Starting phenix.real_space_refine on Mon Aug 25 11:34:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.map" model { file = "/net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u07_8477/08_2025/5u07_8477.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 45 5.16 5 C 17065 2.51 5 N 5076 2.21 5 O 5403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27681 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 9 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1285 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3880 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 453} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2017 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2828 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 351} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 351} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2823 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "I" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2544 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1319 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Chain: "M" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "N" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1891 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 20, 'TRANS': 220} Chain breaks: 1 Chain: "O" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 5.51, per 1000 atoms: 0.20 Number of scatterers: 27681 At special positions: 0 Unit cell: (184.5, 148.83, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 92 15.00 O 5403 8.00 N 5076 7.00 C 17065 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 - 3.00 Amino acid : True - 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: 1.92 Conformation dependent library (CDL) restraints added in 892.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 34 sheets defined 46.1% alpha, 18.2% beta 16 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 138 through 138 No H-bonds generated for 'chain 'A' and resid 138 through 138' Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.705A pdb=" N GLY A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.713A pdb=" N VAL B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.784A pdb=" N ARG B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 35 No H-bonds generated for 'chain 'B' and resid 34 through 35' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.801A pdb=" N HIS B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.679A pdb=" N SER B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.757A pdb=" N THR B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 185 removed outlier: 3.998A pdb=" N HIS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 205 through 227 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 80 removed outlier: 4.184A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.676A pdb=" N VAL C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.524A pdb=" N LEU C 138 " --> pdb=" O ASP C 135 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.527A pdb=" N GLN C 251 " --> pdb=" O PHE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.790A pdb=" N SER C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 446 Processing helix chain 'C' and resid 464 through 486 removed outlier: 3.991A pdb=" N HIS C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 502 through 517 removed outlier: 3.639A pdb=" N LEU C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 522 through 534 Processing helix chain 'C' and resid 535 through 538 removed outlier: 3.511A pdb=" N SER C 538 " --> pdb=" O THR C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.575A pdb=" N PHE D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 56 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.695A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.937A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 152 through 161 removed outlier: 3.553A pdb=" N ILE E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 248 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 309 through 329 removed outlier: 4.139A pdb=" N ARG E 313 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.553A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 350' Processing helix chain 'E' and resid 355 through 368 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.518A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.695A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.982A pdb=" N HIS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 142 Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.564A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 212 through 218 removed outlier: 3.500A pdb=" N HIS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 248 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 309 through 329 removed outlier: 4.289A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.520A pdb=" N GLY F 350 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 368 Processing helix chain 'G' and resid 39 through 56 Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.733A pdb=" N GLU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.928A pdb=" N HIS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 152 through 161 Processing helix chain 'G' and resid 164 through 171 Processing helix chain 'G' and resid 212 through 219 removed outlier: 3.524A pdb=" N HIS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY G 217 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 248 through 266 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 309 through 329 removed outlier: 4.268A pdb=" N ARG G 313 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 350 removed outlier: 3.507A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 350 " --> pdb=" O ALA G 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 350' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 56 removed outlier: 3.530A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.822A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.881A