Starting phenix.real_space_refine on Thu Nov 16 10:27:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_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_13075/11_2023/7ouf_13075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_13075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouf_13075/11_2023/7ouf_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-1.21rc1-5144/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: 8.53, per 1000 atoms: 0.57 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: 6.12 Conformation dependent library (CDL) restraints added in 2.5 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: 6.11 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: 4.43 Time building geometry restraints manager: 6.56 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: 7776 17.00 - 34.00: 755 34.00 - 51.00: 367 51.00 - 68.00: 100 68.00 - 85.00: 22 Dihedral angle restraints: 9020 sinusoidal: 4104 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 9017 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.370 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 47.140 Find NCS groups from input model: 0.930 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.770 ------------------------------------------------------------------------------- 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 : 17.364 85.004 5808 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 *********************** 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 : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 450 average time/residue: 1.3341 time to fit residues: 655.8021 Evaluate side-chains 382 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 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: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15672 Z= 0.286 Angle : 0.622 11.982 21676 Z= 0.323 Chirality : 0.044 0.151 2406 Planarity : 0.006 0.067 2464 Dihedral : 19.404 85.029 2582 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.10 (0.21), residues: 1640 helix: 0.73 (0.19), residues: 756 sheet: 0.23 (0.32), residues: 222 loop : -0.67 (0.25), residues: 662 *********************** 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 443 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 403 time to evaluate : 1.617 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 416 average time/residue: 1.3836 time to fit residues: 627.5454 Evaluate side-chains 404 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 391 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.3117 time to fit residues: 5.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 126 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 152 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 0.0170 chunk 151 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 122 optimal weight: 0.3980 overall best weight: 0.0712 ------------------------------------------------------------------------------- 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 E 59 ASN E 63 GLN E 177 ASN F 48 GLN F 306 ASN ** 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: 0.7339 moved from start: 0.2307 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= 0.144 Angle : 0.549 10.282 21676 Z= 0.280 Chirality : 0.039 0.163 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.110 88.585 2582 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.37 % Allowed : 16.21 % Favored : 80.43 % 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: 0.20 (0.21), residues: 1640 helix: 0.86 (0.19), residues: 752 sheet: 0.28 (0.33), residues: 222 loop : -0.69 (0.25), residues: 666 *********************** 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 446 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 397 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 18 residues processed: 412 average time/residue: 1.4015 time to fit residues: 629.6155 Evaluate side-chains 397 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 379 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 12 average time/residue: 0.7496 time to fit residues: 13.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 0.5980 chunk 162 optimal weight: 0.0030 chunk 80 optimal weight: 0.0670 chunk 145 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 overall best weight: 0.2346 ------------------------------------------------------------------------------- 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 E 59 ASN E 63 GLN E 177 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15672 Z= 0.152 Angle : 0.538 10.823 21676 Z= 0.275 Chirality : 0.039 0.145 2406 Planarity : 0.005 0.064 2464 Dihedral : 19.003 88.994 2582 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.16 % Allowed : 18.61 % Favored : 78.23 % 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: 0.97 (0.19), residues: 746 sheet: 0.28 (0.33), residues: 222 loop : -0.70 (0.25), residues: 672 *********************** 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 437 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 391 time to evaluate : 1.617 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 405 average time/residue: 1.4235 time to fit residues: 627.5707 Evaluate side-chains 402 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 382 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 8 residues processed: 14 average time/residue: 0.8636 time to fit residues: 16.0370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0980 chunk 92 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 120 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15672 Z= 0.189 Angle : 0.551 9.890 21676 Z= 0.281 Chirality : 0.040 0.169 2406 Planarity : 0.005 0.064 2464 Dihedral : 19.072 88.732 2582 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.43 % Allowed : 19.02 % Favored : 77.54 % 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: 0.35 (0.21), residues: 1640 helix: 1.02 (0.19), residues: 748 sheet: 0.33 (0.33), residues: 222 loop : -0.62 (0.25), residues: 670 *********************** 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 444 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 394 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 408 average time/residue: 1.4799 time to fit residues: 662.6176 Evaluate side-chains 415 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 391 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 10 residues processed: 15 average time/residue: 0.8641 time to fit residues: 17.