8800 (tmmt) REVERT: N 198 LYS cc_start: 0.9462 (tppp) cc_final: 0.9089 (tptp) REVERT: N 200 ARG cc_start: 0.9034 (mmm160) cc_final: 0.8828 (mmm160) REVERT: N 204 GLU cc_start: 0.9234 (tp30) cc_final: 0.8545 (tp30) outliers start: 69 outliers final: 27 residues processed: 502 average time/residue: 1.8680 time to fit residues: 1018.4776 Evaluate side-chains 502 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 458 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 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 F residue 205 MET Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain 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 200 ARG 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: 0.9980 chunk 198 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 35 GLN F 35 GLN G 35 GLN H 157 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN K 150 ASN N 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054589 restraints weight = 55439.698| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.89 r_work: 0.2658 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20069 Z= 0.179 Angle : 0.767 12.661 27111 Z= 0.390 Chirality : 0.044 0.202 3150 Planarity : 0.005 0.091 3556 Dihedral : 4.218 39.801 2800 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.28 % Allowed : 25.14 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2464 helix: 1.96 (0.15), residues: 1379 sheet: 1.98 (0.33), residues: 210 loop : -0.19 (0.22), residues: 875 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 0.016 0.001 PHE I 104 TYR 0.030 0.001 TYR B 93 ARG 0.024 0.001 ARG K 200 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 1054) hydrogen bonds : angle 3.80704 ( 3255) covalent geometry : bond 0.00433 (20041) covalent geometry : angle 0.76737 (27111) Misc. bond : bond 0.00044 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 464 time to evaluate : 2.319 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: 0.9188 (mm-40) cc_final: 0.8852 (mm-40) REVERT: A 100 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8649 (mmtt) REVERT: A 108 MET cc_start: 0.8882 (ptp) cc_final: 0.8414 (ptp) REVERT: A 163 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.8882 (tmmm) REVERT: A 176 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8788 (t) REVERT: A 178 GLU cc_start: 0.9386 (pm20) cc_final: 0.9069 (pm20) REVERT: B 39 ARG cc_start: 0.9299 (ttp80) cc_final: 0.8961 (mtp-110) REVERT: B 50 GLN cc_start: 0.9373 (pt0) cc_final: 0.9108 (pt0) REVERT: B 54 ASP cc_start: 0.9239 (m-30) cc_final: 0.9015 (m-30) REVERT: B 58 ASN cc_start: 0.9530 (m-40) cc_final: 0.9128 (m110) REVERT: B 156 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: B 163 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8886 (tmmm) REVERT: C 39 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8723 (mtp-110) REVERT: C 43 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9137 (mm-30) REVERT: C 139 GLN cc_start: 0.8224 (tt0) cc_final: 0.7063 (tt0) REVERT: C 163 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8891 (tmmm) REVERT: D 39 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8641 (mtp-110) REVERT: D 42 ASN cc_start: 0.9597 (m-40) cc_final: 0.9178 (m110) REVERT: D 43 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9133 (mm-30) REVERT: D 93 TYR cc_start: 0.9400 (t80) cc_final: 0.9188 (t80) REVERT: D 100 LYS cc_start: 0.8986 (mptt) cc_final: 0.8597 (mptt) REVERT: D 156 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: D 194 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8609 (mt-10) REVERT: E 39 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8848 (mtp-110) REVERT: E 43 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9144 (mm-30) REVERT: E 50 GLN cc_start: 0.9436 (pt0) cc_final: 0.9197 (pt0) REVERT: E 134 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8725 (mt-10) REVERT: E 163 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8831 (tmmm) REVERT: F 39 ARG cc_start: 0.9197 (ttp80) cc_final: 0.8810 (mtp-110) REVERT: F 100 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8751 (mmtt) REVERT: F 108 MET cc_start: 0.8814 (ptp) cc_final: 0.8564 (ptp) REVERT: F 194 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8758 (mt-10) REVERT: F 205 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8519 (mmp) REVERT: G 50 GLN cc_start: 0.9407 (pt0) cc_final: 0.9192 (pt0) REVERT: G 163 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8795 (tmmm) REVERT: H 91 ARG cc_start: 0.9431 (ptm-80) cc_final: 0.9105 (ptp90) REVERT: H 144 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8807 (ttmt) REVERT: H 150 ASN cc_start: 0.9378 (m110) cc_final: 0.9118 (m-40) REVERT: H 152 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6680 (tmt170) REVERT: H 203 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9352 (tp) REVERT: H 222 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8838 (tp-100) REVERT: I 85 GLU cc_start: 0.8512 (pp20) cc_final: 0.8226 (pp20) REVERT: I 91 ARG cc_start: 0.9493 (mtp85) cc_final: 0.9256 (mtp85) REVERT: I 104 PHE cc_start: 0.8162 (t80) cc_final: 0.7904 (t80) REVERT: I 122 GLN cc_start: 0.8270 (pt0) cc_final: 0.7662 (pm20) REVERT: I 184 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8820 (mp) REVERT: I 204 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8513 (tm-30) REVERT: I 222 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8781 (tp40) REVERT: J 91 ARG cc_start: 0.9467 (mtp85) cc_final: 0.8940 (ptp-110) REVERT: J 144 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8513 (ptpp) REVERT: J 166 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7708 (mm-40) REVERT: J 187 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: J 203 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9228 (tp) REVERT: J 204 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8180 (tm-30) REVERT: K 58 PHE cc_start: 0.9248 (t80) cc_final: 0.8983 (t80) REVERT: K 59 GLU cc_start: 0.9185 (mp0) cc_final: 0.8879 (mp0) REVERT: K 85 GLU cc_start: 0.8825 (pp20) cc_final: 0.8599 (pp20) REVERT: K 91 ARG cc_start: 0.9150 (ttm110) cc_final: 0.8861 (ttp-110) REVERT: K 166 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: K 197 GLU cc_start: 0.9113 (pm20) cc_final: 0.8753 (pm20) REVERT: K 198 LYS cc_start: 0.9268 (tppp) cc_final: 0.8903 (tppp) REVERT: K 201 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: K 203 ILE cc_start: 0.9522 (tp) cc_final: 0.9260 (tp) REVERT: K 204 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8339 (tm-30) REVERT: L 86 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8794 (t) REVERT: L 91 ARG cc_start: 0.9485 (mtp-110) cc_final: 0.9177 (mtp85) REVERT: L 122 GLN cc_start: 0.8384 (pt0) cc_final: 0.7724 (pm20) REVERT: L 152 ARG cc_start: 0.7718 (tmt170) cc_final: 0.7202 (tmt170) REVERT: L 166 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: L 170 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8764 (mp) REVERT: L 200 ARG cc_start: 0.9404 (ttm110) cc_final: 0.8821 (mtm-85) REVERT: L 204 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8429 (tm-30) REVERT: M 51 TYR cc_start: 0.8293 (t80) cc_final: 0.7892 (t80) REVERT: M 122 GLN cc_start: 0.8325 (pt0) cc_final: 0.7611 (pm20) REVERT: M 185 GLU cc_start: 0.8922 (pt0) cc_final: 0.8628 (pt0) REVERT: M 204 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8420 (tm-30) REVERT: N 91 ARG cc_start: 0.9143 (pmm-80) cc_final: 0.8662 (pmm-80) REVERT: N 122 GLN cc_start: 0.7782 (mt0) cc_final: 0.7382 (mt0) REVERT: N 152 ARG cc_start: 0.7728 (tmt170) cc_final: 0.7417 (tmt170) REVERT: N 166 GLN cc_start: 0.8826 (mt0) cc_final: 0.8546 (mt0) REVERT: N 198 LYS cc_start: 0.9512 (tppp) cc_final: 0.9138 (tptp) REVERT: N 204 GLU cc_start: 0.9235 (tp30) cc_final: 0.8515 (tp30) REVERT: N 222 GLN cc_start: 0.8961 (tp40) cc_final: 0.8676 (tp40) outliers start: 68 outliers final: 30 residues processed: 493 average time/residue: 1.9008 time to fit residues: 1016.4176 Evaluate side-chains 508 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 457 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 151 ILE 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 60 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 