pdb=" N HIS H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 142 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 248 through 266 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 309 through 329 removed outlier: 4.246A pdb=" N ARG H 313 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.532A pdb=" N GLY H 350 " --> pdb=" O ALA H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 39 through 56 removed outlier: 3.545A pdb=" N TRP I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.667A pdb=" N GLU I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 93 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.989A pdb=" N HIS I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 142 Processing helix chain 'I' and resid 152 through 161 Processing helix chain 'I' and resid 164 through 171 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 248 through 266 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 309 through 329 removed outlier: 4.124A pdb=" N ARG I 313 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 removed outlier: 3.575A pdb=" N LEU I 349 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'J' and resid 6 through 22 removed outlier: 4.032A pdb=" N VAL J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 33 removed outlier: 3.783A pdb=" N ARG J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.800A pdb=" N HIS J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG J 49 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 75 through 90 Processing helix chain 'J' and resid 138 through 151 removed outlier: 3.679A pdb=" N SER J 142 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 165 removed outlier: 3.756A pdb=" N THR J 157 " --> pdb=" O ASN J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 185 removed outlier: 3.999A pdb=" N HIS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Proline residue: J 177 - end of helix Processing helix chain 'J' and resid 191 through 201 Processing helix chain 'J' and resid 205 through 227 Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 51 through 55 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 121 through 131 removed outlier: 3.551A pdb=" N ILE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA N 131 " --> pdb=" O ASP N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 164 removed outlier: 3.814A pdb=" N GLU N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'N' and resid 236 through 248 removed outlier: 3.741A pdb=" N ASN N 240 " --> pdb=" O ARG N 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.583A pdb=" N LEU C 176 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 293 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 224 Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.561A pdb=" N SER C 318 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.001A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 191 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR D 234 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 191 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 232 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR D 193 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.001A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 191 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR D 234 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 191 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 232 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR D 193 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 5 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 283 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 336 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.046A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 191 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 192 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.046A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 191 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 192 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 203 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.084A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.084A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU F 351 " --> pdb=" O ARG F 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.130A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE G 192 " --> pdb=" O TYR G 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.130A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE G 192 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 351 " --> pdb=" O ARG G 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AC5, first strand: chain 'G' and resid 200 through 203 Processing sheet with id=AC6, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.157A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.157A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU H 351 " --> pdb=" O ARG H 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AC9, first strand: chain 'H' and resid 200 through 203 Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.214A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 192 " --> pdb=" O TYR I 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.214A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 192 " --> pdb=" O TYR I 232 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AD4, first strand: chain 'N' and resid 150 through 152 removed outlier: 6.831A pdb=" N LEU N 5 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL N 112 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR N 60 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP N 183 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ARG N 65 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 13.434A pdb=" N LEU N 181 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG N 213 " --> pdb=" O PRO N 204 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER N 215 " --> pdb=" O ASP N 202 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU N 200 