Starting phenix.real_space_refine on Sat Mar 16 16:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/03_2024/7ouf_13075_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.020 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9426 2.51 5 N 2708 2.21 5 O 2826 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15094 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "B" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, '1L0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, '1L0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 99.207 124.392 25.234 1.00 67.89 S ATOM 260 SG CYS D 38 97.150 126.483 27.367 1.00 71.78 S ATOM 2296 SG CYS E 35 72.024 57.694 37.712 1.00 18.55 S ATOM 2317 SG CYS E 38 68.786 59.299 38.503 1.00 10.83 S ATOM 7744 SG CYS A 35 22.026 43.004 24.693 1.00 59.67 S ATOM 7765 SG CYS A 38 24.048 40.909 26.854 1.00 61.22 S ATOM 9801 SG CYS B 35 48.975 109.678 37.794 1.00 23.48 S ATOM 9822 SG CYS B 38 52.200 108.072 38.634 1.00 10.83 S Time building chain proxies: 8.34, per 1000 atoms: 0.55 Number of scatterers: 15094 At special positions: 0 Unit cell: (122.1, 168.3, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 4 9.00 O 2826 8.00 N 2708 7.00 C 9426 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=0, symmetry=0 Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 8 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 12 sheets defined 45.4% alpha, 10.3% beta 24 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.621A pdb=" N LEU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.673A pdb=" N GLY D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 151 through 174 removed outlier: 5.763A pdb=" N LEU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP E 174 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 38 through 49 removed outlier: 3.698A pdb=" N CYS F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 80 Processing helix chain 'F' and resid 89 through 103 Proline residue: F 93 - end of helix Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.675A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.819A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 213 Processing helix chain 'F' and resid 221 through 234 removed outlier: 4.163A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 261 through 275 Proline residue: F 265 - end of helix removed outlier: 3.924A pdb=" N LEU F 275 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 removed outlier: 3.970A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix removed outlier: 3.656A pdb=" N LYS F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.867A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.621A pdb=" N LEU A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.674A pdb=" N GLY A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 151 through 174 removed outlier: 5.762A pdb=" N LEU B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 174 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.699A pdb=" N CYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 80 Processing helix chain 'C' and resid 89 through 103 Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.675A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.820A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 213 Processing helix chain 'C' and resid 221 through 234 removed outlier: 4.163A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 261 through 275 Proline residue: C 265 - end of helix removed outlier: 3.924A pdb=" N LEU C 275 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.970A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix removed outlier: 3.656A pdb=" N LYS C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.868A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'D' and resid 89 through 94 removed outlier: 7.351A pdb=" N HIS D 118 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY D 64 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN D 120 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ILE D 66 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASP D 122 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 13.968A pdb=" N HIS D 68 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 144 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= C, first strand: chain 'D' and resid 255 through 258 Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 