Starting phenix.real_space_refine on Sat Jan 20 11:12:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/01_2024/7oug_13076_updated.pdb" } resolution = 3.1 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= 0.021 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 9424 2.51 5 N 2710 2.21 5 O 2824 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 101": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15090 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: "L" 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, 'RLT': 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, 'RLT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 105.427 119.943 25.979 1.00 64.43 S ATOM 260 SG CYS D 38 103.330 122.249 27.523 1.00 61.41 S ATOM 2296 SG CYS E 35 73.195 55.648 38.011 1.00 18.21 S ATOM 2317 SG CYS E 38 70.364 57.662 38.953 1.00 8.92 S ATOM 7744 SG CYS A 35 22.183 45.021 25.936 1.00 64.00 S ATOM 7765 SG CYS A 38 24.283 42.718 27.481 1.00 58.68 S ATOM 9801 SG CYS B 35 54.346 109.350 37.975 1.00 18.65 S ATOM 9822 SG CYS B 38 57.179 107.339 38.919 1.00 9.34 S Time building chain proxies: 7.98, per 1000 atoms: 0.53 Number of scatterers: 15090 At special positions: 0 Unit cell: (128.7, 166.1, 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 2 9.00 O 2824 8.00 N 2710 7.00 C 9424 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: 6.00 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 38 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " 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 38 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 6 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 46.0% alpha, 10.6% beta 20 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 158 through 174 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 41 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 174 removed outlier: 6.189A pdb=" N LEU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 204 through 208 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 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 Proline residue: F 93 - end of helix removed outlier: 3.986A pdb=" N VAL F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 213 Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 249 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 258 through 275 removed outlier: 4.556A pdb=" N SER F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS F 264 " --> pdb=" O SER F 261 " (cutoff:3.500A) Proline residue: F 265 - end of helix removed outlier: 4.187A pdb=" N LEU F 275 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix removed outlier: 3.618A pdb=" N LEU F 290 " --> pdb=" O MET F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET F 303 " --> pdb=" O LYS F 300 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 158 through 174 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 41 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 174 removed outlier: 6.190A pdb=" N LEU B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 208 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 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 Proline residue: C 93 - end of helix removed outlier: 3.985A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 258 through 275 removed outlier: 4.555A pdb=" N SER C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 4.187A pdb=" N LEU C 275 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix removed outlier: 3.618A pdb=" N LEU C 290 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) 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: 7.235A pdb=" N HIS D 118 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY D 64 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN D 120 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ILE D 66 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP D 122 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 14.810A pdb=" N HIS D 68 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.498A 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 266 through 269 removed outlier: 3.856A pdb=" N GLN D 250 