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.823A pdb=" N ARG N 24 " --> pdb=" O SER N 106 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N LEU N 108 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD7, first strand: chain 'N' and resid 15 through 16 removed outlier: 4.831A pdb=" N TRP N 15 " --> pdb=" O LEU N 27 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.66 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: 6700 1.33 - 1.45: 6239 1.45 - 1.57: 15239 1.57 - 1.69: 181 1.69 - 1.81: 78 Bond restraints: 28437 Sorted by residual: bond pdb=" C SER F 269 " pdb=" N GLY F 270 " ideal model delta sigma weight residual 1.332 1.369 -0.037 5.00e-03 4.00e+04 5.54e+01 bond pdb=" C VAL C 364 " pdb=" N PRO C 365 " ideal model delta sigma weight residual 1.331 1.391 -0.060 1.27e-02 6.20e+03 2.25e+01 bond pdb=" N PRO J 25 " pdb=" CD PRO J 25 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO C 365 " pdb=" CD PRO C 365 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" N PRO J 56 " pdb=" CD PRO J 56 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 28432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 38000 3.58 - 7.15: 921 7.15 - 10.73: 87 10.73 - 14.31: 22 14.31 - 17.88: 5 Bond angle restraints: 39035 Sorted by residual: angle pdb=" N GLU A 159 " pdb=" CA GLU A 159 " pdb=" C GLU A 159 " ideal model delta sigma weight residual 108.79 123.20 -14.41 1.53e+00 4.27e-01 8.87e+01 angle pdb=" O3' DG O 11 " pdb=" P DC O 12 " pdb=" O5' DC O 12 " ideal model delta sigma weight residual 104.00 115.93 -11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" N ILE A 106 " pdb=" CA ILE A 106 " pdb=" CB ILE A 106 " ideal model delta sigma weight residual 111.45 122.36 -10.91 1.64e+00 3.72e-01 4.43e+01 angle pdb=" N TYR A 104 " pdb=" CA TYR A 104 " pdb=" C TYR A 104 " ideal model delta sigma weight residual 108.99 119.35 -10.36 1.57e+00 4.06e-01 4.35e+01 angle pdb=" N TYR A 104 " pdb=" CA TYR A 104 " pdb=" CB TYR A 104 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.52e+01 ... (remaining 39030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 16468 32.01 - 64.03: 595 64.03 - 96.04: 44 96.04 - 128.05: 2 128.05 - 160.06: 2 Dihedral angle restraints: 17111 sinusoidal: 7521 harmonic: 9590 Sorted by residual: dihedral pdb=" O4' C K 55 " pdb=" C1' C K 55 " pdb=" N1 C K 55 " pdb=" C2 C K 55 " ideal model delta sinusoidal sigma weight residual 200.00 50.12 149.88 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual 200.00 81.53 118.47 1 1.50e+01 4.44e-03 6.30e+01 dihedral pdb=" O4' C K 9 " pdb=" C1' C K 9 " pdb=" N1 C K 9 " pdb=" C2 C K 9 " ideal model delta sinusoidal sigma weight residual -128.00 -58.65 -69.35 1 1.70e+01 3.46e-03 2.15e+01 ... (remaining 17108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3722 0.092 - 0.184: 603 0.184 - 0.276: 84 0.276 - 0.368: 13 0.368 - 0.460: 3 Chirality restraints: 4425 Sorted by residual: chirality pdb=" C1' DA M 39 " pdb=" O4' DA M 39 " pdb=" C2' DA M 39 " pdb=" N9 DA M 39 " both_signs ideal model delta sigma weight residual False 2.42 1.96 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA HIS C 343 " pdb=" N HIS C 343 " pdb=" C HIS C 343 " pdb=" CB HIS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA GLU A 159 " pdb=" N GLU A 159 " pdb=" C GLU A 159 " pdb=" CB GLU A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4422 not shown) Planarity restraints: 4775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA M 39 " 0.021 2.00e-02 2.50e+03 3.27e-02 2.95e+01 pdb=" N9 DA M 39 " -0.087 2.00e-02 2.50e+03 pdb=" C8 DA M 39 " 0.059 2.00e-02 2.50e+03 pdb=" N7 DA M 39 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA M 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA M 39 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA M 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA M 39 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA M 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA M 39 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA M 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.039 2.00e-02 2.50e+03 3.28e-02 2.68e+01 pdb=" CG TRP C 390 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 30 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C TYR E 30 " 0.082 2.00e-02 2.50e+03 pdb=" O TYR E 30 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY E 31 " -0.028 2.00e-02 2.50e+03 ... (remaining 4772 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 368 2.55 - 3.13: 23686 3.13 - 3.72: 44809 3.72 - 4.31: 60836 4.31 - 4.90: 101326 Nonbonded interactions: 231025 Sorted by model distance: nonbonded pdb=" O VAL J 77 " pdb=" N ALA J 80 " model vdw 1.958 3.120 nonbonded pdb=" N2 DG M 54 " pdb=" O2 DC O 1 " model vdw 2.102 2.496 nonbonded pdb=" OD1 ASN F 164 " pdb=" N VAL F 165 " model vdw 2.159 3.120 nonbonded pdb=" O2' C K 6 " pdb=" O4' C K 7 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP N 202 " pdb=" N VAL N 203 " model vdw 2.172 3.120 ... (remaining 231020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 5 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 18 or (resid 19 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 83 or (resi \ d 84 through 86 and (name N or name CA or name C or name O or name CB )) or resi \ d 87 through 166 or (resid 167 and (name N or name CA or name C or name O or nam \ e CB )) or resid 168 through 229)) selection = (chain 'J' and (resid 5 through 35 or resid 41 through 55 or resid 76 through 96 \ or resid 136 through 229)) } ncs_group { reference = (chain 'E' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 198 or resid 227 through 269 or res \ id 279 through 288 or (resid 289 and (name N or name CA or name C or name O or n \ ame CB )) or resid 290 through 345 or (resid 346 through 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 367)) selection = (chain 'F' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 288 or (resid 289 and (name N or name \ CA or name C or name O or name CB )) or resid 290 through 367)) selection = (chain 