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 33 HIS E 63 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 HIS A 209 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** C 166 GLN C 306 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15672 Z= 0.224 Angle : 0.577 10.952 21676 Z= 0.296 Chirality : 0.041 0.164 2406 Planarity : 0.005 0.064 2464 Dihedral : 19.181 89.017 2582 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.09 % Allowed : 20.26 % Favored : 76.65 % 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: 0.33 (0.21), residues: 1640 helix: 0.97 (0.19), residues: 748 sheet: 0.29 (0.33), residues: 222 loop : -0.59 (0.25), residues: 670 *********************** 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 441 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 396 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 415 average time/residue: 1.4318 time to fit residues: 645.8681 Evaluate side-chains 412 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 388 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.4322 time to fit residues: 8.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 59 ASN E 63 GLN E 123 ASN F 306 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15672 Z= 0.248 Angle : 0.593 12.293 21676 Z= 0.303 Chirality : 0.042 0.199 2406 Planarity : 0.005 0.065 2464 Dihedral : 19.256 88.958 2582 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.95 % Allowed : 20.95 % Favored : 76.10 % 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: 0.24 (0.21), residues: 1640 helix: 0.88 (0.19), residues: 750 sheet: 0.20 (0.33), residues: 222 loop : -0.60 (0.25), residues: 668 *********************** 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 448 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 405 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 421 average time/residue: 1.3868 time to fit residues: 636.0498 Evaluate side-chains 419 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 393 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 12 residues processed: 14 average time/residue: 0.6072 time to fit residues: 12.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15672 Z= 0.212 Angle : 0.595 11.613 21676 Z= 0.304 Chirality : 0.041 0.196 2406 Planarity : 0.006 0.068 2464 Dihedral : 19.227 89.430 2582 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 21.98 % Favored : 75.62 % 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: 0.83 (0.19), residues: 752 sheet: 0.19 (0.33), residues: 222 loop : -0.57 (0.25), residues: 666 *********************** 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 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 396 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 413 average time/residue: 1.4704 time to fit residues: 661.6678 Evaluate side-chains 420 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 392 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 17 residues processed: 14 average time/residue: 0.8092 time to fit residues: 15.8160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.0040 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 159 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 ASN D 246 GLN E 15 GLN E 59 ASN E 63 GLN E 123 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 63 GLN B 123 ASN B 134 HIS B 177 ASN B 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15672 Z= 0.221 Angle : 0.619 13.378 21676 Z= 0.315 Chirality : 0.041 0.201 2406 Planarity : 0.006 0.082 2464 Dihedral : 19.212 89.285 2582 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.47 % Allowed : 23.28 % Favored : 74.24 % 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: 0.78 (0.19), residues: 752 sheet: 0.17 (0.33), residues: 222 loop : -0.57 (0.25), residues: 666 *********************** 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 425 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 389 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 409 average time/residue: 1.5069 time to fit residues: 668.5518 Evaluate side-chains 414 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 388 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 12 average time/residue: 0.6908 time to fit residues: 11.9240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 141 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 33 HIS E 59 ASN E 206 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 63 GLN B 134 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15672 Z= 0.248 Angle : 0.657 18.533 21676 Z= 0.333 Chirality : 0.042 0.212 2406 Planarity : 0.006 0.089 2464 Dihedral : 19.256 89.052 2582 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.13 % Allowed : 24.24 % Favored : 73.63 % 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: 0.73 (0.19), residues: 754 sheet: 0.12 (0.33), residues: 222 loop : -0.58 (0.25), residues: 664 ********************** 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 418 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 387 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 23 residues processed: 403 average time/residue: 1.4774 time to fit residues: 646.8319 Evaluate side-chains 409 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 386 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 11 average time/residue: 0.7005 time to fit residues: 11.6894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.0470 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN E 63 GLN E 123 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 134 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118513 restraints weight = 22338.858| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.03 r_work: 0.3319 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15672 Z= 0.216 Angle : 0.648 11.547 21676 Z= 0.331 Chirality : 0.042 0.274 2406 Planarity : 0.006 0.090 2464 Dihedral : 19.220 89.677 2582 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 25.00 % 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: 0.08 (0.21), residues: 1640 helix: 0.66 (0.19), residues: 754 sheet: 0.14 (0.33), residues: 222 loop : -0.58 (0.25), residues: 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8862.66 seconds wall clock time: 156 minutes 28.85 seconds (9388.85 seconds total)