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.081A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.372A 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 255 through 259 Processing sheet with id= G, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.236A pdb=" N HIS A 118 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY A 64 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 120 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ILE A 66 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP A 122 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 14.811A pdb=" N HIS A 68 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.498A 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 266 through 269 removed outlier: 3.856A pdb=" N GLN A 250 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.080A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.372A 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 255 through 259 540 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3564 1.33 - 1.45: 3583 1.45 - 1.57: 8311 1.57 - 1.69: 152 1.69 - 1.81: 62 Bond restraints: 15672 Sorted by residual: bond pdb=" CAV RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 1.450 1.324 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CAV RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 1.450 1.324 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CAU RLT E 304 " pdb=" NAR RLT E 304 " ideal model delta sigma weight residual 1.449 1.329 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CAU RLT B 304 " pdb=" NAR RLT B 304 " ideal model delta sigma weight residual 1.449 1.330 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CBC RLT E 304 " pdb=" NAQ RLT E 304 " ideal model delta sigma weight residual 1.481 1.362 0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 81.93 - 92.34: 4 92.34 - 102.76: 137 102.76 - 113.18: 9465 113.18 - 123.60: 11255 123.60 - 134.02: 817 Bond angle restraints: 21678 Sorted by residual: angle pdb=" CBC RLT B 304 " pdb=" CBF RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 109.47 81.93 27.54 3.00e+00 1.11e-01 8.43e+01 angle pdb=" CBC RLT E 304 " pdb=" CBF RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 109.47 82.19 27.28 3.00e+00 1.11e-01 8.27e+01 angle pdb=" CAD RLT E 304 " pdb=" CBF RLT E 304 " pdb=" CBC RLT E 304 " ideal model delta sigma weight residual 109.46 89.52 19.94 3.00e+00 1.11e-01 4.42e+01 angle pdb=" CAD RLT B 304 " pdb=" CBF RLT B 304 " pdb=" CBC RLT B 304 " ideal model delta sigma weight residual 109.46 89.57 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" CAA RLT E 304 " pdb=" CAW RLT E 304 " pdb=" OAT RLT E 304 " ideal model delta sigma weight residual 134.90 115.25 19.65 3.00e+00 1.11e-01 4.29e+01 ... (remaining 21673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 7649 15.99 - 31.98: 879 31.98 - 47.97: 373 47.97 - 63.96: 175 63.96 - 79.95: 20 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 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+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 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+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 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1790 0.037 - 0.074: 432 0.074 - 0.110: 142 0.110 - 0.147: 40 0.147 - 0.184: 2 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CG LEU B 257 " pdb=" CB LEU B 257 " pdb=" CD1 LEU B 257 " pdb=" CD2 LEU B 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CG LEU E 257 " pdb=" CB LEU E 257 " pdb=" CD1 LEU E 257 " pdb=" CD2 LEU E 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2403 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAV RLT E 304 " 0.081 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" CBA RLT E 304 " -0.176 2.00e-02 2.50e+03 pdb=" CBF RLT E 304 " -0.307 2.00e-02 2.50e+03 pdb=" NAS RLT E 304 " 0.455 2.00e-02 2.50e+03 pdb=" OAF RLT E 304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAV RLT B 304 " 0.080 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" CBA RLT B 304 " -0.175 2.00e-02 2.50e+03 pdb=" CBF RLT B 304 " -0.305 2.00e-02 2.50e+03 pdb=" NAS RLT B 304 " 0.452 2.00e-02 2.50e+03 pdb=" OAF RLT B 304 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAN RLT B 304 " -0.158 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CAU RLT B 304 " 0.052 2.00e-02 2.50e+03 pdb=" CBB RLT B 304 " -0.120 2.00e-02 2.50e+03 pdb=" NAR RLT B 304 " 0.204 2.00e-02 2.50e+03 pdb=" OAE RLT B 304 " 0.022 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8167 3.02 - 3.65: 22423 3.65 - 4.27: 34225 4.27 - 4.90: 55631 Nonbonded interactions: 120497 Sorted by model distance: nonbonded pdb="MG MG B 303 " pdb=" OAE RLT B 304 " model vdw 1.769 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.777 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.785 2.170 nonbonded pdb="MG MG E 303 " pdb=" OAE RLT E 304 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.833 2.170 ... (remaining 120492 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 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 1.430 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: 6.470 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 47.090 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.004 0.126 15672 Z= 0.249 Angle : 0.736 27.544 21678 Z= 0.333 Chirality : 0.039 0.184 2406 Planarity : 0.009 0.261 2466 Dihedral : 17.646 79.953 5884 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.14 % Allowed : 0.07 % Favored : 99.79 % 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: 0.28 (0.20), residues: 1640 helix: 1.16 (0.19), residues: 742 sheet: 0.36 (0.31), residues: 222 loop : -0.94 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 131 HIS 0.004 0.001 HIS D 33 PHE 0.019 0.001 PHE C 274 TYR 0.013 0.001 TYR F 138 ARG 0.004 0.000 ARG E 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 479 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 477 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.7182 (mmm) cc_final: 0.6886 (mmm) REVERT: E 127 TYR cc_start: 0.7630 (m-10) cc_final: 0.7309 (m-10) REVERT: F 45 LYS cc_start: 0.6338 (mtpt) cc_final: 0.5315 (mtpt) REVERT: F 78 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6431 (tm-30) REVERT: F 174 GLU cc_start: 0.6874 (pp20) cc_final: 0.6650 (pp20) REVERT: F 201 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: F 210 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6801 (ttp80) REVERT: F 287 MET cc_start: 0.6472 (mmm) cc_final: 0.6265 (mmm) REVERT: F 308 LEU cc_start: 0.8349 (mt) cc_final: 0.8041 (mt) REVERT: F 310 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 47 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: B 127 TYR cc_start: 0.7441 (m-10) cc_final: 0.7224 (m-10) REVERT: B 175 ASN cc_start: 0.6739 (m110) cc_final: 0.6475 (m110) REVERT: C 41 LEU cc_start: 0.7835 (tt) cc_final: 0.7526 (tt) REVERT: C 45 LYS cc_start: 0.6260 (mtpt) cc_final: 0.4862 (mtpt) REVERT: C 92 TYR cc_start: 0.5749 (m-80) cc_final: 0.5427 (m-80) REVERT: C 139 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6563 (tm-30) REVERT: C 154 ILE cc_start: 0.7912 (mm) cc_final: 0.7697 (pt) REVERT: C 174 GLU cc_start: 0.6887 (pp20) cc_final: 0.6619 (pp20) REVERT: C 201 ARG cc_start: 0.7051 (mtm-85) cc_final: 0.6808 (mtm-85) REVERT: C 241 GLU cc_start: 0.4459 (tm-30) cc_final: 0.4008 (tm-30) REVERT: C 245 ILE cc_start: 0.6937 (mt) cc_final: 0.6410 (mt) REVERT: C 308 LEU cc_start: 0.8335 (mt) cc_final: 0.8061 (mt) outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.3598 time to fit residues: 231.2973 Evaluate side-chains 430 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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: 0.5980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 80 optimal weight: 0.0870 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 195 ASN D 206 GLN D 238 ASN E 21 HIS E 59 ASN E 93 HIS E 241 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN A 118 HIS A 134 HIS A 195 ASN A 238 ASN B 59 ASN B 123 ASN B 161 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15672 Z= 0.179 Angle : 0.588 13.686 21678 Z= 0.301 Chirality : 0.041 0.174 2406 Planarity : 0.006 0.125 2466 Dihedral : 19.100 82.801 2658 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.72 % Allowed : 11.81 % Favored : 86.47 % 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: 0.12 (0.20), residues: 1640 helix: 0.78 (0.19), residues: 758 sheet: 0.38 (0.32), residues: 222 loop : -0.77 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.006 0.001 HIS A 8 PHE 0.010 0.001 PHE A 10 TYR 0.020 0.002 TYR F 79 ARG 0.012 0.001 ARG C 143 *********************** 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 460 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 435 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.7186 (mmm) cc_final: 0.6835 (mmm) REVERT: E 127 TYR cc_start: 0.7568 (m-10) cc_final: 0.7248 (m-10) REVERT: F 78 GLU cc_start: 0.6486 (tm-30) cc_final: 0.6268 (tm-30) REVERT: F 174 GLU cc_start: 0.6999 (pp20) cc_final: 0.6701 (pp20) REVERT: F 210 ARG cc_start: 0.7016 (ttp80) cc_final: 0.6799 (ttp80) REVERT: F 308 LEU cc_start: 0.8355 (mt) cc_final: 0.8061 (mt) REVERT: F 310 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7114 (mm-30) REVERT: B 47 MET cc_start: 0.7127 (mmm) cc_final: 0.6809 (mmm) REVERT: B 127 TYR cc_start: 0.7361 (m-10) cc_final: 0.7112 (m-10) REVERT: C 77 VAL cc_start: 0.7089 (p) cc_final: 0.6765 (p) REVERT: C 201 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6779 (mtm-85) REVERT: C 241 GLU cc_start: 0.4603 (tm-30) cc_final: 0.4044 (tm-30) REVERT: C 245 ILE cc_start: 0.6848 (mt) cc_final: 0.6252 (mt) REVERT: C 308 LEU cc_start: 0.8370 (mt) cc_final: 0.7992 (mt) REVERT: C 310 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7124 (mm-30) outliers start: 25 outliers final: 12 residues processed: 443 average time/residue: 0.3598 time to fit residues: 213.7720 Evaluate side-chains 430 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 418 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 0.0010 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 238 ASN E 59 ASN E 93 HIS E 112 HIS F 203 GLN A 238 ASN B 59 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15672 Z= 0.289 Angle : 0.600 10.596 21678 Z= 0.311 Chirality : 0.042 0.143 2406 Planarity : 0.005 0.062 2466 Dihedral : 19.170 86.224 2658 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 13.67 % Favored : 83.79 % 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: -0.06 (0.20), residues: 1640 helix: 0.58 (0.18), residues: 756 sheet: 0.31 (0.31), residues: 242 loop : -0.82 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 229 HIS 0.006 0.001 HIS F 187 PHE 0.017 0.002 PHE C 99 TYR 0.023 0.002 TYR A 231 ARG 0.012 0.001 ARG C 143 *********************** 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 477 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 440 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.6791 (tp30) cc_final: 0.6518 (tp30) REVERT: E 47 MET cc_start: 0.7204 (mmm) cc_final: 0.6871 (mmm) REVERT: E 246 GLN cc_start: 0.7106 (mm110) cc_final: 0.6821 (mt0) REVERT: F 77 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6465 (p) REVERT: F 78 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6196 (tm-30) REVERT: F 169 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: F 210 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6881 (ttp80) REVERT: F 310 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 18 LEU cc_start: 0.7655 (mt) cc_final: 0.7455 (mp) REVERT: A 182 ASN cc_start: 0.7440 (m-40) cc_final: 0.7234 (m110) REVERT: B 32 LEU cc_start: 0.8488 (mm) cc_final: 0.8201 (mt) REVERT: B 47 MET cc_start: 0.7195 (mmm) cc_final: 0.6868 (mmm) REVERT: B 202 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7427 (mtmm) REVERT: C 169 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6338 (tm-30) REVERT: C 174 GLU cc_start: 0.7155 (pp20) cc_final: 0.6936 (pp20) REVERT: C 201 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6919 (mtm-85) REVERT: C 241 GLU cc_start: 0.4928 (tm-30) cc_final: 0.4320 (tm-30) REVERT: C 245 ILE cc_start: 0.6956 (mt) cc_final: 0.6416 (mt) REVERT: C 308 LEU cc_start: 0.8458 (mt) cc_final: 0.8207 (mt) REVERT: C 310 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7240 (mm-30) outliers start: 37 outliers final: 23 residues processed: 451 average time/residue: 0.3522 time to fit residues: 213.0204 Evaluate side-chains 448 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 422 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 13 CYS Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 286 VAL 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: 2.