'G' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 330 or (resid 331 and (name N or name \ CA or name C or name O or name CB )) or resid 332 through 345 or (resid 346 thr \ ough 348 and (name N or name CA or name C or name O or name CB )) or resid 349 t \ hrough 367)) selection = (chain 'H' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 288 or (resid 289 and (name N or name \ CA or name C or name O or name CB )) or resid 290 through 330 or (resid 331 and \ (name N or name CA or name C or name O or name CB )) or resid 332 through 345 o \ r (resid 346 through 348 and (name N or name CA or name C or name O or name CB ) \ ) or resid 349 through 367)) selection = (chain 'I' and (resid 2 through 140 or (resid 141 through 143 and (name N or nam \ e CA or name C or name O or name CB )) or resid 144 through 288 or (resid 289 an \ d (name N or name CA or name C or name O or name CB )) or resid 290 through 330 \ or (resid 331 and (name N or name CA or name C or name O or name CB )) or resid \ 332 through 345 or (resid 346 through 348 and (name N or name CA or name C or na \ me O or name CB )) or resid 349 through 367)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.470 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.010 0.098 28437 Z= 0.463 Angle : 1.348 17.885 39035 Z= 0.764 Chirality : 0.072 0.460 4425 Planarity : 0.007 0.110 4775 Dihedral : 14.697 160.064 10901 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 1.14 % Allowed : 4.84 % Favored : 94.02 % Rotamer: Outliers : 2.31 % Allowed : 7.74 % Favored : 89.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.13), residues: 3246 helix: -1.18 (0.12), residues: 1326 sheet: -2.23 (0.21), residues: 455 loop : -1.27 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG A 21 TYR 0.052 0.005 TYR J 182 PHE 0.051 0.004 PHE C 276 TRP 0.089 0.006 TRP C 390 HIS 0.020 0.004 HIS J 218 Details of bonding type rmsd covalent geometry : bond 0.01048 (28437) covalent geometry : angle 1.34774 (39035) hydrogen bonds : bond 0.14698 ( 1333) hydrogen bonds : angle 8.88439 ( 3812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 642 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 ARG cc_start: 0.7449 (mtt180) cc_final: 0.7128 (ttm-80) REVERT: C 387 ASP cc_start: 0.8308 (p0) cc_final: 0.8064 (p0) REVERT: D 33 LYS cc_start: 0.9056 (mttm) cc_final: 0.8644 (mtmt) REVERT: D 319 ASN cc_start: 0.8277 (t0) cc_final: 0.7770 (t0) REVERT: E 92 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8418 (tm) REVERT: E 118 TYR cc_start: 0.8847 (t80) cc_final: 0.8384 (t80) REVERT: E 250 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7059 (tm-30) REVERT: F 222 ASN cc_start: 0.8427 (p0) cc_final: 0.8033 (p0) REVERT: G 241 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7041 (tpp80) REVERT: G 312 LEU cc_start: 0.9034 (tp) cc_final: 0.8763 (tp) REVERT: H 173 MET cc_start: 0.7542 (ttt) cc_final: 0.7188 (ttm) REVERT: H 209 ASP cc_start: 0.9131 (m-30) cc_final: 0.8894 (m-30) REVERT: H 244 GLU cc_start: 0.7968 (pp20) cc_final: 0.7721 (pp20) REVERT: H 312 LEU cc_start: 0.9060 (tp) cc_final: 0.8823 (tp) REVERT: I 10 GLN cc_start: 0.7176 (tt0) cc_final: 0.6949 (tt0) REVERT: I 296 PHE cc_start: 0.8815 (m-10) cc_final: 0.8504 (m-10) REVERT: J 148 PHE cc_start: 0.6850 (t80) cc_final: 0.6646 (t80) REVERT: J 190 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7891 (tt) REVERT: J 205 THR cc_start: 0.7697 (p) cc_final: 0.7169 (p) REVERT: J 218 HIS cc_start: 0.7920 (m170) cc_final: 0.7695 (m-70) REVERT: N 164 GLU cc_start: 0.7736 (pm20) cc_final: 0.7499 (pm20) REVERT: N 179 THR cc_start: 0.6893 (m) cc_final: 0.6175 (p) outliers start: 61 outliers final: 15 residues processed: 679 average time/residue: 0.1923 time to fit residues: 196.9386 Evaluate side-chains 338 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 321 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 9 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 283 HIS C 349 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 216 HIS ** E 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 190 HIS ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 49 HIS F 134 HIS F 195 HIS G 18 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 273 ASN H 18 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN H 216 HIS H 225 GLN H 272 GLN I 16 ASN I 18 ASN I 49 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095502 restraints weight = 54839.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095286 restraints weight = 35912.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095877 restraints weight = 27633.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096152 restraints weight = 23285.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096372 restraints weight = 21672.355| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28437 Z= 0.223 Angle : 0.783 10.387 39035 Z= 0.411 Chirality : 0.046 0.214 4425 Planarity : 0.006 0.067 4775 Dihedral : 16.226 159.971 4992 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Rotamer: Outliers : 4.25 % Allowed : 14.15 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3246 helix: -0.05 (0.13), residues: 1354 sheet: -1.52 (0.23), residues: 432 loop : -0.92 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 43 TYR 0.032 0.002 TYR D 14 PHE 0.023 0.002 PHE C 379 TRP 0.031 0.002 TRP C 390 HIS 0.015 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00482 (28437) covalent geometry : angle 0.78336 (39035) hydrogen bonds : bond 0.05271 ( 1333) hydrogen bonds : angle 5.92341 ( 3812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 417 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.6543 (mm-40) cc_final: 0.5920 (mp10) REVERT: B 155 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7308 (p0) REVERT: B 222 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7359 (pt0) REVERT: C 121 GLU cc_start: 0.7649 (tp30) cc_final: 0.7423 (tp30) REVERT: C 127 HIS cc_start: 0.7674 (t-90) cc_final: 0.7429 (t-90) REVERT: C 169 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7589 (m170) REVERT: C 