Starting phenix.real_space_refine on Wed Apr 10 14:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/04_2024/8xop_38537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/04_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_38537/04_2024/8xop_38537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/04_2024/8xop_38537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/04_2024/8xop_38537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xop_38537/04_2024/8xop_38537_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 12474 2.51 5 N 3304 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "L PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.52, per 1000 atoms: 0.53 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: 7.63 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 98 helices and 28 sheets defined 47.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.766A pdb=" N SER A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.921A pdb=" N GLU B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 removed outlier: 3.749A pdb=" N SER B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 148 through 173 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'C' and resid 32 through 43 removed outlier: 3.748A pdb=" N GLU C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.803A pdb=" N SER C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 150 through 173 Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.641A pdb=" N GLU D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.743A pdb=" N SER D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 148 through 173 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'E' and resid 32 through 43 removed outlier: 3.918A pdb=" N GLU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 3.831A pdb=" N SER E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 98 Processing helix chain 'E' and resid 114 through 120 Processing helix chain 'E' and resid 148 through 173 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 192 through 198 Processing helix chain 'F' and resid 32 through 43 removed outlier: 3.909A pdb=" N GLU F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 69 removed outlier: 3.775A pdb=" N SER F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 98 Processing helix chain 'F' and resid 114 through 121 Processing helix chain 'F' and resid 148 through 173 Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 192 through 198 Processing helix chain 'G' and resid 32 through 43 removed outlier: 3.826A pdb=" N GLU G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 69 removed outlier: 3.756A pdb=" N SER G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 114 through 120 Processing helix chain 'G' and resid 148 through 173 Processing helix chain 'G' and resid 177 through 183 Processing helix chain 'G' and resid 192 through 198 Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.616A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 86 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 196 through 202 Processing helix chain 'H' and resid 211 through 217 Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.749A pdb=" N GLU I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU I 60 " --> pdb=" O LYS I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 86 Processing helix chain 'I' and resid 105 through 116 Processing helix chain 'I' and resid 132 through 139 Processing helix chain 'I' and resid 167 through 190 Processing helix chain 'I' and resid 196 through 202 Processing helix chain 'I' and resid 211 through 217 Processing helix chain 'J' and resid 52 through 60 removed outlier: 4.038A pdb=" N GLU J 60 " --> pdb=" O LYS J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 86 Processing helix chain 'J' and resid 104 through 116 Processing helix chain 'J' and resid 131 through 139 Processing helix chain 'J' and resid 167 through 191 Processing helix chain 'J' and resid 196 through 203 Processing helix chain 'J' and resid 211 through 217 Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.795A pdb=" N GLU K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU K 60 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 87 Processing helix chain 'K' and resid 105 through 116 Processing helix chain 'K' and resid 132 through 139 Processing helix chain 'K' and resid 167 through 190 Processing helix chain 'K' and resid 196 through 203 Processing helix chain 'K' and resid 211 through 217 Processing helix chain 'L' and resid 52 through 60 removed outlier: 4.287A pdb=" N GLU L 60 " --> pdb=" O LYS L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 86 Processing helix chain 'L' and resid 104 through 116 Processing helix chain 'L' and resid 131 through 138 Processing helix chain 'L' and resid 167 through 190 Processing helix chain 'L' and resid 196 through 202 Processing helix chain 'L' and resid 211 through 217 Processing helix chain 'M' and resid 52 through 60 removed outlier: 4.156A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 86 Processing helix chain 'M' and resid 104 through 116 Processing helix chain 'M' and resid 132 through 139 Processing helix chain 'M' and resid 167 through 190 Processing helix chain 'M' and resid 196 through 204 removed outlier: 4.139A pdb=" N GLU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 217 Processing helix chain 'N' and resid 52 through 60 removed outlier: 4.425A pdb=" N GLU N 60 " --> pdb=" O LYS N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 86 Processing helix chain 'N' and resid 104 through 116 Processing helix chain 'N' and resid 132 through 138 Processing helix chain 'N' and resid 167 through 191 Processing helix chain 'N' and resid 196 through 202 Processing helix chain 'N' and resid 211 through 217 Processing sheet with id= A, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.435A pdb=" N TYR A 76 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 48 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 78 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.572A pdb=" N GLU A 134 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.814A pdb=" N TYR B 76 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU B 48 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR B 78 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.654A pdb=" N GLU B 134 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.604A pdb=" N TYR C 76 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 48 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR C 78 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.535A pdb=" N GLU C 134 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.736A pdb=" N TYR D 76 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 48 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR D 78 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 110 through 112 removed outlier: 6.628A pdb=" N GLU D 134 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.831A pdb=" N TYR E 76 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU E 48 " --> pdb=" O TYR E 76 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR E 78 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 110 through 112 removed outlier: 6.560A pdb=" N GLU E 134 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.755A pdb=" N TYR F 76 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU F 48 " --> pdb=" O TYR F 76 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR F 78 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 110 through 112 removed outlier: 6.632A pdb=" N GLU F 134 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.834A pdb=" N TYR G 76 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU G 48 " --> pdb=" O TYR G 76 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR G 78 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.466A pdb=" N GLU G 134 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.935A pdb=" N