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 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 59 GLU 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 157 GLN 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 59 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 200 ARG 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 151 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 35 GLN F 35 GLN F 50 GLN F 97 GLN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 122 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 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 = 0.3062 r_free = 0.3062 target = 0.065327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053087 restraints weight = 56150.459| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.86 r_work: 0.2616 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20069 Z= 0.240 Angle : 0.818 12.947 27111 Z= 0.421 Chirality : 0.045 0.212 3150 Planarity : 0.005 0.115 3556 Dihedral : 4.470 45.963 2800 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.28 % Allowed : 25.53 % Favored : 71.19 % 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: 1.63 (0.18), residues: 2464 helix: 1.77 (0.15), residues: 1372 sheet: 2.14 (0.32), residues: 224 loop : -0.29 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.023 0.001 PHE L 58 TYR 0.024 0.001 TYR B 93 ARG 0.012 0.001 ARG K 200 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1054) hydrogen bonds : angle 4.06810 ( 3255) covalent geometry : bond 0.00566 (20041) covalent geometry : angle 0.81797 (27111) Misc. bond : bond 0.00071 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 457 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8935 (ptp) cc_final: 0.8463 (ptp) REVERT: A 163 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.8905 (tmmm) REVERT: A 176 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8829 (t) REVERT: A 178 GLU cc_start: 0.9385 (pm20) cc_final: 0.9074 (pm20) REVERT: B 39 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8960 (mtp-110) REVERT: B 50 GLN cc_start: 0.9384 (pt0) cc_final: 0.9147 (pt0) REVERT: B 58 ASN cc_start: 0.9542 (m-40) cc_final: 0.9254 (m110) REVERT: B 156 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: B 163 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.8911 (tmmm) REVERT: C 39 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8669 (mtp-110) REVERT: C 163 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.8915 (tmmm) REVERT: D 39 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8683 (mtp-110) REVERT: D 42 ASN cc_start: 0.9592 (m-40) cc_final: 0.9157 (m110) REVERT: D 43 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9144 (mm-30) REVERT: D 194 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8661 (mt-10) REVERT: E 39 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8854 (mtp-110) REVERT: E 43 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9173 (mm-30) REVERT: E 50 GLN cc_start: 0.9453 (pt0) cc_final: 0.9203 (pt0) REVERT: E 134 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8753 (mt-10) REVERT: E 163 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8878 (tmmm) REVERT: F 39 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8816 (mtp-110) REVERT: F 108 MET cc_start: 0.8866 (ptp) cc_final: 0.8602 (ptp) REVERT: F 194 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8802 (mt-10) REVERT: G 50 GLN cc_start: 0.9424 (pt0) cc_final: 0.9180 (pt0) REVERT: H 91 ARG cc_start: 0.9389 (ptm-80) cc_final: 0.9080 (ptp90) REVERT: H 144 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8709 (ttmt) REVERT: H 203 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9368 (tp) REVERT: H 222 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8825 (tp-100) REVERT: I 85 GLU cc_start: 0.8559 (pp20) cc_final: 0.8291 (pp20) REVERT: I 91 ARG cc_start: 0.9472 (mtp85) cc_final: 0.9260 (mtp85) REVERT: I 104 PHE cc_start: 0.8156 (t80) cc_final: 0.7898 (t80) REVERT: I 122 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: I 184 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8819 (mp) REVERT: I 197 