Starting phenix.real_space_refine on Mon Jul 22 19:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/07_2024/8xop_38537.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 12474 2.51 5 N 3304 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "L PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.76, per 1000 atoms: 0.55 Number of scatterers: 19740 At special positions: 0 Unit cell: (115.92, 116.76, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3857 8.00 N 3304 7.00 C 12474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 3.9 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 42 sheets defined 51.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 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: 6.88 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3461 1.32 - 1.44: 4785 1.44 - 1.56: 11599 1.56 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 20041 Sorted by residual: bond pdb=" C3 OTT U 1 " pdb=" C4 OTT U 1 " ideal model delta sigma weight residual 1.445 1.388 0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C3 OTT T 1 " pdb=" C4 OTT T 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C3 OTT S 1 " pdb=" C4 OTT S 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C3 OTT R 1 " pdb=" C4 OTT R 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" C3 OTT W 1 " pdb=" C4 OTT W 1 " ideal model delta sigma weight residual 1.445 1.389 0.056 2.00e-02 2.50e+03 7.81e+00 ... (remaining 20036 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.53: 510 105.53 - 112.63: 10677 112.63 - 119.73: 6386 119.73 - 126.84: 9359 126.84 - 133.94: 179 Bond angle restraints: 27111 Sorted by residual: angle pdb=" N GLU J 185 " pdb=" CA GLU J 185 " pdb=" CB GLU J 185 " ideal model delta sigma weight residual 110.28 116.90 -6.62 1.55e+00 4.16e-01 1.82e+01 angle pdb=" C VAL L 77 " pdb=" N MET L 78 " pdb=" CA MET L 78 " ideal model delta sigma weight residual 121.14 113.88 7.26 1.75e+00 3.27e-01 1.72e+01 angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta sigma weight residual 110.12 115.46 -5.34 1.47e+00 4.63e-01 1.32e+01 angle pdb=" C VAL K 77 " pdb=" N MET K 78 " pdb=" CA MET K 78 " ideal model delta sigma weight residual 121.14 114.82 6.32 1.75e+00 3.27e-01 1.31e+01 angle pdb=" N GLU E 156 " pdb=" CA GLU E 156 " pdb=" CB GLU E 156 " ideal model delta sigma weight residual 110.22 115.64 -5.42 1.54e+00 4.22e-01 1.24e+01 ... (remaining 27106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11342 17.94 - 35.89: 699 35.89 - 53.83: 118 53.83 - 71.77: 23 71.77 - 89.71: 19 Dihedral angle restraints: 12201 sinusoidal: 4774 harmonic: 7427 Sorted by residual: dihedral pdb=" CA ARG A 44 " pdb=" C ARG A 44 " pdb=" N ILE A 45 " pdb=" CA ILE A 45 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA b 6 " pdb=" C ALA b 6 " pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " ideal model delta harmonic sigma weight residual 0.00 -26.87 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ALA W 6 " pdb=" C ALA W 6 " pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " ideal model delta harmonic sigma weight residual 0.00 -26.59 26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 12198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2253 0.040 - 0.080: 600 0.080 - 0.120: 257 0.120 - 0.160: 26 0.160 - 0.200: 14 Chirality restraints: 3150 Sorted by residual: chirality pdb=" CG MP8 b 7 " pdb=" CB MP8 b 7 " pdb=" CD MP8 b 7 " pdb=" CE MP8 b 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CG MP8 V 7 " pdb=" CB MP8 V 7 " pdb=" CD MP8 V 7 " pdb=" CE MP8 V 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CG MP8 X 7 " pdb=" CB MP8 X 7 " pdb=" CD MP8 X 7 " pdb=" CE MP8 X 7 " both_signs ideal model delta sigma weight residual False 2.67 2.87 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3147 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 OTT b 1 " 0.075 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C6 OTT b 1 " -0.075 2.00e-02 2.50e+03 pdb=" C7 OTT b 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 OTT b 1 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 OTT Y 1 " 0.072 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" C6 OTT Y 1 " -0.073 2.00e-02 2.50e+03 pdb=" C7 OTT Y 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 OTT Y 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 OTT a 1 " -0.037 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C2 OTT a 1 " 0.036 2.00e-02 2.50e+03 pdb=" C3 OTT a 1 " 0.041 2.00e-02 2.50e+03 pdb=" C4 OTT a 1 " -0.040 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 417 2.68 - 3.23: 19673 3.23 - 3.79: 31202 3.79 - 4.34: 40491 4.34 - 4.90: 67808 Nonbonded interactions: 159591 Sorted by model distance: nonbonded pdb=" OE1 GLN C 139 " pdb=" NE2 GLN K 166 " model vdw 2.120 2.520 nonbonded pdb=" NH2 ARG A 164 " pdb=" OE1 GLU A 167 " model vdw 2.182 2.520 nonbonded pdb=" NH2 ARG F 164 " pdb=" OE1 GLU F 167 " model vdw 2.191 2.520 nonbonded pdb=" NH2 ARG D 164 " pdb=" OE1 GLU D 167 " model vdw 2.197 2.520 nonbonded pdb=" NH2 ARG E 164 " pdb=" OE1 GLU E 167 " model vdw 2.197 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 55.940 Find NCS groups from input model: 0.930 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20041 Z= 0.303 Angle : 0.691 8.958 27111 Z= 0.356 Chirality : 0.045 0.200 3150 Planarity : 0.006 0.074 3556 Dihedral : 12.473 89.713 7399 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2464 helix: 1.54 (0.15), residues: 1358 sheet: 1.74 (0.34), residues: 245 loop : -0.21 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.002 0.000 HIS G 138 PHE 0.022 0.001 PHE I 104 TYR 0.020 0.001 TYR H 51 ARG 0.009 0.001 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 2.431 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: 1.8745 time to fit residues: 1096.6775 Evaluate side-chains 427 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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: 5.9990 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 186 optimal weight: 0.0040 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 50 GLN D 58 ASN D 63 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 122 GLN I 150 ASN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 80 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20041 Z= 0.304 Angle : 0.629 8.194 27111 Z= 0.324 Chirality : 0.043 0.165 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.295 40.590 2800 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 3.81 % Allowed : 14.58 % Favored : 81.61 % 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: 1.90 (0.14), residues: 1372 sheet: 1.72 (0.34), residues: 245 loop : -0.16 (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 0.025 0.001 PHE L 58 TYR 0.019 0.001 TYR H 51 ARG 0.008 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 469 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8731 (mm-40) REVERT: B 50 GLN cc_start: 0.9206 (pt0) cc_final: 0.8966 (pt0) REVERT: B 100 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8362 (mmtt) REVERT: B 205 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: C 43 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9005 (mm-30) REVERT: C 97 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8749 (mm-40) REVERT: D 43 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8994 (mm-30) REVERT: D 100 LYS cc_start: 0.8963 (mmtm) cc_final: 0.8610 (mptt) REVERT: D 194 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8258 (mt-10) REVERT: E 43 GLU cc_start: 0.9250 (mm-30) cc_final: 0.9018 (mm-30) REVERT: E 97 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8909 (mm-40) REVERT: E 134 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8461 (mt-10) REVERT: F 43 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9040 (mm-30) REVERT: F 50 GLN cc_start: 0.9236 (pt0) cc_final: 0.8998 (pt0) REVERT: F 100 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8403 (mmtt) REVERT: F 108 MET cc_start: 0.8494 (ptp) cc_final: 0.8095 (ptp) REVERT: G 50 GLN cc_start: 0.9212 (pt0) cc_final: 0.8961 (pt0) REVERT: G 74 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8691 (p0) REVERT: G 150 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8408 (p0) REVERT: H 59 GLU cc_start: 0.8981 (mp0) cc_final: 0.8659 (mp0) REVERT: H 204 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7924 (tm-30) REVERT: I 85 GLU cc_start: 0.8290 (pp20) cc_final: 0.8033 (pp20) REVERT: J 166 GLN cc_start: 0.7301 (mm-40) cc_final: 0.7045 (mm-40) REVERT: J 204 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7798 (tm-30) REVERT: K 87 MET cc_start: 0.6878 (mtt) cc_final: 0.6612 (mtm) REVERT: K 91 ARG cc_start: 0.9230 (ttm110) cc_final: 0.8633 (ttm110) REVERT: K 152 ARG cc_start: 0.7243 (tmt170) cc_final: 0.6995 (tmt170) REVERT: K 166 GLN cc_start: 0.7897 (tt0) cc_final: 0.7512 (tt0) REVERT: K 197 GLU cc_start: 0.9112 (pm20) cc_final: 0.8776 (pm20) REVERT: K 201 GLU cc_start: 0.8953 (mp0) cc_final: 0.8619 (mp0) REVERT: K 203 ILE cc_start: 0.9574 (tp) cc_final: 0.9247 (tp) REVERT: K 204 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8026 (tm-30) REVERT: L 91 ARG cc_start: 0.9314 (mtp-110) cc_final: 0.9100 (mmm-85) REVERT: L 198 LYS cc_start: 0.9398 (tppp) cc_final: 0.9077 (tppp) REVERT: M 51 TYR cc_start: 0.8262 (t80) cc_final: 0.8034 (t80) REVERT: M 60 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8922 (mm-30) REVERT: M 185 GLU cc_start: 0.8593 (pt0) cc_final: 0.8295 (pt0) REVERT: M 204 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7975 (tm-30) REVERT: N 60 GLU cc_start: 0.8496 (mp0) cc_final: 0.8275 (mp0) REVERT: N 91 ARG cc_start: 0.9095 (ptp90) cc_final: 0.8728 (pmm-80) REVERT: N 122 GLN cc_start: 0.7103 (mt0) cc_final: 0.6753 (mt0) REVERT: N 166 GLN cc_start: 0.7993 (mm110) cc_final: 0.7724 (mm-40) REVERT: N 176 GLU cc_start: 0.8826 (tp30) cc_final: 0.8613 (tp30) REVERT: N 198 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9101 (tptp) REVERT: N 204 GLU cc_start: 0.8688 (tp30) cc_final: 0.7952 (tp30) outliers start: 79 outliers final: 24 residues processed: 492 average time/residue: 1.8410 time to fit residues: 984.0747 Evaluate side-chains 468 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 441 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN G 35 GLN I 122 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20041 Z= 0.305 Angle : 0.628 9.274 27111 Z= 0.322 Chirality : 0.042 0.162 3150 Planarity : 0.005 0.055 3556 Dihedral : 4.352 32.444 2800 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.05 % Allowed : 17.81 % Favored : 78.14 % 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: 1.76 (0.17), residues: 2464 helix: 1.96 (0.14), residues: 1372 sheet: 1.87 (0.32), residues: 259 loop : -0.40 (0.22), residues: 833 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 0.019 0.001 PHE M 58 TYR 0.016 0.001 TYR H 51 ARG 0.014 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 459 time to evaluate : 2.373 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: 0.9084 (mm-40) cc_final: 0.8778 (mm-40) REVERT: B 39 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8837 (mtp-110) REVERT: B 50 GLN cc_start: 0.9214 (pt0) cc_final: 0.8968 (pt0) REVERT: B 100 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8412 (mptt) REVERT: B 156 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: B 163 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8981 (tmmm) REVERT: C 39 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8641 (mtp-110) REVERT: C 43 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9005 (mm-30) REVERT: C 54 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8793 (m-30) REVERT: C 97 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8992 (mm-40) REVERT: C 163 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8713 (tmmm) REVERT: D 39 ARG cc_start: 0.8941 (ttp-110) cc_final: 0.8587 (mtp-110) REVERT: D 43 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8995 (mm-30) REVERT: D 100 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8602 (mptt) REVERT: D 194 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8332 (mt-10) REVERT: E 43 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9018 (mm-30) REVERT: E 50 GLN cc_start: 0.9394 (pt0) cc_final: 0.9157 (pt0) REVERT: E 97 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8869 (mm-40) REVERT: E 134 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8445 (mt-10) REVERT: E 163 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8732 (tmmm) REVERT: F 39 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8810 (mtp-110) REVERT: F 43 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9032 (mm-30) REVERT: F 50 GLN cc_start: 0.9222 (pt0) cc_final: 0.8888 (pt0) REVERT: F 100 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8462 (mmtt) REVERT: G 50 GLN cc_start: 0.9205 (pt0) cc_final: 0.8933 (pt0) REVERT: G 74 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8736 (p0) REVERT: G 150 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8414 (p0) REVERT: G 156 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: G 163 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8679 (tmmm) REVERT: H 91 ARG cc_start: 0.9351 (ptm160) cc_final: 0.9065 (ptp90) REVERT: H 128 GLN cc_start: 0.8917 (tp40) cc_final: 0.8695 (tp40) REVERT: H 203 ILE cc_start: 0.9508 (tp) cc_final: 0.9255 (tp) REVERT: H 204 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7708 (tm-30) REVERT: I 85 GLU cc_start: 0.8324 (pp20) cc_final: 0.8111 (pp20) REVERT: I 118 LYS cc_start: 0.8652 (mptt) cc_final: 0.8377 (tptp) REVERT: I 204 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8038 (tm-30) REVERT: J 59 GLU cc_start: 0.8859 (mp0) cc_final: 0.8545 (mp0) REVERT: J 60 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8951 (mm-30) REVERT: J 91 ARG cc_start: 0.9265 (mtp85) cc_final: 0.8772 (ttm110) REVERT: J 144 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8344 (ptpp) REVERT: J 166 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7031 (mm-40) REVERT: J 170 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8881 (mp) REVERT: J 203 ILE cc_start: 0.9452 (tp) cc_final: 0.9172 (tp) REVERT: J 204 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7802 (tm-30) REVERT: K 87 MET cc_start: 0.6946 (mtt) cc_final: 0.6671 (mtm) REVERT: K 91 ARG cc_start: 0.9193 (ttm110) cc_final: 0.8718 (ttm110) REVERT: K 166 GLN cc_start: 0.7876 (tt0) cc_final: 0.7522 (tt0) REVERT: K 198 LYS cc_start: 0.9180 (tppp) cc_final: 0.8970 (tppp) REVERT: K 203 ILE cc_start: 0.9544 (tp) cc_final: 0.9323 (tp) REVERT: K 204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7994 (tm-30) REVERT: L 91 ARG cc_start: 0.9302 (mtp-110) cc_final: 0.9086 (mmm-85) REVERT: L 200 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8508 (mtm110) REVERT: M 51 TYR cc_start: 0.8318 (t80) cc_final: 0.8069 (t80) REVERT: M 60 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9024 (mm-30) REVERT: M 91 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.9090 (mmm-85) REVERT: M 185 GLU cc_start: 0.8637 (pt0) cc_final: 0.8358 (pt0) REVERT: M 204 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7977 (tm-30) REVERT: N 122 GLN cc_start: 0.7052 (mt0) cc_final: 0.6727 (mt0) REVERT: N 198 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9124 (tptp) REVERT: N 204 GLU cc_start: 0.8687 (tp30) cc_final: 0.7860 (tm-30) outliers start: 84 outliers final: 37 residues processed: 487 average time/residue: 1.8496 time to fit residues: 978.5102 Evaluate side-chains 493 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 444 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 ASP 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 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.1980 chunk 217 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN B 97 GLN E 35 GLN G 35 GLN H 157 GLN K 80 GLN N 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20041 Z= 0.226 Angle : 0.601 9.036 27111 Z= 0.308 Chirality : 0.042 0.163 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.214 28.858 2800 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.67 % Allowed : 19.55 % Favored : 76.79 % 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: 2.02 (0.14), residues: 1386 sheet: 2.15 (0.32), residues: 224 loop : -0.23 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 189 HIS 0.003 0.000 HIS G 138 PHE 0.031 0.001 PHE L 58 TYR 0.018 0.001 TYR M 159 ARG 0.014 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 473 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8736 (mm-40) REVERT: A 176 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8803 (t) REVERT: A 178 GLU cc_start: 0.9211 (pm20) cc_final: 0.8846 (pm20) REVERT: B 39 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8838 (mtp-110) REVERT: B 50 GLN cc_start: 0.9213 (pt0) cc_final: 0.8925 (pt0) REVERT: B 156 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: C 43 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8979 (mm-30) REVERT: C 54 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: C 97 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8781 (mm-40) REVERT: C 100 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8411 (mmtt) REVERT: C 163 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8719 (tmmm) REVERT: D 39 ARG cc_start: 0.8908 (ttp-110) cc_final: 0.8581 (mtp-110) REVERT: D 43 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8997 (mm-30) REVERT: D 156 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: E 39 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8757 (mtp-110) REVERT: E 43 GLU cc_start: 0.9220 (mm-30) cc_final: 0.9001 (mm-30) REVERT: E 50 GLN cc_start: 0.9345 (pt0) cc_final: 0.9062 (pt0) REVERT: E 97 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9031 (mm110) REVERT: E 156 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: E 163 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8712 (tmmm) REVERT: F 39 ARG cc_start: 0.9168 (ttp80) cc_final: 0.8766 (mtp-110) REVERT: F 43 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9020 (mm-30) REVERT: F 50 GLN cc_start: 0.9202 (pt0) cc_final: 0.8870 (pt0) REVERT: F 108 MET cc_start: 0.8513 (ptp) cc_final: 0.8263 (ptp) REVERT: F 156 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: G 50 GLN cc_start: 0.9188 (pt0) cc_final: 0.8921 (pt0) REVERT: G 74 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8768 (p0) REVERT: G 156 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: G 163 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8677 (tmmm) REVERT: H 84 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8768 (mm) REVERT: H 91 ARG cc_start: 0.9318 (ptm160) cc_final: 0.8522 (ptp90) REVERT: H 144 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8698 (ttmp) REVERT: H 203 ILE cc_start: 0.9517 (tp) cc_final: 0.9243 (tp) REVERT: H 204 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7687 (tm-30) REVERT: I 85 GLU cc_start: 0.8295 (pp20) cc_final: 0.8021 (pp20) REVERT: I 118 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8400 (tptp) REVERT: I 204 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8043 (tm-30) REVERT: J 91 ARG cc_start: 0.9272 (mtp85) cc_final: 0.8761 (ttm110) REVERT: J 144 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8405 (ptpp) REVERT: J 166 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7104 (mm-40) REVERT: J 187 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: J 203 ILE cc_start: 0.9449 (tp) cc_final: 0.9169 (tp) REVERT: J 204 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7861 (tm-30) REVERT: K 58 PHE cc_start: 0.9126 (t80) cc_final: 0.8839 (t80) REVERT: K 78 MET cc_start: 0.8932 (pmm) cc_final: 0.8666 (pmm) REVERT: K 87 MET cc_start: 0.6986 (mtt) cc_final: 0.6701 (mtm) REVERT: K 91 ARG cc_start: 0.9171 (ttm110) cc_final: 0.8566 (ttm110) REVERT: K 152 ARG cc_start: 0.7258 (tmt170) cc_final: 0.6988 (tmt170) REVERT: K 166 GLN cc_start: 0.7869 (tt0) cc_final: 0.7389 (tt0) REVERT: K 197 GLU cc_start: 0.9043 (pm20) cc_final: 0.8760 (pm20) REVERT: K 198 LYS cc_start: 0.9191 (tppp) cc_final: 0.8986 (tppp) REVERT: K 200 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8216 (mmm160) REVERT: K 201 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: K 203 ILE cc_start: 0.9578 (tp) cc_final: 0.9287 (tp) REVERT: K 204 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8116 (tm-30) REVERT: L 91 ARG cc_start: 0.9312 (mtp-110) cc_final: 0.9092 (mmm-85) REVERT: L 166 GLN cc_start: 0.7931 (tt0) cc_final: 0.7323 (tt0) REVERT: L 170 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8602 (mp) REVERT: L 198 LYS cc_start: 0.9411 (tppp) cc_final: 0.9128 (tppp) REVERT: L 203 ILE cc_start: 0.9488 (tp) cc_final: 0.9270 (tp) REVERT: M 51 TYR cc_start: 0.8300 (t80) cc_final: 0.8087 (t80) REVERT: M 60 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9007 (mm-30) REVERT: M 91 ARG cc_start: 0.9304 (mtp-110) cc_final: 0.9097 (mmm-85) REVERT: M 185 GLU cc_start: 0.8647 (pt0) cc_final: 0.8324 (pt0) REVERT: M 190 LYS cc_start: 0.9279 (tppt) cc_final: 0.9045 (ttpp) REVERT: M 198 LYS cc_start: 0.9229 (tppp) cc_final: 0.9028 (tppp) REVERT: M 200 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8536 (ppt170) REVERT: M 204 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7967 (tm-30) REVERT: N 122 GLN cc_start: 0.6957 (mt0) cc_final: 0.6620 (mt0) REVERT: N 197 GLU cc_start: 0.9218 (mp0) cc_final: 0.8993 (pm20) REVERT: N 198 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9157 (tptp) REVERT: N 204 GLU cc_start: 0.8715 (tp30) cc_final: 0.7807 (tp30) outliers start: 76 outliers final: 28 residues processed: 502 average time/residue: 1.8016 time to fit residues: 983.5394 Evaluate side-chains 491 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 445 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP 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 B residue 150 ASP Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 169 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN B 97 GLN C 50 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 97 GLN G 35 GLN G 132 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 GLN I 150 ASN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20041 Z= 0.351 Angle : 0.647 9.742 27111 Z= 0.332 Chirality : 0.043 0.171 3150 Planarity : 0.005 0.054 3556 Dihedral : 4.274 28.296 2800 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 4.97 % Allowed : 20.99 % Favored : 74.03 % 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: 1.84 (0.18), residues: 2464 helix: 1.96 (0.14), residues: 1386 sheet: 2.13 (0.32), residues: 224 loop : -0.25 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 189 HIS 0.003 0.001 HIS B 138 PHE 0.012 0.001 PHE I 104 TYR 0.021 0.001 TYR B 93 ARG 0.014 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 450 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8813 (mm-40) REVERT: A 100 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8564 (mmtm) REVERT: A 176 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8798 (t) REVERT: A 178 GLU cc_start: 0.9186 (pm20) cc_final: 0.8783 (pm20) REVERT: B 39 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8858 (mtp-110) REVERT: B 50 GLN cc_start: 0.9220 (pt0) cc_final: 0.8977 (pt0) REVERT: B 156 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: B 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8836 (tmmm) REVERT: C 39 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8620 (mtp-110) REVERT: C 43 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8989 (mm-30) REVERT: C 54 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8827 (m-30) REVERT: C 100 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8479 (mmtt) REVERT: C 163 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8741 (tmmm) REVERT: D 43 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9009 (mm-30) REVERT: E 39 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8795 (mtp-110) REVERT: E 50 GLN cc_start: 0.9349 (pt0) cc_final: 0.9039 (pt0) REVERT: E 156 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: F 39 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8774 (mtp-110) REVERT: F 43 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9038 (mm-30) REVERT: F 50 GLN cc_start: 0.9209 (pt0) cc_final: 0.8946 (pt0) REVERT: F 54 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8817 (m-30) REVERT: F 108 MET cc_start: 0.8549 (ptp) cc_final: 0.8281 (ptp) REVERT: F 156 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: G 50 GLN cc_start: 0.9202 (pt0) cc_final: 0.8919 (pt0) REVERT: G 74 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8844 (p0) REVERT: G 156 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: H 84 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (mm) REVERT: H 91 ARG cc_start: 0.9307 (ptm160) cc_final: 0.8513 (ptp90) REVERT: H 144 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8775 (ttmt) REVERT: H 203 ILE cc_start: 0.9520 (tp) cc_final: 0.9245 (tp) REVERT: H 204 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7726 (tm-30) REVERT: H 222 GLN cc_start: 0.8788 (tp40) cc_final: 0.8562 (tp40) REVERT: I 85 GLU cc_start: 0.8386 (pp20) cc_final: 0.8114 (pp20) REVERT: I 118 LYS cc_start: 0.8700 (mptt) cc_final: 0.8319 (tptp) REVERT: I 203 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9228 (tp) REVERT: I 204 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8032 (tm-30) REVERT: J 144 LYS cc_start: 0.8821 (ptpp) cc_final: 0.8389 (ptpp) REVERT: J 166 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7250 (mm-40) REVERT: J 187 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: J 203 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9184 (tp) REVERT: J 204 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7838 (tm-30) REVERT: K 58 PHE cc_start: 0.9153 (t80) cc_final: 0.8830 (t80) REVERT: K 91 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8818 (ttm-80) REVERT: K 166 GLN cc_start: 0.7916 (tt0) cc_final: 0.7318 (tt0) REVERT: K 185 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7250 (mt-10) REVERT: K 198 LYS cc_start: 0.9221 (tppp) cc_final: 0.8956 (tppp) REVERT: K 201 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: K 203 ILE cc_start: 0.9577 (tp) cc_final: 0.9293 (tp) REVERT: K 204 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7988 (tm-30) REVERT: L 91 ARG cc_start: 0.9290 (mtp-110) cc_final: 0.9068 (mmm-85) REVERT: L 166 GLN cc_start: 0.8038 (tt0) cc_final: 0.7267 (tt0) REVERT: L 170 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8659 (mp) REVERT: L 198 LYS cc_start: 0.9446 (tppp) cc_final: 0.9171 (tppp) REVERT: L 200 ARG cc_start: 0.9109 (ttm110) cc_final: 0.8762 (mtm-85) REVERT: M 51 TYR cc_start: 0.8296 (t80) cc_final: 0.8075 (t80) REVERT: M 60 GLU cc_start: 0.9275 (mm-30) cc_final: 0.9030 (mm-30) REVERT: M 104 PHE cc_start: 0.7867 (t80) cc_final: 0.7575 (t80) REVERT: M 185 GLU cc_start: 0.8640 (pt0) cc_final: 0.8355 (pt0) REVERT: M 198 LYS cc_start: 0.9262 (tppp) cc_final: 0.9025 (tppp) REVERT: M 204 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7966 (tm-30) REVERT: N 122 GLN cc_start: 0.7056 (mt0) cc_final: 0.6694 (mt0) REVERT: N 204 GLU cc_start: 0.8699 (tp30) cc_final: 0.7936 (tp30) outliers start: 103 outliers final: 45 residues processed: 498 average time/residue: 1.7467 time to fit residues: 947.3145 Evaluate side-chains 494 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 431 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP 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 54 ASP 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 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 210 THR 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 J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 122 GLN Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 