SER H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU H 65 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR H 96 " --> pdb=" O LEU H 65 " (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: 7.035A pdb=" N GLN H 222 " --> pdb=" O ALA H 147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 153 through 155 Processing sheet with id= Q, first strand: chain 'I' and resid 62 through 65 removed outlier: 6.736A pdb=" N SER I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU I 65 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR I 96 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 153 through 155 Processing sheet with id= S, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.721A pdb=" N SER J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU J 65 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR J 96 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 153 through 155 Processing sheet with id= U, first strand: chain 'K' and resid 62 through 65 removed outlier: 6.726A pdb=" N SER K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU K 65 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR K 96 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 153 through 155 Processing sheet with id= W, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.713A pdb=" N SER L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU L 65 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR L 96 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 153 through 155 Processing sheet with id= Y, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.721A pdb=" N SER M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU M 65 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR M 96 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 128 through 130 removed outlier: 6.837A pdb=" N ARG M 152 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.737A pdb=" N SER N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU N 65 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR N 96 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 128 through 130 removed outlier: 6.556A pdb=" N ARG N 152 " --> pdb=" O ALA N 129 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2721 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: 5.98 Time building geometry restraints manager: 8.22 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: 420 2.68 - 3.23: 19752 3.23 - 3.79: 31333 3.79 - 4.34: 40702 4.34 - 4.90: 67896 Nonbonded interactions: 160103 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 160098 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.700 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.290 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.770 ------------------------------------------------------------------------------- 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= 0.309 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 : 2.039 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: 1.8195 time to fit residues: 1064.3222 Evaluate side-chains 427 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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: 9.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 chunk 138 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 50 GLN D 58 ASN D 63 GLN E 50 GLN G 35 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20041 Z= 0.273 Angle : 0.604 7.897 27111 Z= 0.308 Chirality : 0.042 0.161 3150 Planarity : 0.005 0.047 3556 Dihedral : 4.169 41.422 2800 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.67 % Allowed : 14.96 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2464 helix: 1.78 (0.15), residues: 1365 sheet: 1.89 (0.33), residues: 259 loop : -0.20 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 189 HIS 0.003 0.001 HIS G 138 PHE 0.026 0.001 PHE L 58 TYR 0.019 0.001 TYR H 51 ARG 0.009 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 538 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 462 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8779 (mm-40) REVERT: A 100 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8425 (mmtt) REVERT: A 171 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8810 (tm-30) REVERT: B 39 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8652 (ttp80) REVERT: B 50 GLN cc_start: 0.9222 (pt0) cc_final: 0.8959 (pt0) REVERT: B 100 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8353 (mmtt) REVERT: B 205 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8053 (mtp) REVERT: C 43 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8981 (mm-30) REVERT: C 97 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8790 (mm-40) REVERT: D 43 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8986 (mm-30) REVERT: D 100 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8684 (mptt) REVERT: D 171 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8787 (tm-30) REVERT: E 43 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8980 (mm-30) REVERT: E 97 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8867 (mm-40) REVERT: E 114 MET cc_start: 0.9055 (tpp) cc_final: 0.8779 (mmm) REVERT: E 134 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8480 (mt-10) REVERT: F 43 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9030 (mm-30) REVERT: F 50 GLN cc_start: 0.9239 (pt0) cc_final: 0.8946 (pt0) REVERT: F 100 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8429 (mmtt) REVERT: F 171 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8860 (tm-30) REVERT: G 50 GLN cc_start: 0.9223 (pt0) cc_final: 0.8938 (pt0) REVERT: G 74 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8687 (p0) REVERT: G 97 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8916 (mm-40) REVERT: H 203 ILE cc_start: 0.9434 (tp) cc_final: 0.9217 (tp) REVERT: H 204 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 222 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8707 (tp-100) REVERT: I 85 GLU cc_start: 0.8241 (pp20) cc_final: 0.7992 (pp20) REVERT: I 203 ILE cc_start: 0.9566 (tp) cc_final: 0.9344 (tp) REVERT: I 204 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8166 (tm-30) REVERT: I 222 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8749 (tp-100) REVERT: J 166 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6990 (mm-40) REVERT: J 200 ARG cc_start: 0.8617 (mpp80) cc_final: 0.8411 (mpp80) REVERT: J 203 ILE cc_start: 0.9371 (tp) cc_final: 0.9135 (tp) REVERT: J 204 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7621 (tm-30) REVERT: K 91 ARG cc_start: 0.9237 (ttm110) cc_final: 0.8618 (ttm110) REVERT: K 200 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8468 (mmm160) REVERT: K 203 ILE cc_start: 0.9578 (tp) cc_final: 0.9257 (tp) REVERT: K 204 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7937 (tm-30) REVERT: L 91 ARG cc_start: 0.9315 (mtp-110) cc_final: 0.9098 (mmm-85) REVERT: L 185 GLU cc_start: 0.8392 (pt0) cc_final: 0.8173 (pt0) REVERT: L 204 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7786 (tm-30) REVERT: M 51 TYR cc_start: 0.8261 (t80) cc_final: 0.8029 (t80) REVERT: M 60 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8960 (mm-30) REVERT: M 104 PHE cc_start: 0.7907 (t80) cc_final: 0.7693 (t80) REVERT: M 185 GLU cc_start: 0.8580 (pt0) cc_final: 0.8245 (pt0) REVERT: M 204 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7947 (tm-30) REVERT: N 60 GLU cc_start: 0.8473 (mp0) cc_final: 0.8271 (mp0) REVERT: N 91 ARG cc_start: 0.9080 (ptp90) cc_final: 0.8720 (pmm-80) REVERT: N 122 GLN cc_start: 0.7255 (mt0) cc_final: 0.6972 (mt0) REVERT: N 166 GLN cc_start: 0.7833 (mm110) cc_final: 0.7419 (mm-40) REVERT: N 204 GLU cc_start: 0.8651 (tp30) cc_final: 0.7977 (tp30) outliers start: 76 outliers final: 26 residues processed: 485 average time/residue: 1.9739 time to fit residues: 1038.7955 Evaluate side-chains 469 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 440 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 