6.875A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 144 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= F, first strand: chain 'E' and resid 266 through 269 removed outlier: 4.159A pdb=" N GLN E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.351A pdb=" N HIS A 118 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLY A 64 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN A 120 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ILE A 66 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ASP A 122 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 13.969A pdb=" N HIS A 68 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 144 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'A' and resid 255 through 258 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.877A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 144 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= L, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.159A pdb=" N GLN B 250 " --> pdb=" O LEU B 257 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2169 1.31 - 1.43: 4841 1.43 - 1.56: 8448 1.56 - 1.68: 152 1.68 - 1.81: 62 Bond restraints: 15672 Sorted by residual: bond pdb=" C09 1L0 E 304 " pdb=" O12 1L0 E 304 " ideal model delta sigma weight residual 1.185 1.402 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C09 1L0 B 304 " pdb=" O12 1L0 B 304 " ideal model delta sigma weight residual 1.185 1.402 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C05 1L0 B 304 " pdb=" N10 1L0 B 304 " ideal model delta sigma weight residual 1.532 1.377 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C05 1L0 E 304 " pdb=" N10 1L0 E 304 " ideal model delta sigma weight residual 1.532 1.379 0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C09 1L0 B 304 " pdb=" N10 1L0 B 304 " ideal model delta sigma weight residual 1.469 1.338 0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 1080 106.41 - 113.32: 8577 113.32 - 120.23: 5515 120.23 - 127.14: 6087 127.14 - 134.04: 417 Bond angle restraints: 21676 Sorted by residual: angle pdb=" C03 1L0 B 304 " pdb=" C02 1L0 B 304 " pdb=" C25 1L0 B 304 " ideal model delta sigma weight residual 107.61 120.93 -13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C03 1L0 E 304 " pdb=" C02 1L0 E 304 " pdb=" C25 1L0 E 304 " ideal model delta sigma weight residual 107.61 120.65 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N VAL F 86 " pdb=" CA VAL F 86 " pdb=" C VAL F 86 " ideal model delta sigma weight residual 112.96 109.29 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N VAL C 86 " pdb=" CA VAL C 86 " pdb=" C VAL C 86 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N GLU F 75 " pdb=" CA GLU F 75 " pdb=" CB GLU F 75 " ideal model delta sigma weight residual 110.28 114.30 -4.02 1.55e+00 4.16e-01 6.72e+00 ... (remaining 21671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 7802 17.00 - 34.00: 793 34.00 - 51.00: 377 51.00 - 68.00: 102 68.00 - 85.00: 22 Dihedral angle restraints: 9096 sinusoidal: 4180 harmonic: 4916 Sorted by residual: dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N TYR E 231 " pdb=" CA TYR E 231 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA TYR B 230 " pdb=" C TYR B 230 " pdb=" N TYR B 231 " pdb=" CA TYR B 231 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR D 230 " pdb=" C TYR D 230 " pdb=" N TYR D 231 " pdb=" CA TYR D 231 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1524 0.030 - 0.059: 548 0.059 - 0.089: 216 0.089 - 0.118: 96 0.118 - 0.148: 22 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE B 147 " pdb=" N ILE B 147 " pdb=" C ILE B 147 " pdb=" CB ILE B 147 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE B 216 " pdb=" N ILE B 216 " pdb=" C ILE B 216 " pdb=" CB ILE B 216 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2403 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 33 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 34 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 33 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO F 34 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 34 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 34 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 210 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO B 211 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.033 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 