Starting phenix.real_space_refine on Mon Sep 14 03:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.cif" model { file = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u07_8477/09_2026/5u07_8477.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 59} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 5.93, per 1000 atoms: 0.21 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.45 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: 6.18 Time building geometry restraints manager: 3.23 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=" C3' DG O 11 " pdb=" O3' DG O 11 " ideal model delta sigma weight residual 1.435 1.509 -0.074 1.30e-02 5.92e+03 3.27e+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 ... (remaining 28432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 37927 3.58 - 7.15: 993 7.15 - 10.73: 88 10.73 - 14.31: 22 14.31 - 17.88: 5 Bond angle restraints: 39035 Sorted by residual: angle pdb=" O5' DC O 12 " pdb=" C5' DC O 12 " pdb=" C4' DC O 12 " ideal model delta sigma weight residual 109.40 116.99 -7.59 8.00e-01 1.56e+00 9.00e+01 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=" C3' DG O 11 " pdb=" O3' DG O 11 " pdb=" P DC O 12 " ideal model delta sigma weight residual 119.70 128.54 -8.84 1.20e+00 6.94e-01 5.43e+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 ... (remaining 39030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 16275 32.01 - 64.03: 569 64.03 - 96.04: 34 96.04 - 128.05: 0 128.05 - 160.06: 1 Dihedral angle restraints: 16879 sinusoidal: 7289 harmonic: 9590 Sorted by residual: dihedral pdb=" C4' A K 44 " pdb=" C3' A K 44 " pdb=" C2' A K 44 " pdb=" C1' A K 44 " ideal model delta sinusoidal sigma weight residual 36.34 -37.84 74.19 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' G K 19 " pdb=" C3' G K 19 " pdb=" C2' G K 19 " pdb=" C1' G K 19 " ideal model delta sinusoidal sigma weight residual 36.34 -36.69 73.04 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' C K 9 " pdb=" C3' C K 9 " pdb=" C2' C K 9 " pdb=" C1' C K 9 " ideal model delta sinusoidal sigma weight residual 36.35 -36.40 72.74 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 16876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3647 0.095 - 0.189: 611 0.189 - 0.284: 144 0.284 - 0.378: 20 0.378 - 0.473: 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 2.43 1.96 0.47 2.00e-01 2.50e+01 5.58e+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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.710 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.011 0.098 28437 Z= 0.487 Angle : 1.374 17.885 39035 Z= 0.779 Chirality : 0.080 0.473 4425 Planarity : 0.007 0.110 4775 Dihedral : 14.424 160.064 10669 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 are 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/Z covalent geometry : bond 0.01053 / 0.49 (28437) covalent geometry : angle 1.37443 / 0.78 (39035) hydrogen bonds : bond 0.14698 / 10.03 ( 1333) hydrogen bonds : angle 8.88439 / 6.34 ( 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 : 0.831 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: 0.8307 (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: 0.7175 (tt0) cc_final: 0.6948 (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: 0.6645 (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: 0.2007 time to fit residues: 207.3737 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 : 0.957 ------------------------------------------------------------------------------- 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... 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 168 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 273 ASN E 18 ASN ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS 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 250 GLN G 273 ASN H 18 ASN H 49 HIS ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN H 225 GLN H 272 GLN H 273 ASN I 16 ASN I 18 ASN I 195 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099307 restraints weight = 55209.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098738 restraints weight = 38608.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099526 restraints weight = 35561.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099701 restraints weight = 27254.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100484 restraints weight = 23933.745| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 28437 Z= 0.251 Angle : 1.086 22.537 39035 Z= 0.512 Chirality : 0.075 1.036 4425 Planarity : 0.006 0.075 4775 Dihedral : 14.223 155.565 4760 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 4.40 % Allowed : 14.07 % Favored : 81.53 % 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 are not related in a simple way. whole: -1.21 (0.14), residues: 3246 helix: -0.18 (0.13), residues: 1344 sheet: -1.55 (0.23), residues: 399 loop : -1.06 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 277 TYR 0.034 0.002 TYR D 14 PHE 0.027 0.002 PHE C 379 TRP 0.038 0.003 TRP C 390 HIS 0.018 0.002 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (28437) covalent geometry : angle 1.08604 / 0.51 (39035) hydrogen bonds : bond 0.05950 / 4.06 ( 1333) hydrogen bonds : angle 6.25839 / 4.45 ( 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 517 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 401 time to evaluate : 0.935 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: B 44 MET cc_start: 0.3282 (ptm) cc_final: 0.3065 (ptm) REVERT: B 155 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7016 (p0) REVERT: C 235 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7090 (t0) REVERT: C 427 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6452 (pm20) REVERT: D 33 LYS cc_start: 0.9030 (mttm) cc_final: 0.8627 (mtmt) REVERT: D 221 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7605 (mtt) REVERT: E 92 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8382 (tm) REVERT: F 316 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6890 (tm-30) REVERT: G 18 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8827 (p0) REVERT: G 118 TYR cc_start: 0.8796 (t80) cc_final: 0.8557 (t80) REVERT: G 205 THR cc_start: 0.9017 (m) cc_final: 0.8766 (p) REVERT: G 316 GLN cc_start: 0.8634 (tp40) cc_final: 0.8387 (tp40) REVERT: H 92 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8862 (mp) REVERT: H 173 MET cc_start: 0.8404 (ttt) cc_final: 0.7696 (ttm) REVERT: H 209 ASP cc_start: 0.9060 (m-30) cc_final: 0.8842 (m-30) REVERT: I 173 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7612 (ttp) REVERT: N 141 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8284 (ppp80) REVERT: N 164 GLU cc_start: 0.7933 (pm20) cc_final: 0.7728 (pm20) REVERT: N 179 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6624 (p) REVERT: N 225 