150 ASP 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 113 THR Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 170 LEU 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 J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 170 LEU 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 113 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: 5.9990 chunk 179 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 97 GLN C 50 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 58 ASN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 GLN 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 ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 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: 0.8642 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20041 Z= 0.368 Angle : 0.640 9.924 27111 Z= 0.326 Chirality : 0.043 0.165 3150 Planarity : 0.005 0.050 3556 Dihedral : 4.348 34.788 2800 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.96 % Allowed : 17.18 % Favored : 78.86 % 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: 1.67 (0.17), residues: 2464 helix: 1.78 (0.15), residues: 1358 sheet: 2.06 (0.32), residues: 224 loop : -0.18 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.003 0.001 HIS B 138 PHE 0.022 0.001 PHE M 58 TYR 0.017 0.001 TYR H 51 ARG 0.009 0.001 ARG H 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 538 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 456 time to evaluate : 2.629 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: 0.9139 (mm-40) cc_final: 0.8760 (mm-40) REVERT: B 39 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8858 (mtp-110) REVERT: B 50 GLN cc_start: 0.9223 (pt0) cc_final: 0.8949 (pt0) REVERT: B 156 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: B 163 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8686 (tmmm) REVERT: B 205 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8049 (mtp) REVERT: C 39 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8623 (mtp-110) REVERT: C 43 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8989 (mm-30) REVERT: C 97 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8959 (mm110) REVERT: C 163 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8717 (tmmm) REVERT: D 39 ARG cc_start: 0.8934 (ttp-110) cc_final: 0.8599 (mtp-110) REVERT: D 43 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8998 (mm-30) REVERT: D 100 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8598 (mptt) REVERT: D 194 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8311 (mt-10) REVERT: E 39 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8702 (mtp-110) REVERT: E 43 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9025 (mm-30) REVERT: E 50 GLN cc_start: 0.9403 (pt0) cc_final: 0.9159 (pt0) REVERT: E 134 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8447 (mt-10) REVERT: F 39 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8832 (mtp-110) REVERT: F 43 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9026 (mm-30) REVERT: F 50 GLN cc_start: 0.9227 (pt0) cc_final: 0.8972 (pt0) REVERT: F 100 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8462 (mmtt) REVERT: G 50 GLN cc_start: 0.9211 (pt0) cc_final: 0.8948 (pt0) REVERT: G 74 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8751 (p0) REVERT: G 163 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8685 (tmmm) REVERT: H 91 ARG cc_start: 0.9348 (ptm160) cc_final: 0.9062 (ptp90) REVERT: H 197 GLU cc_start: 0.9165 (pm20) cc_final: 0.8948 (pm20) REVERT: H 203 ILE cc_start: 0.9482 (tp) cc_final: 0.9241 (tp) REVERT: H 204 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7728 (tm-30) REVERT: H 222 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8726 (tp-100) REVERT: I 85 GLU cc_start: 0.8367 (pp20) cc_final: 0.8094 (pp20) REVERT: I 203 ILE cc_start: 0.9550 (tp) cc_final: 0.9346 (tp) REVERT: I 204 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8155 (tm-30) REVERT: I 222 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8721 (tp-100) REVERT: J 60 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8952 (mm-30) REVERT: J 166 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7091 (mm-40) REVERT: J 200 ARG cc_start: 0.8653 (mpp80) cc_final: 0.8411 (mpp80) REVERT: J 203 ILE cc_start: 0.9426 (tp) cc_final: 0.9159 (tp) REVERT: J 204 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7547 (tm-30) REVERT: K 91 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8604 (ttm110) REVERT: K 203 ILE cc_start: 0.9565 (tp) cc_final: 0.9324 (tp) REVERT: K 204 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7897 (tm-30) REVERT: L 91 ARG cc_start: 0.9301 (mtp-110) cc_final: 0.9095 (mmm-85) REVERT: L 185 GLU cc_start: 0.8421 (pt0) cc_final: 0.8192 (pt0) REVERT: L 204 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7801 (tm-30) REVERT: M 51 TYR cc_start: 0.8297 (t80) cc_final: 0.8079 (t80) REVERT: M 60 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8952 (mm-30) REVERT: M 91 ARG cc_start: 0.9289 (mtp-110) cc_final: 0.9087 (mmm-85) REVERT: M 185 GLU cc_start: 0.8625 (pt0) cc_final: 0.8320 (pt0) REVERT: M 204 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7929 (tm-30) REVERT: N 122 GLN cc_start: 0.7332 (mt0) cc_final: 0.7035 (mt0) REVERT: N 204 GLU cc_start: 0.8620 (tp30) cc_final: 0.7934 (tp30) outliers start: 82 outliers final: 35 residues processed: 485 average time/residue: 1.9886 time to fit residues: 1047.9829 Evaluate side-chains 482 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 438 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 74 ASP 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 193 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 GLN 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: 7.9990 chunk 162 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 0.0870 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN D 97 GLN E 35 GLN F 97 GLN G 35 GLN H 157 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20041 Z= 0.175 Angle : 0.590 9.122 27111 Z= 0.298 Chirality : 0.041 0.158 3150 Planarity : 0.004 0.059 3556 Dihedral : 4.120 28.724 2800 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.33 % Allowed : 19.55 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2464 helix: 1.95 (0.15), residues: 1351 sheet: 1.99 (0.32), residues: 224 loop : -0.15 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.002 0.000 HIS G 138 PHE 0.026 0.001 PHE J 58 TYR 0.021 0.001 TYR F 93 ARG 0.013 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 491 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: A 97 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8689 (mm-40) REVERT: A 163 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8746 (tmmm) REVERT: A 176 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9021 (p) REVERT: A 178 GLU cc_start: 0.9179 (pm20) cc_final: 0.8923 (pm20) REVERT: B 50 GLN cc_start: 0.9223 (pt0) cc_final: 0.8948 (pt0) REVERT: B 100 LYS cc_start: 0.8761 (mptp) cc_final: 0.8347 (mmtt) REVERT: B 156 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 163 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8892 (tmmm) REVERT: C 43 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8946 (mm-30) REVERT: C 97 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8791 (mm-40) REVERT: C 100 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8497 (mmtt) REVERT: D 39 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8522 (mtp-110) REVERT: D 43 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8921 (mm-30) REVERT: D 100 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8696 (mptt) REVERT: D 152 LYS cc_start: 0.8450 (tttt) cc_final: 0.8208 (tttm) REVERT: D 156 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: D 194 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8234 (mt-10) REVERT: E 43 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8955 (mm-30) REVERT: E 50 GLN