235 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7171 (t0) REVERT: C 236 ILE cc_start: 0.8305 (mp) cc_final: 0.8086 (mp) REVERT: C 427 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5928 (pm20) REVERT: C 431 ARG cc_start: 0.8468 (ptt-90) cc_final: 0.7684 (mtm110) REVERT: C 530 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: D 30 TYR cc_start: 0.9038 (t80) cc_final: 0.8836 (t80) REVERT: D 33 LYS cc_start: 0.8984 (mttm) cc_final: 0.8595 (mtmt) REVERT: D 44 LYS cc_start: 0.9183 (tttt) cc_final: 0.8782 (tttp) REVERT: E 92 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8429 (tm) REVERT: F 183 ASP cc_start: 0.8244 (p0) cc_final: 0.7646 (p0) REVERT: F 363 MET cc_start: 0.9125 (mmt) cc_final: 0.8756 (mmm) REVERT: G 74 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8425 (ptp-170) REVERT: G 221 MET cc_start: 0.7101 (tpp) cc_final: 0.6607 (mmm) REVERT: G 316 GLN cc_start: 0.8668 (tp40) cc_final: 0.8399 (tp40) REVERT: I 119 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8378 (pp) REVERT: I 173 MET cc_start: 0.8232 (tmm) cc_final: 0.7883 (ttp) REVERT: I 234 TYR cc_start: 0.8005 (t80) cc_final: 0.7774 (t80) REVERT: J 205 THR cc_start: 0.7605 (p) cc_final: 0.7370 (p) REVERT: N 93 ARG cc_start: 0.8739 (mpt90) cc_final: 0.8498 (mmt180) REVERT: N 141 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8091 (ppp80) REVERT: N 164 GLU cc_start: 0.8072 (pm20) cc_final: 0.7871 (pm20) REVERT: N 179 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6675 (p) REVERT: N 225 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7435 (mm-30) outliers start: 112 outliers final: 50 residues processed: 490 average time/residue: 0.1782 time to fit residues: 136.2734 Evaluate side-chains 361 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 104 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 334 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 174 HIS C 235 ASN C 491 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 273 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 216 HIS F 272 GLN G 18 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS H 18 ASN H 89 GLN H 316 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092850 restraints weight = 55260.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092066 restraints weight = 35249.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092204 restraints weight = 27802.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092593 restraints weight = 24703.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092812 restraints weight = 21918.611| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28437 Z= 0.202 Angle : 0.711 10.716 39035 Z= 0.368 Chirality : 0.044 0.220 4425 Planarity : 0.005 0.074 4775 Dihedral : 16.077 157.316 4972 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 4.63 % Allowed : 16.16 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3246 helix: 0.38 (0.14), residues: 1359 sheet: -1.24 (0.23), residues: 439 loop : -0.75 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 217 TYR 0.024 0.002 TYR E 234 PHE 0.019 0.002 PHE N 243 TRP 0.027 0.002 TRP C 390 HIS 0.026 0.002 HIS H 216 Details of bonding type rmsd covalent geometry : bond 0.00454 (28437) covalent geometry : angle 0.71104 (39035) hydrogen bonds : bond 0.04737 ( 1333) hydrogen bonds : angle 5.44176 ( 3812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 351 time to evaluate : 0.882 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: A 179 ARG cc_start: -0.3450 (OUTLIER) cc_final: -0.3864 (mpt-90) REVERT: B 20 LEU cc_start: 0.7242 (mm) cc_final: 0.6804 (mt) REVERT: B 158 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: B 174 ARG cc_start: 0.7410 (tpt-90) cc_final: 0.6580 (mtm110) REVERT: B 183 LEU cc_start: 0.8367 (tp) cc_final: 0.8009 (tt) REVERT: B 222 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7499 (pt0) REVERT: C 169 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7191 (m-70) REVERT: C 235 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7888 (t0) REVERT: C 249 TRP cc_start: 0.7823 (p-90) cc_final: 0.7552 (p-90) REVERT: C 312 TYR cc_start: 0.8206 (m-10) cc_final: 0.7715 (m-80) REVERT: C 386 ARG cc_start: 0.7506 (ttp-170) cc_final: 0.7045 (ttm-80) REVERT: C 427 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5721 (pm20) REVERT: C 431 ARG cc_start: 0.8323 (ptt-90) cc_final: 0.7694 (mtm110) REVERT: C 520 CYS cc_start: 0.7140 (t) cc_final: 0.5965 (m) REVERT: D 14 TYR cc_start: 0.8952 (t80) cc_final: 0.8627 (t80) REVERT: D 33 LYS cc_start: 0.9000 (mttm) cc_final: 0.8576 (mtmt) REVERT: D 232 TYR cc_start: 0.9232 (t80) cc_final: 0.9031 (t80) REVERT: E 10 GLN cc_start: 0.8247 (tt0) cc_final: 0.8012 (tt0) REVERT: E 12 LEU cc_start: 0.8851 (mt) cc_final: 0.8650 (mt) REVERT: E 41 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: E 92 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8509 (tm) REVERT: F 183 ASP cc_start: 0.8198 (p0) cc_final: 0.7931 (p0) REVERT: G 74 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8412 (ptp90) REVERT: G 140 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (ptpp) REVERT: G 221 MET cc_start: 0.7018 (tpp) cc_final: 0.6817 (tpp) REVERT: G 307 SER cc_start: 0.8686 (t) cc_final: 0.8448 (p) REVERT: G 316 GLN cc_start: 0.8658 (tp40) cc_final: 0.8397 (tp40) REVERT: I 173 MET cc_start: 0.8198 (tmm) cc_final: 0.7606 (tmm) REVERT: N 58 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8123 (mmmt) REVERT: N 141 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8222 (ppp80) REVERT: N 179 THR cc_start: 0.7059 (m) cc_final: 0.6304 (p) REVERT: N 225 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7468 (mm-30) outliers start: 122 outliers final: 64 residues processed: 439 average time/residue: 0.1557 time to fit residues: 109.9728 Evaluate side-chains 373 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 165 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS C 235 ASN C 491 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN G 18 ASN G 89 GLN H 18 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN I 190 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091257 restraints weight = 55108.