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.0870 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 43 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 59 ASN D 238 ASN E 59 ASN E 112 HIS F 233 ASN F 243 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN C 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15672 Z= 0.221 Angle : 0.562 7.542 21678 Z= 0.291 Chirality : 0.040 0.148 2406 Planarity : 0.005 0.074 2466 Dihedral : 19.094 88.223 2658 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.30 % Allowed : 16.62 % 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: -0.01 (0.20), residues: 1640 helix: 0.61 (0.19), residues: 756 sheet: 0.34 (0.31), residues: 242 loop : -0.79 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.004 0.001 HIS A 8 PHE 0.021 0.001 PHE C 246 TYR 0.021 0.002 TYR C 158 ARG 0.011 0.001 ARG F 143 *********************** 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 483 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 435 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.6826 (tp30) cc_final: 0.6536 (tp30) REVERT: E 47 MET cc_start: 0.7174 (mmm) cc_final: 0.6861 (mmm) REVERT: E 246 GLN cc_start: 0.7030 (mm110) cc_final: 0.6765 (mt0) REVERT: F 165 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7251 (mm) REVERT: F 169 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: F 210 ARG cc_start: 0.7066 (ttp80) cc_final: 0.6857 (ttp80) REVERT: F 219 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6751 (p0) REVERT: F 247 LEU cc_start: 0.8513 (tp) cc_final: 0.8296 (tp) REVERT: F 254 LEU cc_start: 0.6517 (tp) cc_final: 0.6147 (tt) REVERT: F 310 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 29 LEU cc_start: 0.8367 (mm) cc_final: 0.8072 (mt) REVERT: B 47 MET cc_start: 0.7203 (mmm) cc_final: 0.6885 (mmm) REVERT: B 202 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7398 (mtmm) REVERT: C 169 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: C 201 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6824 (mtm-85) REVERT: C 210 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6883 (mtm-85) REVERT: C 241 GLU cc_start: 0.4983 (tm-30) cc_final: 0.4342 (tm-30) REVERT: C 245 ILE cc_start: 0.7010 (mt) cc_final: 0.6457 (mt) REVERT: C 308 LEU cc_start: 0.8445 (mt) cc_final: 0.8200 (mt) REVERT: C 310 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7212 (mm-30) outliers start: 48 outliers final: 25 residues processed: 456 average time/residue: 0.3558 time to fit residues: 217.3914 Evaluate side-chains 454 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 425 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 59 ASN E 112 HIS E 118 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 41 ASN B 59 ASN B 60 HIS B 112 HIS B 118 HIS B 195 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15672 Z= 0.286 Angle : 0.590 7.253 21678 Z= 0.306 Chirality : 0.042 0.154 2406 Planarity : 0.005 0.060 2466 Dihedral : 19.121 89.011 2658 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.23 % Allowed : 18.27 % Favored : 78.50 % 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: -0.07 (0.20), residues: 1640 helix: 0.59 (0.19), residues: 752 sheet: 0.37 (0.31), residues: 242 loop : -0.87 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 65 HIS 0.007 0.001 HIS F 187 PHE 0.019 0.001 PHE C 99 TYR 0.025 0.002 TYR F 269 ARG 0.009 0.000 ARG A 142 *********************** 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 483 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 436 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.6885 (tp30) cc_final: 0.6646 (tp30) REVERT: E 47 MET cc_start: 0.7200 (mmm) cc_final: 0.6883 (mmm) REVERT: E 246 GLN cc_start: 0.7088 (mm110) cc_final: 0.6831 (mt0) REVERT: F 165 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7253 (mm) REVERT: F 219 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6724 (p0) REVERT: F 254 LEU cc_start: 0.6682 (tp) cc_final: 0.6245 (tt) REVERT: F 310 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 29 LEU cc_start: 0.8368 (mm) cc_final: 