cc_start: 0.9349 (pt0) cc_final: 0.9133 (pt0) REVERT: E 97 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8738 (mm-40) REVERT: E 134 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8411 (mt-10) REVERT: E 163 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8727 (tmmm) REVERT: F 39 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8704 (mtp-110) REVERT: F 43 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8982 (mm-30) REVERT: F 50 GLN cc_start: 0.9200 (pt0) cc_final: 0.8916 (pt0) REVERT: F 108 MET cc_start: 0.8566 (ptp) cc_final: 0.8242 (ptp) REVERT: G 50 GLN cc_start: 0.9209 (pt0) cc_final: 0.8931 (pt0) REVERT: G 74 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8796 (p0) REVERT: G 97 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8888 (mm-40) REVERT: G 163 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8686 (tmmm) REVERT: H 85 GLU cc_start: 0.8955 (pm20) cc_final: 0.8730 (pm20) REVERT: H 91 ARG cc_start: 0.9333 (ptm160) cc_final: 0.8528 (ptp90) REVERT: H 144 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8706 (ttmt) REVERT: H 198 LYS cc_start: 0.9160 (tppp) cc_final: 0.8914 (tppp) REVERT: H 203 ILE cc_start: 0.9455 (tp) cc_final: 0.9212 (tp) REVERT: H 204 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7955 (tm-30) REVERT: H 222 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8691 (tp-100) REVERT: I 104 PHE cc_start: 0.7898 (t80) cc_final: 0.7663 (t80) REVERT: I 150 ASN cc_start: 0.9267 (m-40) cc_final: 0.8876 (m110) REVERT: I 201 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: I 204 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8174 (tm-30) REVERT: I 222 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8741 (tp-100) REVERT: J 166 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7022 (mm-40) REVERT: J 203 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9092 (tp) REVERT: J 204 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7685 (tm-30) REVERT: K 91 ARG cc_start: 0.9173 (ttm110) cc_final: 0.8554 (ttm110) REVERT: K 152 ARG cc_start: 0.7157 (tmt170) cc_final: 0.6776 (tmt170) REVERT: K 166 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: K 203 ILE cc_start: 0.9526 (tp) cc_final: 0.9298 (tp) REVERT: K 204 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7937 (tm-30) REVERT: L 59 GLU cc_start: 0.8952 (mp0) cc_final: 0.8611 (mp0) REVERT: L 91 ARG cc_start: 0.9323 (mtp-110) cc_final: 0.9100 (mmm-85) REVERT: L 170 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8625 (mp) REVERT: L 185 GLU cc_start: 0.8272 (pt0) cc_final: 0.8046 (pt0) REVERT: L 204 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7895 (tm-30) REVERT: M 51 TYR cc_start: 0.8340 (t80) cc_final: 0.8113 (t80) REVERT: M 60 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8858 (mm-30) REVERT: M 91 ARG cc_start: 0.9320 (mtp-110) cc_final: 0.9021 (mtp85) REVERT: M 185 GLU cc_start: 0.8584 (pt0) cc_final: 0.8229 (pt0) REVERT: M 198 LYS cc_start: 0.9132 (tppp) cc_final: 0.8896 (tppp) REVERT: M 204 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7946 (tm-30) REVERT: N 60 GLU cc_start: 0.8638 (mp0) cc_final: 0.8415 (mp0) REVERT: N 91 ARG cc_start: 0.8693 (pmm-80) cc_final: 0.8414 (pmm-80) REVERT: N 122 GLN cc_start: 0.7323 (mt0) cc_final: 0.6999 (mt0) REVERT: N 198 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9003 (tptp) REVERT: N 204 GLU cc_start: 0.8659 (tp30) cc_final: 0.7790 (tp30) outliers start: 69 outliers final: 23 residues processed: 511 average time/residue: 1.9383 time to fit residues: 1076.8476 Evaluate side-chains 490 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 455 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR 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 55 ASP Chi-restraints excluded: chain C residue 150 ASP 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 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain H residue 59 GLU 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 108 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 180 MET Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 171 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN B 97 GLN D 97 GLN E 35 GLN F 35 GLN G 35 GLN G 132 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20041 Z= 0.232 Angle : 0.609 9.397 27111 Z= 0.308 Chirality : 0.041 0.183 3150 Planarity : 0.004 0.051 3556 Dihedral : 3.986 26.965 2800 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.62 % Allowed : 21.19 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2464 helix: 1.94 (0.15), residues: 1351 sheet: 2.08 (0.32), residues: 224 loop : -0.16 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 189 HIS 0.003 0.001 HIS G 138 PHE 0.013 0.001 PHE M 58 TYR 0.015 0.001 TYR B 93 ARG 0.011 0.001 ARG N 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 460 time to evaluate : 2.051 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: 0.9084 (mm-40) cc_final: 0.8705 (mm-40) REVERT: A 100 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8365 (mmtt) REVERT: A 163 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8748 (tmmm) REVERT: A 176 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 178 GLU cc_start: 0.9152 (pm20) cc_final: 0.8909 (pm20) REVERT: B 39 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8843 (mtp-110) REVERT: B 50 GLN cc_start: 0.9210 (pt0) cc_final: 0.8932 (pt0) REVERT: B 100 LYS cc_start: 0.8738 (mptp) cc_final: 0.8291 (mmtt) REVERT: B 156 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: C 39 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8589 (mtp-110) REVERT: C 43 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8962 (mm-30) REVERT: C 97 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8870 (mm-40) REVERT: C 100 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8437 (mmtt) REVERT: C 163 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8660 (tmmm) REVERT: D 43 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8997 (mm-30) REVERT: D 194 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8251 (mt-10) REVERT: E 43 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8970 (mm-30) REVERT: E 50 GLN cc_start: 0.9330 (pt0) cc_final: 0.9083 (pt0) REVERT: E 134 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8293 (mt-10) REVERT: E 163 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8736 (tmmm) REVERT: F 39 ARG cc_start: 0.9176 (ttp80) cc_final: 0.8744 (mtp-110) REVERT: F 43 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8998 (mm-30) REVERT: F 100 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8384 (mmtt) REVERT: F 163 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8762 (tmmm) REVERT: G 50 GLN cc_start: 0.9202 (pt0) cc_final: 0.8916 (pt0) REVERT: G 74 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8867 (p0) REVERT: H 91 ARG cc_start: 0.9332 (ptm160) cc_final: 0.8535 (ptp90) REVERT: H 128 GLN cc_start: 0.8910 (tp40) cc_final: 0.8670 (tp40) REVERT: H 198 LYS cc_start: 0.9073 (tppp) cc_final: 0.8856 (tppp) REVERT: H 203 ILE cc_start: 0.9448 (tp) cc_final: 0.9175 (tp) REVERT: H 204 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7732 (tm-30) REVERT: H 222 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8724 (tp-100) REVERT: I 201 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: I 204 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8100 (tm-30) REVERT: I 222 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8743 (tp-100) REVERT: J 166 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7147 (mm-40) REVERT: J 197 GLU cc_start: 0.9197 (pm20) cc_final: 0.8985 (pm20) REVERT: J 203 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9075 (tp) REVERT: J 204 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7673 (tm-30) REVERT: K 58 PHE cc_start: 0.9095 (t80) cc_final: 0.8796 (t80) REVERT: K 91 ARG cc_start: 0.9128 (ttm110) cc_final: 0.8705 (ttm110) REVERT: K 203 ILE cc_start: 0.9537 (tp) cc_final: 0.9161 (tp) REVERT: K 204 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7926 (tm-30) REVERT: L 60 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8981 (mm-30) REVERT: L 91 ARG cc_start: 0.9304 (mtp-110) cc_final: 0.9081 (mmm-85) REVERT: L 166 GLN cc_start: 0.8090 (tt0) cc_final: 0.7378 (tt0) REVERT: L 170 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8636 (mp) REVERT: L 185 GLU cc_start: 0.8386 (pt0) cc_final: 0.8122 (pt0) REVERT: L 200 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8751 (mtm-85) REVERT: L 203 ILE cc_start: 0.9315 (tp) cc_final: 0.9101 (tp) REVERT: L 204 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7639 (tm-30) REVERT: M 51 TYR cc_start: 0.8310 (t80) cc_final: 0.8079 (t80) REVERT: M 91 ARG cc_start: 0.9326 (mtp-110) cc_final: 0.9126 (mmm-85) REVERT: M 185 GLU cc_start: 0.8604 (pt0) cc_final: 0.8301 (pt0) REVERT: M 198 LYS cc_start: 0.9138 (tppp) cc_final: 0.8865 (tppp) REVERT: M 204 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7971 (tm-30) REVERT: N 91 ARG cc_start: 0.8738 (pmm-80) cc_final: 0.8447 (pmm-80) REVERT: N 122 GLN cc_start: 0.7344 (mt0) cc_final: 0.7027 (mt0) REVERT: N 166 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7547 (mm-40) REVERT: N 197 GLU cc_start: 0.9181 (mp0) cc_final: 0.8957 (pm20) REVERT: N 198 LYS cc_start: 0.9465 (mmmm) cc_final: 0.9057 (tptp) REVERT: N 204 GLU cc_start: 0.8646 (tp30) cc_final: 0.7797 (tp30) outliers start: 75 outliers final: 32 residues processed: 490 average time/residue: 1.9567 time to fit residues: 1040.9811 Evaluate side-chains 494 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 450 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 39 ARG 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 163 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 59 GLU 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 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 GLN 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 169 ASP Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 132 ASN F 50 GLN G 35 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20041 Z= 0.409 Angle : 0.692 10.166 27111 Z= 0.353 Chirality : 0.044 0.191 3150 Planarity : 0.005 0.071 3556 Dihedral : 4.271 26.916 2800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.44 % Allowed : 22.10 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.17), residues: 2464 helix: 1.77 (0.15), residues: 1344 sheet: 2.00 (0.33), residues: 224 loop : -0.22 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.004 0.001 HIS B 138 PHE 0.028 0.002 PHE L 58 TYR 0.013 0.001 TYR D 93 ARG 0.014 0.001 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 446 time to evaluate : 2.108 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 100 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8399 (mmtt) REVERT: A 163 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8753 (tmmm) REVERT: A 176 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8913 (t) REVERT: A 178 GLU cc_start: 0.9155 (pm20) cc_final: 0.8788 (pm20) REVERT: B 39 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8846 (mtp-110) REVERT: B 50 GLN cc_start: 0.9206 (pt0) cc_final: 0.8933 (pt0) REVERT: B 156 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: B 163 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8737 (tmmm) REVERT: B 194 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: C 39 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8629 (mtp-110) REVERT: C 43 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9023 (mm-30) REVERT: C 163 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8694 (tmmm) REVERT: D 43 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9018 (mm-30) REVERT: D 194 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8360 (mt-10) REVERT: E 43 GLU cc_start: 0.9235 (mm-30) cc_final: 0.9033 (mm-30) REVERT: E 50 GLN cc_start: 0.9351 (pt0) cc_final: 0.9032 (pt0) REVERT: E 163 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8757 (tmmm) REVERT: F 39 ARG cc_start: 0.9176 (ttp80) cc_final: 0.8781 (mtp-110) REVERT: F 43 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9032 (mm-30) REVERT: F 100 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8374 (mmtt) REVERT: G 74 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8851 (p0) REVERT: G 150 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8324 (p0) REVERT: G 163 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8700 (tmmm) REVERT: H 91 ARG cc_start: 0.9290 (ptm160) cc_final: 0.8576 (ptp90) REVERT: H 203 ILE cc_start: 0.9464 (tp) cc_final: 0.9193 (tp) REVERT: H 204 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7746 (tm-30) REVERT: H 222 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8675 (tp40) REVERT: I 204 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8151 (tm-30) REVERT: I 222 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8713 (tp-100) REVERT: J 166 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7159 (mm-40) REVERT: J 203 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9125 (tp) REVERT: J 204 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7468 (tm-30) REVERT: K 58 PHE cc_start: 0.9164 (t80) cc_final: 0.8866 (t80) REVERT: K 91 ARG cc_start: 0.9068 (ttm110) cc_final: 0.8528 (ttm110) REVERT: K 197 GLU cc_start: 0.9233 (pm20) cc_final: 0.9013 (pm20) REVERT: K 203 ILE cc_start: 0.9514 (tp) cc_final: 0.9272 (tp) REVERT: K 204 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7958 (tm-30) REVERT: L 60 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9007 (mm-30) REVERT: L 91 ARG cc_start: 0.9269 (mtp-110) cc_final: 0.9065 (mmm-85) REVERT: L 166 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: L 170 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8692 (mp) REVERT: L 185 GLU cc_start: 0.8482 (pt0) cc_final: 0.8240 (pt0) REVERT: L 200 ARG cc_start: 0.8977 (ttm110) cc_final: 0.8702 (mtm-85) REVERT: L 204 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7685 (tm-30) REVERT: M 51 TYR cc_start: 0.8368 (t80) cc_final: 0.8121 (t80) REVERT: M 80 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.9018 (mt0) REVERT: M 185 GLU cc_start: 0.8645 (pt0) cc_final: 0.8329 (pt0) REVERT: M 204 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7997 (tm-30) REVERT: N 91 ARG cc_start: 0.8773 (pmm-80) cc_final: 0.8438 (pmm-80) REVERT: N 122 GLN cc_start: 0.7409 (mt0) cc_final: 0.7042 (mt0) REVERT: N 166 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7736 (mm-40) REVERT: N 198 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9040 (tptp) REVERT: N 203 ILE cc_start: 0.9566 (tp) cc_final: 0.9327 (tp) REVERT: N 204 GLU cc_start: 0.8638 (tp30) cc_final: 0.7924 (tp30) outliers start: 92 outliers final: 37 residues processed: 477 average time/residue: 1.9622 time to fit residues: 1017.6455 Evaluate side-chains 482 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 429 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 204 VAL 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 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 113 THR 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 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 J residue 59 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 223 VAL 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 L residue 170 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 122 GLN 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 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN C 50 GLN D 97 GLN E 35 GLN G 35 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN M 80 GLN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20041 Z= 0.333 Angle : 0.685 10.835 27111 Z= 0.348 Chirality : 0.043 0.193 3150 Planarity : 0.005 0.049 3556 Dihedral : 4.207 27.276 2800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.44 % Allowed : 23.89 % Favored : 71.67 % 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: 1.56 (0.17), residues: 