GLU cc_start: 0.9242 (mp0) cc_final: 0.8832 (mp0) REVERT: I 201 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8245 (mp0) REVERT: I 204 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8618 (tm-30) REVERT: J 91 ARG cc_start: 0.9416 (mtp85) cc_final: 0.8938 (ptp-110) REVERT: J 144 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8489 (ptpp) REVERT: J 166 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7589 (mm-40) REVERT: J 187 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: J 198 LYS cc_start: 0.9461 (tppp) cc_final: 0.9221 (tppp) REVERT: J 203 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9256 (tp) REVERT: J 204 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8337 (tm-30) REVERT: K 58 PHE cc_start: 0.9260 (t80) cc_final: 0.8986 (t80) REVERT: K 91 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8836 (ttp-110) REVERT: K 166 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: K 201 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: K 204 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8339 (tm-30) REVERT: L 60 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9124 (mm-30) REVERT: L 91 ARG cc_start: 0.9471 (mtp-110) cc_final: 0.9170 (mtp85) REVERT: L 122 GLN cc_start: 0.8414 (pt0) cc_final: 0.7700 (pm20) REVERT: L 152 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7044 (tmt170) REVERT: L 170 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8787 (mp) REVERT: L 200 ARG cc_start: 0.9402 (ttm110) cc_final: 0.8852 (mtm-85) REVERT: L 204 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8446 (tm-30) REVERT: M 51 TYR cc_start: 0.8295 (t80) cc_final: 0.8079 (t80) REVERT: M 122 GLN cc_start: 0.8389 (pt0) cc_final: 0.7703 (pm20) REVERT: M 152 ARG cc_start: 0.7660 (tmt170) cc_final: 0.7242 (tmt170) REVERT: M 166 GLN cc_start: 0.9155 (mt0) cc_final: 0.8756 (pt0) REVERT: M 185 GLU cc_start: 0.8919 (pt0) cc_final: 0.8622 (pt0) REVERT: M 204 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8436 (tm-30) REVERT: N 91 ARG cc_start: 0.9127 (pmm-80) cc_final: 0.8621 (pmm-80) REVERT: N 122 GLN cc_start: 0.7903 (mt0) cc_final: 0.7473 (mt0) REVERT: N 166 GLN cc_start: 0.8849 (mt0) cc_final: 0.8571 (mt0) REVERT: N 198 LYS cc_start: 0.9488 (tppp) cc_final: 0.9139 (tptp) REVERT: N 203 ILE cc_start: 0.9569 (tp) cc_final: 0.9362 (tp) REVERT: N 204 GLU cc_start: 0.9227 (tp30) cc_final: 0.8485 (tp30) outliers start: 68 outliers final: 30 residues processed: 486 average time/residue: 1.8897 time to fit residues: 996.0414 Evaluate side-chains 494 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 447 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN 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 180 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 200 ARG 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: 4.9990 chunk 231 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 35 GLN E 97 GLN F 35 GLN F 50 GLN F 97 GLN G 35 GLN I 150 ASN I 157 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN N 80 GLN N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055026 restraints weight = 56003.241| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.92 r_work: 0.2664 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20069 Z= 0.158 Angle : 0.806 12.977 27111 Z= 0.412 Chirality : 0.044 0.215 3150 Planarity : 0.005 0.106 3556 Dihedral : 4.292 29.215 2800 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.65 % Allowed : 26.21 % Favored : 71.14 % 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: 1.86 (0.15), residues: 1372 sheet: 2.07 (0.31), residues: 224 loop : -0.30 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 189 HIS 0.003 0.000 HIS G 138 PHE 0.017 0.001 PHE M 58 TYR 0.026 0.001 TYR D 93 ARG 0.010 0.001 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 1054) hydrogen bonds : angle 3.93122 ( 3255) covalent geometry : bond 0.00388 (20041) covalent geometry : angle 0.80610 (27111) Misc. bond : bond 0.00029 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16979.82 seconds wall clock time: 288 minutes 36.45 seconds (17316.45 seconds total)