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090209 restraints weight = 34098.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090596 restraints weight = 27783.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.090930 restraints weight = 25917.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091107 restraints weight = 22475.058| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28437 Z= 0.207 Angle : 0.687 11.060 39035 Z= 0.356 Chirality : 0.043 0.267 4425 Planarity : 0.005 0.074 4775 Dihedral : 16.074 157.866 4972 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.21 % Rotamer: Outliers : 4.97 % Allowed : 17.45 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.14), residues: 3246 helix: 0.60 (0.14), residues: 1363 sheet: -1.02 (0.23), residues: 453 loop : -0.72 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 174 TYR 0.028 0.002 TYR E 234 PHE 0.019 0.002 PHE D 170 TRP 0.023 0.002 TRP C 390 HIS 0.010 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00460 (28437) covalent geometry : angle 0.68686 (39035) hydrogen bonds : bond 0.04457 ( 1333) hydrogen bonds : angle 5.20300 ( 3812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 334 time to evaluate : 0.897 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: B 183 LEU cc_start: 0.8241 (tp) cc_final: 0.7867 (tt) REVERT: B 187 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6575 (mm110) REVERT: B 212 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 222 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7597 (pt0) REVERT: C 169 HIS cc_start: 0.7968 (m90) cc_final: 0.7682 (m-70) REVERT: C 249 TRP cc_start: 0.7875 (p-90) cc_final: 0.7517 (p-90) REVERT: C 312 TYR cc_start: 0.8297 (m-10) cc_final: 0.8037 (m-10) REVERT: C 427 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: C 519 TYR cc_start: 0.8160 (m-80) cc_final: 0.7783 (m-80) REVERT: D 14 TYR cc_start: 0.8931 (t80) cc_final: 0.8585 (t80) REVERT: D 33 LYS cc_start: 0.8970 (mttm) cc_final: 0.8641 (mtmt) REVERT: D 41 GLN cc_start: 0.8978 (pm20) cc_final: 0.8763 (pm20) REVERT: E 35 ARG cc_start: 0.8624 (mpp80) cc_final: 0.8370 (mtt-85) REVERT: E 41 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: E 92 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8607 (tm) REVERT: E 216 HIS cc_start: 0.4358 (OUTLIER) cc_final: 0.3815 (p-80) REVERT: F 183 ASP cc_start: 0.8359 (p0) cc_final: 0.8120 (p0) REVERT: G 74 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8418 (ptp90) REVERT: G 173 MET cc_start: 0.8517 (ttp) cc_final: 0.8210 (ttp) REVERT: G 221 MET cc_start: 0.7128 (tpp) cc_final: 0.6915 (tpp) REVERT: G 307 SER cc_start: 0.8717 (t) cc_final: 0.8468 (p) REVERT: G 316 GLN cc_start: 0.8727 (tp40) cc_final: 0.8449 (tp40) REVERT: H 114 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.7906 (m) REVERT: I 168 ASN cc_start: 0.8697 (m-40) cc_final: 0.8462 (m-40) REVERT: I 169 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8815 (mp) REVERT: I 173 MET cc_start: 0.8287 (tmm) cc_final: 0.7713 (tmm) REVERT: I 346 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7011 (mt) REVERT: N 141 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8305 (ppp80) REVERT: N 179 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6312 (p) REVERT: N 225 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7463 (mm-30) outliers start: 131 outliers final: 82 residues processed: 431 average time/residue: 0.1552 time to fit residues: 108.0813 Evaluate side-chains 376 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 284 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 228 optimal weight: 0.1980 chunk 306 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 236 ASN G 18 ASN H 18 ASN H 316 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 GLN ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090243 restraints weight = 55123.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089732 restraints weight = 35150.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089889 restraints weight = 29732.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090292 restraints weight = 24292.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090515 restraints weight = 22717.544| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28437 Z= 0.194 Angle : 0.675 14.064 39035 Z= 0.346 Chirality : 0.043 0.234 4425 Planarity : 0.005 0.065 4775 Dihedral : 16.015 159.091 4966 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.76 % Favored : 96.09 % Rotamer: Outliers : 5.35 % Allowed : 18.44 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3246 helix: 0.73 (0.14), residues: 1372 sheet: -1.06 (0.22), residues: 453 loop : -0.72 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 241 TYR 0.034 0.002 TYR E 234 PHE 0.020 0.002 PHE G 203 TRP 0.022 0.002 TRP C 390 HIS 0.010 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00435 (28437) covalent geometry : angle 0.67455 (39035) hydrogen bonds : bond 0.04306 ( 1333) hydrogen bonds : angle 5.08770 ( 3812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 323 time to evaluate : 1.185 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: B 8 GLN cc_start: 0.6602 (mm-40) cc_final: 0.6121 (mp10) REVERT: B 20 LEU cc_start: 0.7519 (mm) cc_final: 0.7106 (mt) REVERT: B 24 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5444 (tm-30) REVERT: B 158 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: B 183 LEU cc_start: 0.8264 (tp) cc_final: 0.7880 (tt) REVERT: B 187 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6598 (mm110) REVERT: B 222 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7759 (pt0) REVERT: C 164 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8088 (pp) REVERT: C 388 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7817 (ttpp) REVERT: C 427 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5995 (pm20) REVERT: C 519 TYR cc_start: 0.8203 (m-80) cc_final: 0.7935 (m-80) REVERT: D 14 TYR