0.8041 (mt) REVERT: B 47 MET cc_start: 0.7285 (mmm) cc_final: 0.6986 (mmm) REVERT: B 202 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7491 (mtmm) REVERT: C 95 VAL cc_start: 0.8186 (t) cc_final: 0.7965 (p) REVERT: C 169 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: C 201 ARG cc_start: 0.7184 (mtm-85) cc_final: 0.6896 (mtm-85) REVERT: C 228 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7835 (tt) REVERT: C 241 GLU cc_start: 0.5023 (tm-30) cc_final: 0.4415 (tm-30) REVERT: C 245 ILE cc_start: 0.7128 (mt) cc_final: 0.6709 (mt) REVERT: C 254 LEU cc_start: 0.6526 (tp) cc_final: 0.6185 (tt) REVERT: C 308 LEU cc_start: 0.8487 (mt) cc_final: 0.8241 (mt) REVERT: C 310 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7206 (mm-30) outliers start: 47 outliers final: 31 residues processed: 451 average time/residue: 0.3398 time to fit residues: 205.9614 Evaluate side-chains 460 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 425 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 MET 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: 0.0470 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 0.0020 chunk 134 optimal weight: 0.0060 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 41 ASN E 59 ASN E 112 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN B 112 HIS B 118 HIS C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15672 Z= 0.169 Angle : 0.556 7.931 21678 Z= 0.287 Chirality : 0.039 0.191 2406 Planarity : 0.005 0.057 2466 Dihedral : 18.983 89.811 2658 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.09 % Allowed : 19.37 % 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: -0.01 (0.20), residues: 1640 helix: 0.53 (0.19), residues: 758 sheet: 0.36 (0.31), residues: 242 loop : -0.69 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 267 HIS 0.010 0.001 HIS B 134 PHE 0.014 0.001 PHE C 141 TYR 0.026 0.002 TYR F 269 ARG 0.010 0.000 ARG A 142 *********************** 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 476 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 431 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.6832 (tp30) cc_final: 0.6619 (tp30) REVERT: E 47 MET cc_start: 0.7166 (mmm) cc_final: 0.6856 (mmm) REVERT: F 169 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: F 174 GLU cc_start: 0.7043 (pp20) cc_final: 0.6793 (pp20) REVERT: F 201 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6947 (mtm-85) REVERT: F 210 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6678 (ttp80) REVERT: F 219 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6572 (p0) REVERT: F 244 LYS cc_start: 0.6891 (mtmt) cc_final: 0.6643 (mtmt) REVERT: F 254 LEU cc_start: 0.6541 (tp) cc_final: 0.6334 (tt) REVERT: F 310 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7035 (mm-30) REVERT: B 29 LEU cc_start: 0.8241 (mm) cc_final: 0.7909 (mt) REVERT: B 32 LEU cc_start: 0.8433 (mm) cc_final: 0.8173 (mt) REVERT: B 47 MET cc_start: 0.7250 (mmm) cc_final: 0.6953 (mmm) REVERT: B 202 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7413 (mtmm) REVERT: C 169 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: C 201 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6825 (mtm-85) REVERT: C 219 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6617 (p0) REVERT: C 310 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7237 (mm-30) outliers start: 45 outliers final: 29 residues processed: 448 average time/residue: 0.3582 time to fit residues: 215.2233 Evaluate side-chains 446 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 413 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 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 238 ASN E 59 ASN E 112 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15672 Z= 0.278 Angle : 0.601 9.180 21678 Z= 0.315 Chirality : 0.042 0.200 2406 Planarity : 0.005 0.052 2466 Dihedral : 19.049 89.575 2658 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.30 % Allowed : 20.74 % Favored : 75.96 % 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: -0.14 (0.20), residues: 1640 helix: 0.43 (0.18), residues: 762 sheet: 0.41 (0.31), residues: 242 loop : -0.82 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 