33 2.33 - 2.97: 6860 2.97 - 3.61: 21791 3.61 - 4.26: 35167 4.26 - 4.90: 56611 Nonbonded interactions: 120462 Sorted by model distance: nonbonded pdb="MG MG B 302 " pdb=" O11 1L0 B 304 " model vdw 1.686 2.170 nonbonded pdb="MG MG E 302 " pdb=" O11 1L0 E 304 " model vdw 1.705 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.760 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.769 2.170 nonbonded pdb="MG MG B 303 " pdb=" O12 1L0 B 304 " model vdw 1.771 2.170 ... (remaining 120457 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' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'B' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) selection = (chain 'D' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'E' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.340 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.340 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 0.217 15672 Z= 0.267 Angle : 0.564 13.325 21676 Z= 0.305 Chirality : 0.040 0.148 2406 Planarity : 0.005 0.067 2464 Dihedral : 17.507 85.004 5884 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.10 (0.21), residues: 1640 helix: 0.78 (0.19), residues: 750 sheet: 0.48 (0.33), residues: 222 loop : -0.83 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 229 HIS 0.005 0.001 HIS E 112 PHE 0.009 0.001 PHE E 10 TYR 0.007 0.001 TYR D 231 ARG 0.003 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 450 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.7087 (t0) cc_final: 0.6808 (t0) REVERT: D 274 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8213 (ptmt) REVERT: E 49 ARG cc_start: 0.6782 (mtp180) cc_final: 0.6442 (mtp180) REVERT: E 78 LEU cc_start: 0.7960 (mt) cc_final: 0.7704 (mt) REVERT: F 67 GLU cc_start: 0.5378 (tp30) cc_final: 0.5172 (mm-30) REVERT: A 186 VAL cc_start: 0.8273 (t) cc_final: 0.7993 (t) REVERT: B 101 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6783 (mt-10) REVERT: B 122 ASP cc_start: 0.8101 (p0) cc_final: 0.7870 (p0) REVERT: C 202 LYS cc_start: 0.7284 (mttt) cc_final: 0.7063 (mttt) REVERT: C 269 TYR cc_start: 0.8417 (t80) cc_final: 0.7974 (t80) REVERT: C 300 LYS cc_start: 0.8085 (pptt) cc_final: 0.7773 (pptt) outliers start: 2 outliers final: 1 residues processed: 450 average time/residue: 1.2672 time to fit residues: 623.4977 Evaluate side-chains 381 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 93 HIS D 123 ASN D 192 ASN D 228 HIS D 238 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 59 ASN E 63 GLN E 68 HIS E 161 ASN E 182 ASN E 195 ASN E 206 GLN E 250 GLN F 48 GLN F 166 GLN F 306 ASN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 143 HIS A 146 HIS A 161 ASN A 182 ASN A 201 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 42 ASN B 63 GLN B 123 ASN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 306 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15672 Z= 0.291 Angle : 0.623 11.333 21676 Z= 0.323 Chirality : 0.044 0.170 2406 Planarity : 0.006 0.065 2464 Dihedral : 19.631 85.094 2660 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.75 % Allowed : 13.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.12 (0.21), residues: 1640 helix: 0.77 (0.19), residues: 756 sheet: 0.20 (0.32), residues: 222 loop : -0.67 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 65 HIS 0.012 0.001 HIS E 33 PHE 0.024 0.002 PHE C 144 TYR 0.020 0.002 TYR C 79 ARG 0.006 0.001 ARG C 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 400 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.6881 (mtp180) cc_final: 0.6554 (mtp180) REVERT: F 75 GLU cc_start: 0.6811 (mp0) cc_final: 0.6526 (mp0) REVERT: F 223 GLU cc_start: 0.6815 (mp0) cc_final: 0.6601 (mp0) REVERT: F 305 LEU cc_start: 0.7959 (tp) cc_final: 0.7727 (tm) REVERT: F 306 ASN cc_start: 0.8043 (m-40) cc_final: 0.7533 (m-40) REVERT: A 186 VAL cc_start: 0.8360 (t) cc_final: 0.8129 (t) REVERT: B 78 LEU cc_start: 0.8188 (mt) cc_final: 0.7909 (mt) REVERT: C 103 MET cc_start: 0.7969 (mmt) cc_final: 0.7742 (mmm) REVERT: C 202 LYS cc_start: 0.7329 (mttt) cc_final: 0.7103 (mttt) REVERT: C 223 GLU cc_start: 0.6868 (mp0) cc_final: 0.6588 (mp0) REVERT: C 269 TYR cc_start: 0.8453 (t80) cc_final: 0.7901 (t80) REVERT: C 300 LYS cc_start: 0.8180 (pptt) cc_final: 0.7837 (pptt) outliers start: 40 outliers final: 13 residues processed: 413 average time/residue: 1.3541 time to fit residues: 610.2344 Evaluate side-chains 404 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 391 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 126 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 0.0070 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 151 optimal weight: 0.6980 chunk 52 optimal weight: 0.0060 chunk 122 optimal weight: 0.9990 overall best weight: 0.