cc_start: 0.8911 (t80) cc_final: 0.8576 (t80) REVERT: D 33 LYS cc_start: 0.8992 (mttm) cc_final: 0.8653 (mtmt) REVERT: D 41 GLN cc_start: 0.9007 (pm20) cc_final: 0.8779 (pm20) REVERT: E 92 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8663 (tm) REVERT: E 216 HIS cc_start: 0.4079 (OUTLIER) cc_final: 0.3604 (p-80) REVERT: F 183 ASP cc_start: 0.8341 (p0) cc_final: 0.8108 (p0) REVERT: G 41 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: G 74 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8427 (ptp90) REVERT: G 173 MET cc_start: 0.8749 (ttp) cc_final: 0.8502 (ttp) REVERT: G 278 MET cc_start: 0.8235 (mmm) cc_final: 0.7976 (mmm) REVERT: G 307 SER cc_start: 0.8707 (t) cc_final: 0.8453 (p) REVERT: G 316 GLN cc_start: 0.8748 (tp40) cc_final: 0.8504 (tp40) REVERT: H 114 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8102 (m) REVERT: I 109 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.3907 (pm20) REVERT: I 169 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8747 (mp) REVERT: I 173 MET cc_start: 0.8384 (tmm) cc_final: 0.7717 (tmm) REVERT: I 346 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7205 (mt) REVERT: J 158 GLU cc_start: 0.8011 (tp30) cc_final: 0.7686 (tp30) REVERT: J 205 THR cc_start: 0.7321 (p) cc_final: 0.7108 (p) REVERT: N 141 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.8494 (ppp80) outliers start: 141 outliers final: 95 residues processed: 422 average time/residue: 0.1498 time to fit residues: 102.2749 Evaluate side-chains 396 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 288 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 275 optimal weight: 8.9990 chunk 321 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 ASN G 18 ASN G 216 HIS G 272 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 GLN ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091058 restraints weight = 54844.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091329 restraints weight = 33194.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090956 restraints weight = 27922.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091369 restraints weight = 25317.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091551 restraints weight = 22589.336| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28437 Z= 0.153 Angle : 0.653 12.853 39035 Z= 0.333 Chirality : 0.042 0.240 4425 Planarity : 0.004 0.060 4775 Dihedral : 15.957 159.099 4966 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.36 % Rotamer: Outliers : 5.05 % Allowed : 19.31 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3246 helix: 0.82 (0.14), residues: 1376 sheet: -1.03 (0.23), residues: 433 loop : -0.73 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 241 TYR 0.025 0.001 TYR F 234 PHE 0.017 0.001 PHE J 81 TRP 0.018 0.001 TRP C 390 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00340 (28437) covalent geometry : angle 0.65307 (39035) hydrogen bonds : bond 0.04144 ( 1333) hydrogen bonds : angle 4.94851 ( 3812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 332 time to evaluate : 0.770 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: B 8 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6519 (mp10) REVERT: B 20 LEU cc_start: 0.7515 (mm) cc_final: 0.7115 (mt) REVERT: B 24 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: B 158 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: B 183 LEU cc_start: 0.8223 (tp) cc_final: 0.7860 (tt) REVERT: B 212 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 222 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7722 (pt0) REVERT: C 132 TRP cc_start: 0.8160 (t-100) cc_final: 0.7649 (t-100) REVERT: C 164 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8039 (pp) REVERT: C 312 TYR cc_start: 0.7934 (m-10) cc_final: 0.7721 (m-10) REVERT: C 388 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7831 (ttpp) REVERT: C 427 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.6010 (pm20) REVERT: C 439 GLU cc_start: 0.7879 (tt0) cc_final: 0.7515 (tt0) REVERT: C 519 TYR cc_start: 0.8125 (m-80) cc_final: 0.7902 (m-80) REVERT: D 14 TYR cc_start: 0.8813 (t80) cc_final: 0.8598 (t80) REVERT: D 33 LYS cc_start: 0.8998 (mttm) cc_final: 0.8656 (mtmt) REVERT: D 187 GLN cc_start: 0.8656 (tt0) cc_final: 0.8365 (tt0) REVERT: D 216 HIS cc_start: 0.6963 (m170) cc_final: 0.6476 (m90) REVERT: E 92 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8647 (tm) REVERT: E 109 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5575 (pm20) REVERT: E 317 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7535 (mm-30) REVERT: F 183 ASP cc_start: 0.8362 (p0) cc_final: 0.8144 (p0) REVERT: F 250 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 41 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: G 74 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8517 (ptp90) REVERT: G 173 MET cc_start: 0.8667 (ttp) cc_final: 0.8300 (ttp) REVERT: G 221 MET cc_start: 0.7269 (tpp) cc_final: 0.6902 (tpp) REVERT: G 278 MET cc_start: 0.8268 (mmm) cc_final: 0.8052 (mmm) REVERT: G 307 SER cc_start: 0.8563 (t) cc_final: 0.8313 (p) REVERT: G 341 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: H 7 HIS cc_start: 0.9353 (OUTLIER) cc_final: 0.7824 (m-70) REVERT: H 114 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8187 (m) REVERT: I 109 GLU cc_start: 0.4575 (OUTLIER) cc_final: 0.3967 (pm20) REVERT: I 169 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8718 (mp) REVERT: I 173 MET cc_start: 0.8359 (tmm) cc_final: 0.7745 (tmm) REVERT: I 236 ASN cc_start: 0.7998 (m110) cc_final: 0.7692 (m-40) REVERT: N 141 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8344 (ppp80) outliers start: 133 outliers final: 80 residues processed: 418 average time/residue: 0.1503 time to fit residues: 101.5782 Evaluate side-chains 386 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 292 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 140 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 315 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 309 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 491 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 285 HIS ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN F 18 ASN G 18 ASN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 HIS ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088393 restraints weight = 55458.