35 GLN G 35 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20041 Z= 0.293 Angle : 0.658 10.298 27111 Z= 0.336 Chirality : 0.043 0.182 3150 Planarity : 0.005 0.057 3556 Dihedral : 4.213 28.534 2800 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.21 % Allowed : 22.68 % 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: 1.80 (0.18), residues: 2464 helix: 1.95 (0.14), residues: 1379 sheet: 2.10 (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 G 189 HIS 0.003 0.001 HIS B 138 PHE 0.023 0.001 PHE L 58 TYR 0.020 0.001 TYR N 159 ARG 0.011 0.001 ARG L 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 451 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8769 (mm-40) REVERT: A 100 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8389 (mmtt) REVERT: A 176 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8804 (t) REVERT: A 178 GLU cc_start: 0.9196 (pm20) cc_final: 0.8863 (pm20) REVERT: B 39 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8853 (mtp-110) REVERT: B 50 GLN cc_start: 0.9223 (pt0) cc_final: 0.8975 (pt0) REVERT: B 156 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: B 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8733 (tmmm) REVERT: C 39 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8622 (mtp-110) REVERT: C 43 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8980 (mm-30) REVERT: C 54 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8790 (m-30) REVERT: D 43 GLU cc_start: 0.9236 (mm-30) cc_final: 0.9010 (mm-30) REVERT: E 39 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8808 (mtp-110) REVERT: E 50 GLN cc_start: 0.9334 (pt0) cc_final: 0.9084 (pt0) REVERT: E 156 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: E 163 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8728 (tmmm) REVERT: F 39 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8750 (mtp-110) REVERT: F 43 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9028 (mm-30) REVERT: F 50 GLN cc_start: 0.9222 (pt0) cc_final: 0.8959 (pt0) REVERT: F 100 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8491 (mmtt) REVERT: F 108 MET cc_start: 0.8545 (ptp) cc_final: 0.8307 (ptp) REVERT: F 156 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: G 50 GLN cc_start: 0.9198 (pt0) cc_final: 0.8911 (pt0) REVERT: G 74 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8815 (p0) REVERT: G 108 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8103 (ptp) REVERT: G 156 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: G 163 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8678 (tmmm) REVERT: H 84 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (mm) REVERT: H 91 ARG cc_start: 0.9292 (ptm160) cc_final: 0.8635 (ptp90) REVERT: H 144 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8817 (ttmt) REVERT: H 197 GLU cc_start: 0.9212 (pm20) cc_final: 0.8925 (pm20) REVERT: H 203 ILE cc_start: 0.9534 (tp) cc_final: 0.9302 (tp) REVERT: H 204 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7779 (tm-30) REVERT: H 222 GLN cc_start: 0.8853 (tp40) cc_final: 0.8628 (tp40) REVERT: I 85 GLU cc_start: 0.8364 (pp20) cc_final: 0.8132 (pp20) REVERT: I 118 LYS cc_start: 0.8702 (mptt) cc_final: 0.8325 (tptp) REVERT: I 204 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7979 (tm-30) REVERT: J 144 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8412 (ptpp) REVERT: J 166 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7232 (mm-40) REVERT: J 187 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: J 203 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9177 (tp) REVERT: J 204 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7937 (tm-30) REVERT: K 58 PHE cc_start: 0.9156 (t80) cc_final: 0.8829 (t80) REVERT: K 91 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8811 (ttm-80) REVERT: K 126 MET cc_start: 0.8033 (mtp) cc_final: 0.7822 (mtp) REVERT: K 166 GLN cc_start: 0.7884 (tt0) cc_final: 0.7255 (tt0) REVERT: K 197 GLU cc_start: 0.9011 (pm20) cc_final: 0.8645 (pm20) REVERT: K 198 LYS cc_start: 0.9164 (tppp) cc_final: 0.8958 (tppp) REVERT: K 201 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: K 203 ILE cc_start: 0.9578 (tp) cc_final: 0.9294 (tp) REVERT: K 204 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8068 (tm-30) REVERT: L 91 ARG cc_start: 0.9288 (mtp-110) cc_final: 0.9073 (mmm-85) REVERT: L 152 ARG cc_start: 0.7616 (tmt170) cc_final: 0.7402 (tmt-80) REVERT: L 166 GLN cc_start: 0.8008 (tt0) cc_final: 0.7382 (tt0) REVERT: L 170 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8627 (mp) REVERT: L 198 LYS cc_start: 0.9467 (tppp) cc_final: 0.9202 (tppp) REVERT: L 200 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8730 (mtm-85) REVERT: M 51 TYR cc_start: 0.8357 (t80) cc_final: 0.7891 (t80) REVERT: M 185 GLU cc_start: 0.8649 (pt0) cc_final: 0.8302 (pt0) REVERT: M 198 LYS cc_start: 0.9289 (tppp) cc_final: 0.9042 (tppp) REVERT: M 204 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8018 (tm-30) REVERT: N 91 ARG cc_start: 0.8686 (pmm-80) cc_final: 0.8385 (pmm-80) REVERT: N 122 GLN cc_start: 0.6952 (mt0) cc_final: 0.6639 (mt0) REVERT: N 198 LYS cc_start: 0.9490 (tppp) cc_final: 0.9056 (tptp) REVERT: N 204 GLU cc_start: 0.8720 (tp30) cc_final: 0.7876 (tp30) outliers start: 108 outliers final: 52 residues processed: 498 average time/residue: 1.8127 time to fit residues: 982.2846 Evaluate side-chains 504 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 434 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP 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 C residue 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 35 GLN G 35 GLN H 157 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20041 Z= 0.228 Angle : 0.658 10.876 27111 Z= 0.335 Chirality : 0.043 0.211 3150 Planarity : 0.005 0.076 3556 Dihedral : 4.040 28.933 2800 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.39 % Allowed : 24.23 % Favored : 71.38 % 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: 1.88 (0.18), residues: 2464 helix: 2.02 (0.15), residues: 1379 sheet: 2.14 (0.32), residues: 224 loop : -0.25 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 189 HIS 0.003 0.001 HIS G 138 PHE 0.014 0.001 PHE M 58 TYR 0.016 0.001 TYR B 93 ARG 0.016 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 469 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8699 (mm-40) REVERT: A 100 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8476 (mmtm) REVERT: A 108 MET cc_start: 0.8624 (ptp) cc_final: 0.8114 (ptp) REVERT: A 176 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 178 GLU cc_start: 0.9215 (pm20) cc_final: 0.8874 (pm20) REVERT: B 39 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8845 (mtp-110) REVERT: B 50 GLN cc_start: 0.9234 (pt0) cc_final: 0.8948 (pt0) REVERT: B 100 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8356 (mmtt) REVERT: B 156 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: B 163 