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 246 GLN E 59 ASN E 63 GLN E 177 ASN F 48 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 250 GLN B 59 ASN B 63 GLN B 123 ASN B 130 GLN B 177 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15672 Z= 0.150 Angle : 0.537 10.314 21676 Z= 0.276 Chirality : 0.039 0.151 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.303 88.025 2660 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.02 % Allowed : 16.90 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.21 (0.21), residues: 1640 helix: 0.86 (0.19), residues: 756 sheet: 0.26 (0.33), residues: 222 loop : -0.65 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 65 HIS 0.012 0.001 HIS D 93 PHE 0.018 0.001 PHE C 144 TYR 0.026 0.002 TYR F 190 ARG 0.006 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 407 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6538 (mtp180) REVERT: F 75 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: F 103 MET cc_start: 0.6945 (mmt) cc_final: 0.6703 (mmm) REVERT: F 165 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6125 (mp) REVERT: F 305 LEU cc_start: 0.7999 (tp) cc_final: 0.7697 (tm) REVERT: A 186 VAL cc_start: 0.8350 (t) cc_final: 0.8091 (t) REVERT: B 78 LEU cc_start: 0.8115 (mt) cc_final: 0.7859 (mt) REVERT: C 202 LYS cc_start: 0.7382 (mttt) cc_final: 0.7174 (mttt) REVERT: C 223 GLU cc_start: 0.6788 (mp0) cc_final: 0.6445 (mp0) REVERT: C 282 THR cc_start: 0.6884 (p) cc_final: 0.6641 (p) REVERT: C 300 LYS cc_start: 0.8145 (pptt) cc_final: 0.7809 (pptt) outliers start: 44 outliers final: 15 residues processed: 419 average time/residue: 1.3257 time to fit residues: 605.4611 Evaluate side-chains 404 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 387 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 219 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 145 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 246 GLN E 59 ASN E 63 GLN E 130 GLN E 177 ASN F 48 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 250 GLN B 59 ASN B 63 GLN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS C 306 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15672 Z= 0.188 Angle : 0.546 10.920 21676 Z= 0.280 Chirality : 0.040 0.151 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.226 88.369 2660 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.37 % Allowed : 17.65 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.26 (0.21), residues: 1640 helix: 0.94 (0.19), residues: 752 sheet: 0.23 (0.32), residues: 222 loop : -0.65 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 65 HIS 0.016 0.001 HIS A 93 PHE 0.015 0.001 PHE C 144 TYR 0.024 0.002 TYR C 190 ARG 0.009 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 401 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6829 (t0) REVERT: E 49 ARG cc_start: 0.6893 (mtp180) cc_final: 0.6542 (mtp180) REVERT: E 175 ASN cc_start: 0.7801 (t0) cc_final: 0.7597 (t0) REVERT: F 103 MET cc_start: 0.7094 (mmt) cc_final: 0.6887 (mmm) REVERT: F 165 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6152 (mp) REVERT: A 186 VAL cc_start: 0.8367 (t) cc_final: 0.8108 (t) REVERT: B 78 LEU cc_start: 0.8078 (mt) cc_final: 0.7861 (mt) REVERT: C 43 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7849 (mt) REVERT: C 202 LYS cc_start: 0.7513 (mttt) cc_final: 0.7310 (mttt) REVERT: C 223 GLU cc_start: 0.6831 (mp0) cc_final: 0.6475 (mp0) REVERT: C 269 TYR cc_start: 0.8306 (t80) cc_final: 0.7776 (t80) REVERT: C 311 ILE cc_start: 0.7926 (mp) cc_final: 0.7701 (mp) outliers start: 49 outliers final: 19 residues processed: 415 average time/residue: 1.3575 time to fit residues: 613.6622 Evaluate side-chains 409 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 387 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 59 ASN E 63 GLN E 123 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 59 ASN B 63 GLN B 123 ASN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15672 Z= 0.221 Angle : 0.565 10.900 21676 Z= 0.290 Chirality : 0.041 0.151 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.304 88.407 2658 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 18.48 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.26 (0.21), residues: 1640 helix: 0.95 (0.19), residues: 750 sheet: 0.20 (0.32), residues: 222 loop : -0.65 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 65 HIS 0.016 0.001 HIS A 93 PHE 0.014 0.001 PHE C 144 TYR 0.032 0.002 TYR C 190 ARG 0.010 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 398 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7227 (mtt-85) REVERT: E 49 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6564 (mtp85) REVERT: E 101 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: F 48 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: F 103 MET cc_start: 0.7353 (mmt) cc_final: 0.7099 (mmm) REVERT: F 165 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6600 (mt) REVERT: F 216 GLU cc_start: 0.5359 (mp0) cc_final: 0.3485 (mp0) REVERT: A 186 VAL cc_start: 0.8390 (t) cc_final: 0.8140 (t) REVERT: B 78 LEU cc_start: 0.8091 (mt) cc_final: 0.7878 (mt) REVERT: B 101 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: C 43 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7902 (mt) REVERT: C 79 TYR cc_start: 0.8360 (t80) cc_final: 0.8133 (t80) REVERT: C 105 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5671 (pmt170) REVERT: C 165 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7800 (mm) REVERT: C 202 LYS cc_start: 0.7574 (mttt) cc_final: 0.7368 (mttt) outliers start: 59 outliers final: 28 residues processed: 415 average time/residue: 1.4086 time to fit residues: 634.6887 Evaluate side-chains 429 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 393 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 15 GLN E 63 GLN E 206 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 250 GLN B 59 ASN B 63 GLN B 123 ASN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15672 Z= 0.231 Angle : 0.578 10.892 21676 Z= 0.298 Chirality : 0.041 0.170 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.337 88.838 2658 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.85 % Allowed : 19.37 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.22 (0.21), residues: 1640 helix: 0.86 (0.19), residues: 752 sheet: 0.14 (0.32), residues: 222 loop : -0.59 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 65 HIS 0.015 0.001 HIS A 93 PHE 0.014 0.001 PHE C 104 TYR 0.022 0.002 TYR C 92 ARG 0.012 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 395 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7280 (mtt-85) REVERT: E 49 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6580 (mtp85) REVERT: E 101 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: F 103 MET cc_start: 0.7568 (mmt) cc_final: 0.7331 (mmm) REVERT: F 165 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7044 (mt) REVERT: F 216 GLU cc_start: 0.5555 (mp0) cc_final: 0.3891 (mp0) REVERT: F 303 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5934 (ttp) REVERT: A 186 VAL cc_start: 0.8392 (t) cc_final: 0.8151 (t) REVERT: B 78 LEU cc_start: 0.8149 (mt) cc_final: 0.7938 (mt) REVERT: B 101 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: B 201 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7281 (mm-40) REVERT: C 43 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7958 (mt) REVERT: C 105 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5904 (pmt170) REVERT: C 163 PHE cc_start: 0.7759 (t80) cc_final: 0.7555 (t80) REVERT: C 165 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7469 (mm) REVERT: C 202 LYS cc_start: 0.7783 (mttt) cc_final: 0.7575 (mttt) outliers start: 56 outliers final: 27 residues processed: 414 average time/residue: 1.3856 time to fit residues: 623.1301 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 395 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 248 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 63 GLN E 206 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 59 ASN B 63 GLN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15672 Z= 0.230 Angle : 0.589 10.927 21676 Z= 0.303 Chirality : 0.042 0.178 2406 Planarity : 0.006 0.065 2464 Dihedral : 19.345 89.152 2658 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.64 % Allowed : 20.54 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.13 (0.21), residues: 1640 helix: 0.78 (0.19), residues: 756 sheet: 0.11 (0.32), residues: 222 loop : -0.62 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 65 HIS 0.017 0.001 HIS A 93 PHE 0.013 0.001 PHE C 99 TYR 0.029 0.002 TYR F 199 ARG 0.015 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 403 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7284 (mtt-85) REVERT: E 49 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6594 (mtp85) REVERT: E 101 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: F 137 VAL cc_start: 0.8198 (p) cc_final: 0.7943 (m) REVERT: F 165 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7049 (mt) REVERT: F 202 LYS cc_start: 0.7430 (mttt) cc_final: 0.7137 (mttt) REVERT: F 216 GLU cc_start: 0.5653 (mp0) cc_final: 0.4138 (mp0) REVERT: B 78 LEU cc_start: 0.8148 (mt) cc_final: 0.7936 (mt) REVERT: B 101 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: B 201 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7299 (mm-40) REVERT: C 43 ILE cc_start: 0.8227 (mm) cc_final: 0.7950 (mt) REVERT: C 76 MET cc_start: 0.7508 (mpp) cc_final: 0.7288 (mpp) REVERT: C 103 MET cc_start: 0.7881 (mmt) cc_final: 0.7678 (mmt) REVERT: C 165 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7485 (mp) REVERT: C 269 TYR cc_start: 0.8236 (t80) cc_final: 0.7694 (t80) REVERT: C 274 PHE cc_start: 0.7699 (m-80) cc_final: 0.7465 (t80) REVERT: C 282 THR cc_start: 0.7106 (p) cc_final: 0.6901 (p) outliers start: 53 outliers final: 31 residues processed: 423 average time/residue: 1.3788 time to fit residues: 634.2988 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 394 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.0270 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 15 GLN E 63 GLN E 206 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 59 ASN B 63 GLN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15672 Z= 0.212 Angle : 0.592 11.385 21676 Z= 0.306 Chirality : 0.041 0.186 2406 Planarity : 0.006 0.068 2464 Dihedral : 19.308 89.679 2658 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.43 % Allowed : 21.70 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.12 (0.21), residues: 1640 helix: 0.78 (0.19), residues: 754 sheet: 0.12 (0.33), residues: 222 loop : -0.64 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 65 HIS 0.017 0.001 HIS A 93 PHE 0.014 0.001 PHE C 99 TYR 0.023 0.002 TYR C 199 ARG 0.015 0.001 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 387 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7291 (mtt-85) REVERT: E 49 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6604 (mtp85) REVERT: E 101 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: F 137 VAL cc_start: 0.8217 (p) cc_final: 0.7953 (m) REVERT: F 165 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6943 (mt) REVERT: F 202 LYS cc_start: 0.7507 (mttt) cc_final: 0.7224 (mttt) REVERT: F 216 GLU cc_start: 0.5691 (mp0) cc_final: 0.4588 (mp0) REVERT: B 101 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: B 201 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: C 43 ILE cc_start: 0.8268 (mm) cc_final: 0.7962 (mt) REVERT: C 216 GLU cc_start: 0.6067 (mp0) cc_final: 0.5383 (mp0) REVERT: C 269 TYR cc_start: 0.8223 (t80) cc_final: 0.7691 (t80) outliers start: 50 outliers final: 32 residues processed: 409 average time/residue: 1.3670 time to fit residues: 607.8652 Evaluate side-chains 420 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 383 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 0.0030 chunk 142 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 15 GLN E 63 GLN E 206 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 HIS A 250 GLN B 59 ASN B 63 GLN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15672 Z= 0.184 Angle : 0.615 12.496 21676 Z= 0.314 Chirality : 0.041 0.201 2406 Planarity : 0.006 0.091 2464 Dihedral : 19.238 89.792 2658 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.02 % Allowed : 22.66 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.17 (0.21), residues: 1640 helix: 0.80 (0.19), residues: 748 sheet: 0.14 (0.33), residues: 222 loop : -0.58 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 65 HIS 0.018 0.001 HIS A 93 PHE 0.034 0.001 PHE C 99 TYR 0.032 0.002 TYR F 199 ARG 0.018 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 389 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7270 (mtt-85) REVERT: E 49 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6591 (mtp85) REVERT: E 101 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: F 137 VAL cc_start: 0.8121 (p) cc_final: 0.7900 (m) REVERT: F 165 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7071 (mt) REVERT: F 202 LYS cc_start: 0.7519 (mttt) cc_final: 0.7242 (mttt) REVERT: F 210 ARG cc_start: 0.6689 (mtp85) cc_final: 0.6478 (mtm180) REVERT: F 216 GLU cc_start: 0.5709 (mp0) cc_final: 0.4502 (mp0) REVERT: F 265 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7648 (Cg_exo) REVERT: B 101 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: B 201 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7296 (mm-40) REVERT: C 43 ILE cc_start: 0.8233 (mm) cc_final: 0.7985 (mt) REVERT: C 162 LYS cc_start: 0.6922 (tptt) cc_final: 0.6677 (tptp) REVERT: C 216 GLU cc_start: 0.6074 (mp0) cc_final: 0.5667 (mp0) REVERT: C 235 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: C 269 TYR cc_start: 0.8202 (t80) cc_final: 0.7721 (t80) outliers start: 44 outliers final: 28 residues processed: 407 average time/residue: 1.4023 time to fit residues: 620.3576 Evaluate side-chains 418 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 384 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 102 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 15 GLN E 59 ASN E 63 GLN E 123 ASN E 206 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 250 GLN B 59 ASN B 63 GLN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15672 Z= 0.238 Angle : 0.654 19.929 21676 Z= 0.330 Chirality : 0.042 0.207 2406 Planarity : 0.006 0.088 2464 Dihedral : 19.312 89.494 2658 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.61 % Allowed : 23.49 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.10 (0.21), residues: 1640 helix: 0.78 (0.19), residues: 746 sheet: 0.06 (0.33), residues: 222 loop : -0.65 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 293 HIS 0.019 0.001 HIS A 93 PHE 0.025 0.002 PHE C 99 TYR 0.026 0.002 TYR F 190 ARG 0.020 0.001 ARG F 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 394 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7280 (mtt-85) REVERT: E 49 ARG cc_start: 0.6979 (mtp180) cc_final: 0.6598 (mtp85) REVERT: E 101 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: F 137 VAL cc_start: 0.8293 (p) cc_final: 0.8027 (m) REVERT: F 165 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7075 (mt) REVERT: F 202 LYS cc_start: 0.7616 (mttt) cc_final: 0.7325 (mttt) REVERT: F 210 ARG cc_start: 0.6761 (mtp85) cc_final: 0.6487 (mtm180) REVERT: F 216 GLU cc_start: 0.5844 (mp0) cc_final: 0.4912 (mp0) REVERT: F 265 PRO cc_start: 0.7901 (Cg_exo) cc_final: 0.7589 (Cg_exo) REVERT: B 101 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: B 201 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7313 (mm-40) REVERT: C 43 ILE cc_start: 0.8301 (mm) cc_final: 0.8037 (mt) REVERT: C 216 GLU cc_start: 0.6544 (mp0) cc_final: 0.6065 (mp0) REVERT: C 265 PRO cc_start: 0.7897 (Cg_exo) cc_final: 0.7617 (Cg_exo) REVERT: C 269 TYR cc_start: 0.8209 (t80) cc_final: 0.7726 (t80) outliers start: 38 outliers final: 27 residues processed: 409 average time/residue: 1.3873 time to fit residues: 616.5138 Evaluate side-chains 428 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 396 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 15 GLN E 59 ASN E 63 GLN E 123 ASN E 206 GLN ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 59 ASN B 63 GLN B 177 ASN B 206 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116528 restraints weight = 22202.261| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.02 r_work: 0.3295 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15672 Z= 0.277 Angle : 0.662 12.480 21676 Z= 0.339 Chirality : 0.044 0.216 2406 Planarity : 0.006 0.091 2464 Dihedral : 19.436 89.431 2658 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.75 % Allowed : 24.11 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % 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: 0.03 (0.21), residues: 1640 helix: 0.70 (0.19), residues: 742 sheet: -0.02 (0.33), residues: 222 loop : -0.62 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 293 HIS 0.020 0.001 HIS A 93 PHE 0.021 0.002 PHE C 99 TYR 0.026 0.002 TYR C 79 ARG 0.021 0.001 ARG F 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8434.84 seconds wall clock time: 148 minutes 11.86 seconds (8891.86 seconds total)