65 HIS 0.010 0.001 HIS B 134 PHE 0.022 0.001 PHE C 99 TYR 0.029 0.002 TYR F 269 ARG 0.009 0.000 ARG A 142 *********************** 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 470 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 422 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.6869 (tp30) cc_final: 0.6628 (tp30) REVERT: E 47 MET cc_start: 0.7304 (mmm) cc_final: 0.6992 (mmm) REVERT: F 44 GLN cc_start: 0.8203 (mp10) cc_final: 0.7782 (pm20) REVERT: F 169 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: F 174 GLU cc_start: 0.7075 (pp20) cc_final: 0.6816 (pp20) REVERT: F 201 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.7039 (mtm-85) REVERT: F 210 ARG cc_start: 0.7028 (ttp80) cc_final: 0.6743 (ttp80) REVERT: F 219 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6685 (p0) REVERT: F 244 LYS cc_start: 0.6974 (mtmt) cc_final: 0.6707 (mtmt) REVERT: F 254 LEU cc_start: 0.6760 (tp) cc_final: 0.6329 (tt) REVERT: F 310 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 29 LEU cc_start: 0.8321 (mm) cc_final: 0.8024 (mt) REVERT: B 47 MET cc_start: 0.7306 (mmm) cc_final: 0.7017 (mmm) REVERT: B 202 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7488 (mtmm) REVERT: C 44 GLN cc_start: 0.8129 (mp10) cc_final: 0.7527 (mp10) REVERT: C 169 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6436 (tm-30) REVERT: C 201 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6904 (mtm-85) REVERT: C 228 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7810 (tt) REVERT: C 245 ILE cc_start: 0.7176 (mt) cc_final: 0.6946 (mm) REVERT: C 254 LEU cc_start: 0.6624 (tp) cc_final: 0.6266 (tt) REVERT: C 310 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7136 (mm-30) outliers start: 48 outliers final: 39 residues processed: 440 average time/residue: 0.3609 time to fit residues: 212.5234 Evaluate side-chains 453 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 411 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.3053 > 50: distance: 29 - 48: 7.833 distance: 35 - 59: 7.189 distance: 39 - 65: 13.447 distance: 43 - 48: 11.283 distance: 48 - 49: 9.215 distance: 49 - 50: 10.008 distance: 49 - 52: 9.198 distance: 50 - 51: 19.181 distance: 50 - 59: 15.144 distance: 52 - 53: 6.135 distance: 53 - 54: 12.073 distance: 53 - 55: 10.154 distance: 54 - 56: 11.108 distance: 55 - 57: 9.080 distance: 56 - 58: 8.989 distance: 57 - 58: 14.387 distance: 59 - 60: 14.383 distance: 60 - 61: 5.998 distance: 60 - 63: 8.673 distance: 61 - 62: 6.140 distance: 61 - 65: 3.648 distance: 63 - 64: 11.905 distance: 65 - 66: 5.279 distance: 66 - 67: 6.822 distance: 66 - 69: 12.631 distance: 67 - 68: 7.818 distance: 67 - 73: 4.935 distance: 69 - 70: 14.922 distance: 70 - 71: 9.124 distance: 70 - 72: 12.210 distance: 73 - 74: 9.168 distance: 74 - 75: 6.835 distance: 74 - 77: 10.923 distance: 75 - 76: 8.032 distance: 75 - 81: 12.826 distance: 77 - 78: 5.950 distance: 78 - 79: 13.011 distance: 78 - 80: 5.979 distance: 81 - 82: 6.464 distance: 81 - 87: 11.841 distance: 82 - 83: 5.613 distance: 82 - 85: 10.450 distance: 83 - 84: 5.978 distance: 83 - 88: 11.721 distance: 85 - 86: 12.222 distance: 86 - 87: 9.871 distance: 89 - 90: 10.607 distance: 89 - 92: 10.362 distance: 90 - 91: 15.450 distance: 90 - 96: 8.954 distance: 92 - 93: 18.070 distance: 93 - 94: 10.415 distance: 93 - 95: 8.350 distance: 96 - 97: 10.451 distance: 97 - 98: 13.838 distance: 97 - 100: 14.696 distance: 98 - 99: 11.557 distance: 98 - 104: 11.404 distance: 100 - 101: 26.548 distance: 101 - 103: 6.225 distance: 104 - 105: 5.157 distance: 104 - 110: 23.518 distance: 105 - 106: 5.404 distance: 105 - 108: 17.903 distance: 106 - 107: 16.024 distance: 106 - 111: 13.681 distance: 108 - 109: 8.531 distance: 109 - 110: 13.012 distance: 111 - 112: 3.852 distance: 112 - 113: 18.190 distance: 112 - 115: 18.554 distance: 113 - 114: 17.677 distance: 113 - 119: 5.304 distance: 115 - 116: 11.808 distance: 116 - 117: 44.886 distance: 117 - 118: 21.865 distance: 119 - 120: 6.527 distance: 120 - 121: 12.467 distance: 120 - 123: 23.237 distance: 121 - 122: 15.703 distance: 121 - 127: 7.401 distance: 123 - 124: 5.438 distance: 124 - 125: 3.752