2464 helix: 1.70 (0.15), residues: 1358 sheet: 1.97 (0.32), residues: 224 loop : -0.23 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 189 HIS 0.003 0.001 HIS B 138 PHE 0.015 0.001 PHE M 58 TYR 0.023 0.001 TYR B 93 ARG 0.010 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 530 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 438 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8842 (mm-40) REVERT: A 100 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8403 (mmtt) REVERT: A 163 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8766 (tmmm) REVERT: A 176 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8864 (t) REVERT: A 178 GLU cc_start: 0.9158 (pm20) cc_final: 0.8781 (pm20) REVERT: B 39 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8829 (mtp-110) REVERT: B 50 GLN cc_start: 0.9216 (pt0) cc_final: 0.8943 (pt0) REVERT: B 100 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9094 (mmtt) REVERT: B 156 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: B 163 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8726 (tmmm) REVERT: B 194 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: B 205 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7995 (mtp) REVERT: C 39 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8621 (mtp-110) REVERT: C 43 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9012 (mm-30) REVERT: C 100 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8385 (mmtt) REVERT: C 163 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8722 (tmmm) REVERT: D 43 GLU cc_start: 0.9244 (mm-30) cc_final: 0.9018 (mm-30) REVERT: D 194 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8346 (mt-10) REVERT: E 43 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9027 (mm-30) REVERT: E 50 GLN cc_start: 0.9336 (pt0) cc_final: 0.9029 (pt0) REVERT: E 163 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8773 (tmmm) REVERT: F 39 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8746 (mtp-110) REVERT: F 100 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8434 (mmtt) REVERT: G 74 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8831 (p0) REVERT: G 150 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8307 (p0) REVERT: H 91 ARG cc_start: 0.9287 (ptm160) cc_final: 0.8602 (ptp90) REVERT: H 203 ILE cc_start: 0.9457 (tp) cc_final: 0.9176 (tp) REVERT: H 204 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7977 (tm-30) REVERT: H 222 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8718 (tp-100) REVERT: I 104 PHE cc_start: 0.7821 (t80) cc_final: 0.6515 (t80) REVERT: I 180 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: I 184 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8675 (mp) REVERT: I 204 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8083 (tm-30) REVERT: I 222 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8714 (tp-100) REVERT: J 166 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7230 (mm-40) REVERT: J 203 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9132 (tp) REVERT: J 204 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7827 (tm-30) REVERT: K 58 PHE cc_start: 0.9155 (t80) cc_final: 0.8854 (t80) REVERT: K 91 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8517 (ttm110) REVERT: K 152 ARG cc_start: 0.7277 (tmt170) cc_final: 0.7067 (tmt170) REVERT: K 203 ILE cc_start: 0.9531 (tp) cc_final: 0.9278 (tp) REVERT: K 204 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7970 (tm-30) REVERT: L 60 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8999 (mm-30) REVERT: L 91 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.9074 (mmm-85) REVERT: L 126 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7878 (pmm) REVERT: L 166 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: L 200 ARG cc_start: 0.9005 (ttm110) cc_final: 0.8647 (mtm-85) REVERT: L 204 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7702 (tm-30) REVERT: M 51 TYR cc_start: 0.8344 (t80) cc_final: 0.7903 (t80) REVERT: M 152 ARG cc_start: 0.7325 (tmt170) cc_final: 0.6701 (tmt170) REVERT: M 185 GLU cc_start: 0.8651 (pt0) cc_final: 0.8333 (pt0) REVERT: M 190 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8638 (ttpp) REVERT: M 204 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7967 (tm-30) REVERT: N 91 ARG cc_start: 0.8851 (pmm-80) cc_final: 0.8498 (pmm-80) REVERT: N 122 GLN cc_start: 0.7415 (mt0) cc_final: 0.7047 (mt0) REVERT: N 166 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7659 (mm-40) REVERT: N 203 ILE cc_start: 0.9578 (tp) cc_final: 0.9344 (tp) REVERT: N 204 GLU cc_start: 0.8653 (tp30) cc_final: 0.7823 (tp30) outliers start: 92 outliers final: 43 residues processed: 472 average time/residue: 1.9343 time to fit residues: 993.1729 Evaluate side-chains 487 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 427 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 151 ILE 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 85 SER Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP 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 113 THR Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 170 LEU 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 180 MET 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 71 ASP Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 169 ASP 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 121 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2292 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= 0.265 Angle : 0.700 11.885 27111 Z= 0.354 Chirality : 0.043 0.209 3150 Planarity : 0.005 0.066 3556 Dihedral : 4.068 27.382 2800 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.01 % Allowed : 24.47 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2464 helix: 1.79 (0.15), residues: 1351 sheet: 2.01 (0.32), residues: 224 loop : -0.23 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 189 HIS 0.003 0.001 HIS D 138 PHE 0.021 0.001 PHE L 58 TYR 0.037 0.001 TYR B 93 ARG 0.015 0.001 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 533 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 450 time to evaluate : 2.395 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: 0.9153 (mm-40) cc_final: 0.8813 (mm-40) REVERT: A 100 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8370 (mmtt) REVERT: A 163 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8762 (tmmm) REVERT: A 176 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 178 GLU cc_start: 0.9162 (pm20) cc_final: 0.8777 (pm20) REVERT: B 39 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8828 (mtp-110) REVERT: B 50 GLN cc_start: 0.9208 (pt0) cc_final: 0.8952 (pt0) REVERT: B 156 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: B 163 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8720 (tmmm) REVERT: B 194 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: B 205 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7946 (mtp) REVERT: C 39 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8601 (mtp-110) REVERT: C 43 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8966 (mm-30) REVERT: C 150 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (p0) REVERT: C 163 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8713 (tmmm) REVERT: D 43 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9013 (mm-30) REVERT: E 50 GLN cc_start: 0.9327 (pt0) cc_final: 0.9090 (pt0) REVERT: E 163 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8766 (tmmm) REVERT: F 39 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8766 (mtp-110) REVERT: F 100 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8392 (mmtt) REVERT: F 108 MET cc_start: 0.8621 (ptp) cc_final: 0.8215 (ptp) REVERT: G 74 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8787 (p0) REVERT: G 108 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8579 (ptp) REVERT: G 150 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8328 (p0) REVERT: H 91 ARG cc_start: 0.9287 (ptm160) cc_final: 