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8731 (tmmm) REVERT: C 39 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8615 (mtp-110) REVERT: C 43 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8979 (mm-30) REVERT: C 54 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: C 163 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8694 (tmmm) REVERT: D 43 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9011 (mm-30) REVERT: E 39 ARG cc_start: 0.9152 (tpp80) cc_final: 0.8793 (mtp-110) REVERT: E 50 GLN cc_start: 0.9315 (pt0) cc_final: 0.9082 (pt0) REVERT: E 163 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8706 (tmmm) REVERT: F 39 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8734 (mtp-110) REVERT: F 43 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9029 (mm-30) REVERT: F 50 GLN cc_start: 0.9211 (pt0) cc_final: 0.8877 (pt0) REVERT: F 54 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8789 (m-30) REVERT: F 108 MET cc_start: 0.8530 (ptp) cc_final: 0.8279 (ptp) REVERT: G 50 GLN cc_start: 0.9188 (pt0) cc_final: 0.8929 (pt0) REVERT: G 74 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (p0) REVERT: G 156 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: G 163 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8686 (tmmm) REVERT: H 84 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8774 (mm) REVERT: H 91 ARG cc_start: 0.9300 (ptm160) cc_final: 0.8660 (ptp90) REVERT: H 150 ASN cc_start: 0.9240 (m-40) cc_final: 0.8905 (m-40) REVERT: H 203 ILE cc_start: 0.9534 (tp) cc_final: 0.9307 (tp) REVERT: H 204 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7768 (tm-30) REVERT: H 222 GLN cc_start: 0.8877 (tp40) cc_final: 0.8675 (tp40) REVERT: I 85 GLU cc_start: 0.8278 (pp20) cc_final: 0.8008 (pp20) REVERT: I 118 LYS cc_start: 0.8667 (mptt) cc_final: 0.8318 (tptp) REVERT: J 144 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8461 (ptpp) REVERT: J 166 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7150 (mm-40) REVERT: J 187 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: J 203 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9171 (tp) REVERT: J 204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7914 (tm-30) REVERT: K 58 PHE cc_start: 0.9107 (t80) cc_final: 0.8784 (t80) REVERT: K 91 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8593 (ttm110) REVERT: K 126 MET cc_start: 0.8036 (mtp) cc_final: 0.7826 (mtp) REVERT: K 166 GLN cc_start: 0.7878 (tt0) cc_final: 0.7245 (tt0) REVERT: K 185 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6696 (mp0) REVERT: K 198 LYS cc_start: 0.9146 (tppp) cc_final: 0.8876 (tppp) REVERT: K 201 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: K 204 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8074 (tm-30) REVERT: L 91 ARG cc_start: 0.9300 (mtp-110) cc_final: 0.9083 (mmm-85) REVERT: L 152 ARG cc_start: 0.7568 (tmt170) cc_final: 0.6985 (tmt170) REVERT: L 166 GLN cc_start: 0.7974 (tt0) cc_final: 0.7498 (tt0) REVERT: L 198 LYS cc_start: 0.9463 (tppp) cc_final: 0.9183 (tppp) REVERT: L 200 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8853 (ttm110) REVERT: M 51 TYR cc_start: 0.8335 (t80) cc_final: 0.7935 (t80) REVERT: M 185 GLU cc_start: 0.8628 (pt0) cc_final: 0.8278 (pt0) REVERT: M 204 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8051 (tm-30) REVERT: N 91 ARG cc_start: 0.8686 (pmm-80) cc_final: 0.8369 (pmm-80) REVERT: N 198 LYS cc_start: 0.9483 (tppp) cc_final: 0.9109 (tptp) REVERT: N 203 ILE cc_start: 0.9497 (tp) cc_final: 0.9229 (tp) REVERT: N 204 GLU cc_start: 0.8728 (tp30) cc_final: 0.7948 (tp30) outliers start: 91 outliers final: 42 residues processed: 505 average time/residue: 1.7752 time to fit residues: 976.4193 Evaluate side-chains 509 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 451 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP 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 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 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 169 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 180 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 35 GLN G 35 GLN I 150 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 GLN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20041 Z= 0.244 Angle : 0.694 11.991 27111 Z= 0.351 Chirality : 0.043 0.204 3150 Planarity : 0.005 0.090 3556 Dihedral : 4.013 28.712 2800 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.01 % Allowed : 25.00 % Favored : 70.99 % 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 (0.18), residues: 2464 helix: 1.96 (0.15), residues: 1379 sheet: 2.14 (0.31), residues: 224 loop : -0.19 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.016 0.001 PHE I 104 TYR 0.022 0.001 TYR N 159 ARG 0.016 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 460 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8727 (mm-40) REVERT: A 100 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8329 (mmtt) REVERT: A 108 MET cc_start: 0.8612 (ptp) cc_final: 0.8086 (ptp) REVERT: A 176 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8704 (t) REVERT: A 178 GLU cc_start: 0.9225 (pm20) cc_final: 0.8872 (pm20) REVERT: B 39 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8852 (mtp-110) REVERT: B 50 GLN cc_start: 0.9225 (pt0) cc_final: 0.8933 (pt0) REVERT: B 156 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: B 163 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8731 (tmmm) REVERT: C 39 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8618 (mtp-110) REVERT: C 43 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8978 (mm-30) REVERT: C 54 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8721 (m-30) REVERT: C 100 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8368 (mmtt) REVERT: C 163 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8701 (tmmm) REVERT: D 43 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9019 (mm-30) REVERT: E 39 ARG cc_start: 0.9160 (tpp80) cc_final: 0.8822 (mtp-110) REVERT: E 50 GLN cc_start: 0.9310 (pt0) cc_final: 0.9084 (pt0) REVERT: E 163 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8686 (tmmm) REVERT: F 39 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8735 (mtp-110) REVERT: F 43 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9026 (mm-30) REVERT: F 54 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8787 (m-30) REVERT: F 108 MET cc_start: 0.8530 (ptp) cc_final: 0.8265 (ptp) REVERT: F 205 MET cc_start: 0.8533 (mmp) cc_final: 0.8299 (mtp) REVERT: G 50 GLN cc_start: 0.9187 (pt0) cc_final: 0.8926 (pt0) REVERT: G 74 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8829 (p0) REVERT: G 156 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: H 84 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8765 (mm) REVERT: H 91 ARG cc_start: 0.9294 (ptm160) cc_final: 0.8635 (ptp90) REVERT: H 144 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8586 (ttmt) REVERT: H 150 ASN cc_start: 0.9231 (m-40) cc_final: 0.8820 (m-40) REVERT: H 203 ILE cc_start: 0.9529 (tp) cc_final: 0.9299 (tp) REVERT: H 204 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8032 (tm-30) REVERT: H 222 GLN cc_start: 0.8901 (tp40) cc_final: 0.8694 (tp40) REVERT: I 85 GLU cc_start: 0.8298 (pp20) cc_final: 0.8026 (pp20) REVERT: I 118 LYS cc_start: 0.8670 (mptt) cc_final: 0.8312 (tptp) REVERT: I 204 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 144 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8607 (ptpp) REVERT: J 166 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7257 (mm-40) REVERT: J 187 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: J 203 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9168 (tp) REVERT: J 204 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7989 (tm-30) REVERT: K 58 PHE cc_start: 0.9109 (t80) cc_final: 0.8788 (t80) REVERT: K 91 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8557 (ttm110) REVERT: K 166 GLN cc_start: 0.7895 (tt0) cc_final: 0.7254 (tt0) REVERT: K 197 GLU cc_start: 0.8954 (pm20) cc_final: 0.8730 (pm20) REVERT: K 204 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8072 (tm-30) REVERT: L 91 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.9073 (mmm-85) REVERT: L 166 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: L 198 LYS cc_start: 0.9464 (tppp) cc_final: 0.9213 (tppp) REVERT: M 51 TYR cc_start: 0.8348 (t80) cc_final: 0.7931 (t80) REVERT: M 104 PHE cc_start: 0.7810 (t80) cc_final: 0.7607 (t80) REVERT: M 185 GLU cc_start: 0.8646 (pt0) cc_final: 0.8306 (pt0) REVERT: M 204 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8132 (tm-30) REVERT: N 91 ARG cc_start: 0.8713 (pmm-80) cc_final: 0.8381 (pmm-80) REVERT: N 198 LYS cc_start: 0.9505 (tppp) cc_final: 0.9152 (tptp) REVERT: N 203 ILE cc_start: 0.9493 (tp) cc_final: 0.9237 (tp) REVERT: N 204 GLU cc_start: 0.8722 (tp30) cc_final: 0.7934 (tp30) outliers start: 83 outliers final: 44 residues processed: 493 average time/residue: 1.7987 time to fit residues: 964.3241 Evaluate side-chains 504 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 445 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP 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 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 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 157 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN J 175 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20041 Z= 0.415 Angle : 0.776 12.753 27111 Z= 0.397 Chirality : 0.045 0.203 3150 Planarity : 0.005 0.065 3556 Dihedral : 4.382 28.579 2800 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 4.30 % Allowed : 25.29 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2464 helix: 1.72 (0.15), residues: 1379 sheet: 2.15 (0.32), residues: 224 loop : -0.33 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 189 HIS 0.004 0.001 HIS B 138 PHE 0.015 0.001 PHE M 58 TYR 0.015 0.001 TYR B 93 ARG 0.017 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 441 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8792 (tmmm) REVERT: A 176 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8754 (t) REVERT: A 178 GLU cc_start: 0.9215 (pm20) cc_final: 0.8844 (pm20) REVERT: B 39 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8869 (mtp-110) REVERT: B 50 GLN cc_start: 0.9215 (pt0) cc_final: 0.8926 (pt0) REVERT: B 156 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: B 163 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8751 (tmmm) REVERT: C 39 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8613 (mtp-110) REVERT: C 43 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9057 (mm-30) REVERT: C 54 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8864 (m-30) REVERT: C 163 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8736 (tmmm) REVERT: E 39 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8835 (mtp-110) REVERT: E 50 GLN cc_start: 0.9339 (pt0) cc_final: 0.9023 (pt0) REVERT: E 163 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8741 (tmmm) REVERT: F 39 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8794 (mtp-110) REVERT: F 43 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9059 (mm-30) REVERT: G 50 GLN cc_start: 0.9230 (pt0) cc_final: 0.8939 (pt0) REVERT: G 74 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8850 (p0) REVERT: G 97 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8580 (mp10) REVERT: G 156 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: H 91 ARG cc_start: 0.9271 (ptm160) cc_final: 0.8582 (ptp90) REVERT: H 203 ILE cc_start: 0.9545 (tp) cc_final: 0.9305 (tp) REVERT: H 204 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8046 (tm-30) REVERT: H 222 GLN cc_start: 0.8913 (tp40) cc_final: 0.8703 (tp40) REVERT: I 85 GLU cc_start: 0.8378 (pp20) cc_final: 0.8072 (pp20) REVERT: I 104 PHE cc_start: 0.7858 (t80) cc_final: 0.7614 (t80) REVERT: I 118 LYS cc_start: 0.8757 (mptt) cc_final: 0.8332 (tptp) REVERT: I 184 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8777 (mp) REVERT: I 204 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8007 (tm-30) REVERT: J 144 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8312 (ptpp) REVERT: J 166 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7308 (mm-40) REVERT: J 187 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: J 198 LYS cc_start: 0.9365 (tppp) cc_final: 0.9154 (tppp) REVERT: J 203 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9227 (tp) REVERT: J 204 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7972 (tm-30) REVERT: K 58 PHE cc_start: 0.9174 (t80) cc_final: 0.8879 (t80) REVERT: K 91 ARG cc_start: 0.9045 (ttm110) cc_final: 0.8770 (ttp-110) REVERT: K 201 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8610 (mp0) REVERT: K 204 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8053 (tm-30) REVERT: L 91 ARG cc_start: 0.9275 (mtp-110) cc_final: 0.9059 (mmm-85) REVERT: L 200 ARG cc_start: 0.9016 (ttp-110) cc_final: 0.8530 (mtm-85) REVERT: M 51 TYR cc_start: 0.8375 (t80) cc_final: 0.8150 (t80) REVERT: M 185 GLU cc_start: 0.8677 (pt0) cc_final: 0.8398 (pt0) REVERT: M 190 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8719 (ttpp) REVERT: M 204 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8046 (tm-30) REVERT: N 185 GLU cc_start: 0.8423 (pp20) cc_final: 0.8129 (pp20) REVERT: N 190 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8766 (tmmt) REVERT: N 203 ILE cc_start: 0.9544 (tp) cc_final: 0.9296 (tp) REVERT: N 204 GLU cc_start: 0.8734 (tp30) cc_final: 0.7938 (tp30) outliers start: 89 outliers final: 43 residues processed: 480 average time/residue: 1.8435 time to fit residues: 963.1061 Evaluate side-chains 484 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 426 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 55 ASP 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 69 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 