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.086774 restraints weight = 37163.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087044 restraints weight = 33954.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087384 restraints weight = 27494.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087619 restraints weight = 24633.655| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28437 Z= 0.263 Angle : 0.715 12.275 39035 Z= 0.370 Chirality : 0.044 0.255 4425 Planarity : 0.005 0.073 4775 Dihedral : 16.008 161.625 4966 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.04 % Favored : 95.81 % Rotamer: Outliers : 5.46 % Allowed : 20.03 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3246 helix: 0.82 (0.14), residues: 1364 sheet: -0.88 (0.23), residues: 442 loop : -0.84 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 43 TYR 0.027 0.002 TYR F 234 PHE 0.031 0.002 PHE D 203 TRP 0.024 0.002 TRP C 390 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00591 (28437) covalent geometry : angle 0.71473 (39035) hydrogen bonds : bond 0.04472 ( 1333) hydrogen bonds : angle 5.07292 ( 3812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 304 time to evaluate : 1.032 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: B 8 GLN cc_start: 0.6928 (mm-40) cc_final: 0.6563 (mp10) REVERT: B 20 LEU cc_start: 0.7542 (mm) cc_final: 0.7143 (mt) REVERT: B 24 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5511 (tm-30) REVERT: B 158 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: C 427 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6014 (pm20) REVERT: C 519 TYR cc_start: 0.8499 (m-80) cc_final: 0.8149 (m-80) REVERT: D 33 LYS cc_start: 0.8953 (mttm) cc_final: 0.8604 (mtmt) REVERT: D 173 MET cc_start: 0.8255 (mmm) cc_final: 0.7905 (mmm) REVERT: E 92 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8637 (tm) REVERT: E 109 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: E 118 TYR cc_start: 0.9236 (t80) cc_final: 0.8729 (t80) REVERT: F 183 ASP cc_start: 0.8396 (p0) cc_final: 0.8192 (p0) REVERT: F 250 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7840 (tm-30) REVERT: G 7 HIS cc_start: 0.9184 (OUTLIER) cc_final: 0.8973 (m90) REVERT: G 74 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8613 (ptp90) REVERT: G 144 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: G 173 MET cc_start: 0.8880 (ttp) cc_final: 0.8390 (ttp) REVERT: G 221 MET cc_start: 0.7104 (tpp) cc_final: 0.6662 (tpp) REVERT: G 307 SER cc_start: 0.8846 (t) cc_final: 0.8557 (p) REVERT: G 316 GLN cc_start: 0.8772 (tp40) cc_final: 0.8490 (tp40) REVERT: H 7 HIS cc_start: 0.9378 (OUTLIER) cc_final: 0.7811 (m-70) REVERT: H 114 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8325 (m) REVERT: H 136 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8279 (p0) REVERT: I 34 GLU cc_start: 0.7512 (pm20) cc_final: 0.7245 (pm20) REVERT: I 92 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8984 (tt) REVERT: I 169 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8770 (mp) REVERT: I 173 MET cc_start: 0.8493 (tmm) cc_final: 0.7961 (tmm) REVERT: I 346 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7350 (mt) REVERT: J 41 ASP cc_start: 0.8039 (t70) cc_final: 0.7477 (t70) REVERT: N 24 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7794 (mmt180) outliers start: 144 outliers final: 101 residues processed: 413 average time/residue: 0.1577 time to fit residues: 105.4208 Evaluate side-chains 391 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 275 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.2192 > 50: distance: 63 - 64: 8.534 distance: 64 - 65: 8.126 distance: 64 - 67: 9.326 distance: 65 - 66: 11.366 distance: 65 - 71: 3.948 distance: 67 - 68: 10.682 distance: 68 - 69: 16.330 distance: 68 - 70: 20.491 distance: 71 - 72: 8.909 distance: 72 - 73: 3.271 distance: 72 - 75: 17.783 distance: 73 - 74: 9.425 distance: 73 - 79: 6.417 distance: 75 - 76: 13.681 distance: 76 - 77: 5.729 distance: 76 - 78: 14.581 distance: 79 - 80: 11.152 distance: 80 - 81: 4.319 distance: 81 - 82: 8.838 distance: 81 - 83: 6.536 distance: 83 - 84: 3.618 distance: 84 - 85: 12.900 distance: 84 - 87: 10.471 distance: 85 - 86: 7.178 distance: 85 - 89: 16.540 distance: 87 - 88: 7.843 distance: 89 - 90: 13.267 distance: 89 - 95: 18.333 distance: 90 - 91: 7.788 distance: 90 - 93: 6.315 distance: 91 - 92: 9.809 distance: 91 - 96: 12.096 distance: 93 - 94: 25.597 distance: 94 - 95: 4.545 distance: 96 - 97: 4.709 distance: 97 - 98: 5.750 distance: 97 - 100: 5.648 distance: 98 - 99: 12.857 distance: 98 - 105: 9.524 distance: 100 - 101: 3.330 distance: 101 - 102: 9.288 distance: 102 - 103: 8.752 distance: 103 - 104: 17.375 distance: 105 - 106: 6.363 distance: 106 - 109: 10.985 distance: 107 - 108: 5.799 distance: 107 - 112: 6.856 distance: 109 - 110: 14.971 distance: 109 - 111: 20.313 distance: 112 - 113: 17.793 distance: 112 - 162: 15.439 distance: 113 - 114: 15.723 distance: 113 - 116: 12.508 distance: 114 - 115: 14.143 distance: 114 - 119: 28.839 distance: 115 - 159: 28.169 distance: 116 - 117: 10.708 distance: 116 - 118: 16.767 distance: 119 - 120: 15.904 distance: 120 - 121: 33.783 distance: 120 - 123: 18.802 distance: 121 - 122: 8.156 distance: 121 - 126: 30.963 distance: 123 - 124: 7.730 distance: 123 - 125: 11.071 distance: 126 - 127: 5.086 distance: 126 - 149: 17.038 distance: 127 - 128: 10.388 distance: 127 - 130: 9.000 distance: 128 - 129: 16.055 distance: 128 - 138: 6.533 distance: 129 - 146: 15.595 distance: 130 - 131: 9.410 distance: 131 - 132: 10.568 distance: 131 - 133: 19.554 distance: 132 - 134: 6.557 distance: 133 - 135: 9.200 distance: 134 - 136: 10.508 distance: 135 - 136: 18.197 distance: 136 - 137: 8.163