0.8628 (ptp90) REVERT: H 144 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8685 (ttmp) REVERT: H 203 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9153 (tp) REVERT: H 204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7987 (tm-30) REVERT: H 222 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8707 (tp-100) REVERT: I 184 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8829 (mp) REVERT: I 204 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8177 (tm-30) REVERT: I 222 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8717 (tp-100) REVERT: J 144 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8467 (ptpp) REVERT: J 166 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7207 (mm-40) REVERT: J 203 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9116 (tp) REVERT: J 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7832 (tm-30) REVERT: K 58 PHE cc_start: 0.9145 (t80) cc_final: 0.8877 (t80) REVERT: K 91 ARG cc_start: 0.9049 (ttm110) cc_final: 0.8485 (ttm110) REVERT: K 152 ARG cc_start: 0.7291 (tmt170) cc_final: 0.6998 (tmt170) REVERT: K 203 ILE cc_start: 0.9523 (tp) cc_final: 0.9249 (tp) REVERT: K 204 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7924 (tm-30) REVERT: L 60 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8980 (mm-30) REVERT: L 91 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.9090 (mmm-85) REVERT: L 152 ARG cc_start: 0.7090 (tmt170) cc_final: 0.6544 (tmt170) REVERT: L 166 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: L 198 LYS cc_start: 0.9399 (tppp) cc_final: 0.9177 (tppp) REVERT: L 204 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7972 (tm-30) REVERT: M 51 TYR cc_start: 0.8348 (t80) cc_final: 0.7920 (t80) REVERT: M 185 GLU cc_start: 0.8642 (pt0) cc_final: 0.8317 (pt0) REVERT: M 190 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8636 (ttpp) REVERT: M 204 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8003 (tm-30) REVERT: N 91 ARG cc_start: 0.8845 (pmm-80) cc_final: 0.8475 (pmm-80) REVERT: N 122 GLN cc_start: 0.7376 (mt0) cc_final: 0.7026 (mt0) REVERT: N 166 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7604 (mm-40) REVERT: N 198 LYS cc_start: 0.9397 (tppp) cc_final: 0.8960 (tptp) REVERT: N 203 ILE cc_start: 0.9572 (tp) cc_final: 0.9353 (tp) REVERT: N 204 GLU cc_start: 0.8659 (tp30) cc_final: 0.7741 (tp30) outliers start: 83 outliers final: 36 residues processed: 483 average time/residue: 1.9674 time to fit residues: 1033.3715 Evaluate side-chains 491 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 437 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 204 VAL 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 74 ASP Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 203 ILE 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 184 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 201 GLU 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 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 86 SER 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 87 MET Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 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: 0.8615 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20041 Z= 0.228 Angle : 0.721 12.269 27111 Z= 0.361 Chirality : 0.043 0.315 3150 Planarity : 0.005 0.066 3556 Dihedral : 3.954 27.397 2800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.14 % Allowed : 25.68 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2464 helix: 1.73 (0.15), residues: 1344 sheet: 2.07 (0.32), residues: 224 loop : -0.20 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 189 HIS 0.002 0.000 HIS D 138 PHE 0.020 0.001 PHE I 104 TYR 0.040 0.001 TYR B 93 ARG 0.016 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 520 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 455 time to evaluate : 2.226 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: 0.9119 (mm-40) cc_final: 0.8702 (mm-40) REVERT: A 100 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8469 (mmtm) REVERT: A 163 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8754 (tmmm) REVERT: A 176 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8845 (t) REVERT: A 178 GLU cc_start: 0.9163 (pm20) cc_final: 0.8808 (pm20) REVERT: B 39 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8819 (mtp-110) REVERT: B 50 GLN cc_start: 0.9204 (pt0) cc_final: 0.8911 (pt0) REVERT: B 100 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9077 (mmtt) REVERT: B 156 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 163 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8747 (tmmm) REVERT: B 194 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 205 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: C 39 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8604 (mtp-110) REVERT: C 43 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8976 (mm-30) REVERT: C 150 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8238 (p0) REVERT: C 163 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8726 (tmmm) REVERT: D 43 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8958 (mm-30) REVERT: E 50 GLN cc_start: 0.9307 (pt0) cc_final: 0.9077 (pt0) REVERT: F 39 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8802 (mtp-110) REVERT: F 100 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8473 (mmtt) REVERT: F 108 MET cc_start: 0.8578 (ptp) cc_final: 0.8177 (ptp) REVERT: G 74 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8826 (p0) REVERT: G 150 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8347 (p0) REVERT: H 84 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8706 (mm) REVERT: H 91 ARG cc_start: 0.9286 (ptm160) cc_final: 0.8622 (ptp90) REVERT: H 204 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8031 (tm-30) REVERT: H 222 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8712 (tp-100) REVERT: I 104 PHE cc_start: 0.7775 (t80) cc_final: 0.6500 (t80) REVERT: I 180 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8241 (tmm) REVERT: I 184 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8570 (mp) REVERT: I 197 GLU cc_start: 0.8961 (mp0) cc_final: 0.8350 (mp0) REVERT: I 201 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: I 204 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8190 (tm-30) REVERT: I 222 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8737 (tp-100) REVERT: J 166 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7234 (mm-40) REVERT: J 187 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7924 (mtp) REVERT: J 203 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9109 (tp) REVERT: J 204 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7834 (tm-30) REVERT: K 58 PHE cc_start: 0.9115 (t80) cc_final: 0.8835 (t80) REVERT: K 91 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8509 (ttm110) REVERT: K 152 ARG cc_start: 0.7301 (tmt170) cc_final: 0.7025 (tmt170) REVERT: K 185 GLU cc_start: 0.8207 (pp20) cc_final: 0.7978 (pp20) REVERT: K 203 ILE cc_start: 0.9510 (tp) cc_final: 0.9236 (tp) REVERT: K 204 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7996 (tm-30) REVERT: L 91 ARG cc_start: 0.9305 (mtp-110) cc_final: 0.9094 (mmm-85) REVERT: L 152 ARG cc_start: 0.7045 (tmt170) cc_final: 0.6580 (tmt170) REVERT: L 166 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: L 198 LYS cc_start: 0.9408 (tppp) cc_final: 0.9197 (tppp) REVERT: L 200 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8634 (mtm-85) REVERT: L 204 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7942 (tm-30) REVERT: M 51 TYR cc_start: 0.8343 (t80) cc_final: 0.7921 (t80) REVERT: M 84 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8763 (mm) REVERT: M 185 GLU cc_start: 0.8637 (pt0) cc_final: 0.8314 (pt0) REVERT: M 190 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8621 (ttpp) REVERT: M 204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8008 (tm-30) REVERT: N 91 ARG cc_start: 0.8823 (pmm-80) cc_final: 0.8443 (pmm-80) REVERT: N 122 GLN cc_start: 0.7313 (mt0) cc_final: 0.6959 (mt0) REVERT: N 166 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7501 (mm-40) REVERT: N 198 LYS cc_start: 0.9402 (tppp) cc_final: 0.8968 (tptp) REVERT: N 203 ILE cc_start: 0.9539 (tp) cc_final: 0.9337 (tp) REVERT: N 204 GLU cc_start: 0.8693 (tp30) cc_final: 0.7682 (tp30) outliers start: 65 outliers final: 29 residues processed: 482 average time/residue: 1.9596 time to fit residues: 1026.6085 Evaluate side-chains 478 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 429 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 55 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 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 180 MET Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU 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 121 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 146 MET Chi-restraints excluded: chain N residue 169 ASP 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: 8.9990 chunk 137 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 188 optimal weight: 0.0040 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 GLN N 157 GLN N 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20041 Z= 0.314 Angle : 0.766 12.841 27111 Z= 0.389 Chirality : 0.044 0.322 3150 Planarity : 0.005 0.069 3556 Dihedral : 4.074 27.242 2800 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.33 % Allowed : 25.92 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2464 helix: 1.53 (0.15), residues: 1358 sheet: 2.07 (0.32), residues: 224 loop : -0.13 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS G 138 PHE 0.026 0.001 PHE M 104 TYR 0.031 0.001 TYR B 93 ARG 0.017 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 501 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 432 time to evaluate : 2.258 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: 0.9147 (mm-40) cc_final: 0.8725 (mm-40) REVERT: A 100 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8340 (mmtt) REVERT: A 163 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8762 (tmmm) REVERT: A 176 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8844 (t) REVERT: A 178 GLU cc_start: 0.9172 (pm20) cc_final: 0.8809 (pm20) REVERT: B 39 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8862 (mtp-110) REVERT: B 50 GLN cc_start: 0.9195 (pt0) cc_final: 0.8904 (pt0) REVERT: B 156 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: B 194 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: B 205 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7933 (mtp) REVERT: C 39 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8632 (mtp-110) REVERT: C 43 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8977 (mm-30) REVERT: C 163 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8742 (tmmm) REVERT: D 43 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9026 (mm-30) REVERT: E 50 GLN cc_start: 0.9316 (pt0) cc_final: 0.9075 (pt0) REVERT: F 39 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8764 (mtp-110) REVERT: F 194 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8826 (mt-10) REVERT: G 74 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8804 (p0) REVERT: G 150 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8406 (p0) REVERT: H 84 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8565 (mm) REVERT: H 91 ARG cc_start: 0.9288 (ptm160) cc_final: 0.8962 (ptp90) REVERT: H 200 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8375 (mtm110) REVERT: H 204 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7759 (tm-30) REVERT: H 222 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8708 (tp-100) REVERT: I 104 PHE cc_start: 0.7867 (t80) cc_final: 0.6572 (t80) REVERT: I 180 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8121 (tmm) REVERT: I 184 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8561 (mp) REVERT: I 197 GLU cc_start: 0.8993 (mp0) cc_final: 0.8470 (mp0) REVERT: I 201 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: I 204 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8097 (tm-30) REVERT: I 222 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8710 (tp-100) REVERT: J 122 GLN cc_start: 0.8223 (mm-40) cc_final: 0.6779 (mt0) REVERT: J 152 ARG cc_start: 0.6471 (tmt170) cc_final: 0.6117 (tmt170) REVERT: J 185 GLU cc_start: 0.8285 (pp20) cc_final: 0.8057 (pp20) REVERT: J 187 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: J 203 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9121 (tp) REVERT: J 204 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7804 (tm-30) REVERT: K 58 PHE cc_start: 0.9150 (t80) cc_final: 0.8856 (t80) REVERT: K 91 ARG cc_start: 0.9032 (ttm110) cc_final: 0.8469 (ttm110) REVERT: K 203 ILE cc_start: 0.9523 (tp) cc_final: 0.9254 (tp) REVERT: K 204 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 59 GLU cc_start: 0.8904 (mp0) cc_final: 0.8604 (mp0) REVERT: L 91 ARG cc_start: 0.9292 (mtp-110) cc_final: 0.9084 (mmm-85) REVERT: L 152 ARG cc_start: 0.7162 (tmt170) cc_final: 0.6680 (tmt170) REVERT: L 166 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: L 198 LYS cc_start: 0.9403 (tppp) cc_final: 0.9161 (tppp) REVERT: L 200 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8664 (mtm-85) REVERT: L 204 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7683 (tm-30) REVERT: M 51 TYR cc_start: 0.8351 (t80) cc_final: 0.8147 (t80) REVERT: M 84 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8814 (mm) REVERT: M 185 GLU cc_start: 0.8650 (pt0) cc_final: 0.8327 (pt0) REVERT: M 190 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8628 (ttpp) REVERT: M 204 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8004 (tm-30) REVERT: N 122 GLN cc_start: 0.7343 (mt0) cc_final: 0.6987 (mt0) REVERT: N 166 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7595 (mm-40) REVERT: N 185 GLU cc_start: 0.8346 (pp20) cc_final: 0.7926 (pp20) REVERT: N 198 LYS cc_start: 0.9400 (tppp) cc_final: 0.8944 (tptp) REVERT: N 200 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8652 (mmm160) REVERT: N 203 ILE cc_start: 0.9549 (tp) cc_final: 0.9345 (tp) REVERT: N 204 GLU cc_start: 0.8578 (tp30) cc_final: 0.7846 (tp30) outliers start: 69 outliers final: 34 residues processed: 464 average time/residue: 1.9336 time to fit residues: 974.6198 Evaluate side-chains 479 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 427 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain 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 180 MET Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 59 GLU 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 121 VAL Chi-restraints excluded: chain L residue 122 GLN 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 84 LEU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 146 MET Chi-restraints excluded: chain N residue 169 ASP 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: 3.9990 chunk 57 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN E 35 GLN F 35 GLN F 50 GLN G 35 GLN I 150 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.054109 restraints weight = 56116.157| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.90 r_work: 0.2650 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20041 Z= 0.265 Angle : 0.757 13.215 27111 Z= 0.386 Chirality : 0.044 0.286 3150 Planarity : 0.005 0.086 3556 Dihedral : 4.162 27.404 2800 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.90 % Allowed : 26.54 % Favored : 70.56 % 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: 1.44 (0.18), residues: 2464 helix: 1.52 (0.15), residues: 1358 sheet: 2.04 (0.31), residues: 224 loop : -0.14 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 189 HIS 0.003 0.000 HIS G 138 PHE 0.016 0.001 PHE I 104 TYR 0.036 0.001 TYR B 93 ARG 0.015 0.001 ARG H 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12442.01 seconds wall clock time: 221 minutes 42.87 seconds (13302.87 seconds total)