156 GLU 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 118 LYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 210 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 226 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 0.0770 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 218 optimal weight: 0.0270 chunk 188 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 35 GLN F 35 GLN F 50 GLN F 97 GLN G 35 GLN H 157 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20041 Z= 0.297 Angle : 0.773 13.109 27111 Z= 0.396 Chirality : 0.044 0.229 3150 Planarity : 0.005 0.106 3556 Dihedral : 4.349 29.164 2800 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.43 % Allowed : 26.50 % Favored : 70.08 % 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: 1.53 (0.18), residues: 2464 helix: 1.67 (0.15), residues: 1379 sheet: 2.11 (0.31), residues: 224 loop : -0.32 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS B 138 PHE 0.015 0.001 PHE H 58 TYR 0.024 0.001 TYR I 159 ARG 0.019 0.001 ARG I 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 439 time to evaluate : 2.372 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 100 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8959 (mmtt) REVERT: A 108 MET cc_start: 0.8646 (ptp) cc_final: 0.8141 (ptp) REVERT: A 163 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8774 (tmmm) REVERT: A 176 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8739 (t) REVERT: A 178 GLU cc_start: 0.9228 (pm20) cc_final: 0.8883 (pm20) REVERT: B 39 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8848 (mtp-110) REVERT: B 50 GLN cc_start: 0.9214 (pt0) cc_final: 0.8953 (pt0) REVERT: B 156 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 163 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8755 (tmmm) REVERT: C 39 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8651 (mtp-110) REVERT: C 43 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8965 (mm-30) REVERT: C 54 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8766 (m-30) REVERT: C 163 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8719 (tmmm) REVERT: E 39 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8806 (mtp-110) REVERT: E 50 GLN cc_start: 0.9321 (pt0) cc_final: 0.9078 (pt0) REVERT: E 163 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8734 (tmmm) REVERT: F 39 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8753 (mtp-110) REVERT: F 43 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9025 (mm-30) REVERT: G 50 GLN cc_start: 0.9239 (pt0) cc_final: 0.8947 (pt0) REVERT: G 74 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8849 (p0) REVERT: G 100 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9048 (mttp) REVERT: G 156 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: H 91 ARG cc_start: 0.9273 (ptm160) cc_final: 0.8606 (ptp90) REVERT: H 144 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8706 (ttmt) REVERT: H 185 GLU cc_start: 0.8394 (pp20) cc_final: 0.8133 (pp20) REVERT: H 203 ILE cc_start: 0.9555 (tp) cc_final: 0.9319 (tp) REVERT: H 204 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 222 GLN cc_start: 0.8901 (tp40) cc_final: 0.8689 (tp40) REVERT: I 85 GLU cc_start: 0.8340 (pp20) cc_final: 0.8088 (pp20) REVERT: I 118 LYS cc_start: 0.8709 (mptt) cc_final: 0.8349 (tptp) REVERT: I 184 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8767 (mp) REVERT: I 204 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8022 (tm-30) REVERT: J 144 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8600 (ptpp) REVERT: J 166 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7321 (mm-40) REVERT: J 187 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7964 (mtp) REVERT: J 198 LYS cc_start: 0.9369 (tppp) cc_final: 0.9105 (tppp) REVERT: J 203 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9254 (tp) REVERT: J 204 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8004 (tm-30) REVERT: K 58 PHE cc_start: 0.9162 (t80) cc_final: 0.8817 (t80) REVERT: K 91 ARG cc_start: 0.9040 (ttm110) cc_final: 0.8782 (ttp-110) REVERT: K 197 GLU cc_start: 0.9071 (pm20) cc_final: 0.8831 (pm20) REVERT: K 201 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: K 204 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8016 (tm-30) REVERT: L 91 ARG cc_start: 0.9295 (mtp-110) cc_final: 0.9080 (mmm-85) REVERT: L 152 ARG cc_start: 0.7311 (tmt170) cc_final: 0.7079 (tmt170) REVERT: L 200 ARG cc_start: 0.8982 (ttp-110) cc_final: 0.8415 (mtm-85) REVERT: M 51 TYR cc_start: 0.8361 (t80) cc_final: 0.8156 (t80) REVERT: M 185 GLU cc_start: 0.8685 (pt0) cc_final: 0.8360 (pt0) REVERT: M 204 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8136 (tm-30) REVERT: N 91 ARG cc_start: 0.8695 (pmm-80) cc_final: 0.8421 (pmm-80) REVERT: N 185 GLU cc_start: 0.8399 (pp20) cc_final: 0.8023 (pp20) REVERT: N 190 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8748 (tmmt) REVERT: N 198 LYS cc_start: 0.9404 (tppp) cc_final: 0.9014 (tptp) REVERT: N 203 ILE cc_start: 0.9541 (tp) cc_final: 0.9303 (tp) REVERT: N 204 GLU cc_start: 0.8766 (tp30) cc_final: 0.7963 (tp30) outliers start: 71 outliers final: 46 residues processed: 468 average time/residue: 1.8430 time to fit residues: 937.0757 Evaluate side-chains 488 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 427 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 55 ASP 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 69 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 156 GLU 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 118 LYS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 167 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 210 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 201 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 27 optimal weight: 0.0070 chunk 52 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.5604 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 35 GLN F 50 GLN F 97 GLN G 35 GLN H 157 GLN J 175 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.066770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054452 restraints weight = 56428.180| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.89 r_work: 0.2655 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20041 Z= 0.277 Angle : 0.775 13.036 27111 Z= 0.398 Chirality : 0.044 0.238 3150 Planarity : 0.005 0.069 3556 Dihedral : 4.336 29.221 2800 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.47 % Allowed : 26.74 % Favored : 69.79 % 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: 1.55 (0.18), residues: 2464 helix: 1.65 (0.15), residues: 1386 sheet: 2.15 (0.31), residues: 224 loop : -0.28 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 189 HIS 0.003 0.000 HIS B 138 PHE 0.020 0.001 PHE I 104 TYR 0.022 0.001 TYR N 51 ARG 0.018 0.001 ARG I 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12258.64 seconds wall clock time: 212 minutes 7.30 seconds (12727.30 seconds total)