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7367 (mm-30) outliers start: 116 outliers final: 54 residues processed: 479 average time/residue: 0.1789 time to fit residues: 134.4116 Evaluate side-chains 371 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 LYS 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 313 LEU Chi-restraints excluded: chain C residue 347 ASP 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 427 GLU Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 305 TYR 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 27 THR 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 F residue 266 THR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 177 LEU 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 159 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 183 LEU 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 206 SER Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 104 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 334 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN E 18 ASN E 190 HIS ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN F 18 ASN F 216 HIS F 272 GLN G 18 ASN G 89 GLN H 18 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091207 restraints weight = 55907.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091963 restraints weight = 35933.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092092 restraints weight = 28356.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092387 restraints weight = 24339.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092596 restraints weight = 21381.814| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28437 Z= 0.299 Angle : 0.919 13.268 39035 Z= 0.451 Chirality : 0.062 0.784 4425 Planarity : 0.006 0.074 4775 Dihedral : 14.648 158.255 4746 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 5.24 % Allowed : 15.52 % Favored : 79.25 % 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 are not related in a simple way. whole: -0.78 (0.14), residues: 3246 helix: 0.20 (0.14), residues: 1348 sheet: -1.22 (0.23), residues: 436 loop : -0.86 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 43 TYR 0.029 0.002 TYR C 315 PHE 0.016 0.002 PHE H 231 TRP 0.031 0.002 TRP C 390 HIS 0.012 0.002 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.30 (28437) covalent geometry : angle 0.91941 / 0.45 (39035) hydrogen bonds : bond 0.05352 / 3.66 ( 1333) hydrogen bonds : angle 5.78552 / 4.11 ( 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 479 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 341 time to evaluate : 0.943 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: B 8 GLN cc_start: 0.6680 (mm-40) cc_final: 0.6061 (mp10) REVERT: B 208 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.5869 (m90) REVERT: C 315 TYR cc_start: 0.8345 (m-80) cc_final: 0.8114 (m-80) REVERT: C 427 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: C 439 GLU cc_start: 0.8373 (tt0) cc_final: 0.7987 (tt0) REVERT: C 530 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: D 17 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8290 (mt) REVERT: D 33 LYS cc_start: 0.9093 (mttm) cc_final: 0.8651 (mtmt) REVERT: E 92 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8445 (tm) REVERT: F 316 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6892 (tm-30) REVERT: G 118 TYR cc_start: 0.8929 (t80) cc_final: 0.8715 (t80) REVERT: G 221 MET cc_start: 0.7172 (tpp) cc_final: 0.6905 (tpp) REVERT: G 316 GLN cc_start: 0.8650 (tp40) cc_final: 0.8390 (tp40) REVERT: H 136 ASP cc_start: 0.8189 (p0) cc_final: 0.7186 (p0) REVERT: H 173 MET cc_start: 0.8498 (ttt) cc_final: 0.8107 (ttt) REVERT: I 119 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8636 (pp) REVERT: J 41 ASP cc_start: 0.7790 (t70) cc_final: 0.7102 (t70) REVERT: J 194 ILE cc_start: 0.8219 (mm) cc_final: 0.8017 (tp) REVERT: N 17 GLU cc_start: 0.8494 (pp20) cc_final: 0.8045 (pp20) REVERT: N 58 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8096 (mmmt) REVERT: N 141 ARG cc_start: 0.9499 (OUTLIER) cc_final: 0.8202 (ppp80) REVERT: N 179 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.6318 (p) REVERT: N 225 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7446 (mm-30) outliers start: 138 outliers final: 80 residues processed: 438 average time/residue: 0.1758 time to fit residues: 125.1282 Evaluate side-chains 376 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 288 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 208 HIS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 392 THR 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 437 CYS Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 ILE 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 239 LEU Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 22 LEU 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 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 6 ILE Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 VAL 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 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 18 ASN Chi-restraints excluded: chain G residue 27 THR 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 266 THR Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 18 ASN 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 199 VAL Chi-restraints excluded: chain H residue 216 HIS 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 38 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 94 SER 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 183 LEU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 82 LYS Chi-restraints excluded: chain N residue 85 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 165 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 287 optimal weight: 0.0870 chunk 140 optimal weight: 0.8980 chunk 296 optimal weight: 0.0170 chunk 278 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS C 235 ASN ** C 445 ASN ** 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** D 272 GLN E 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN G 18 ASN G 195 HIS H 89 GLN ** H 316 GLN ** 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096446 restraints weight = 54779.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097043 restraints weight = 38803.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097342 restraints weight = 32762.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097609 restraints weight = 25288.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097886 restraints weight = 22580.997| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 28437 Z= 0.157 Angle : 0.810 14.235 39035 Z= 0.393 Chirality : 0.055 0.614 4425 Planarity : 0.005 0.058 4775 Dihedral : 14.352 153.450 4742 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.64 % Favored : 96.21 % Rotamer: Outliers : 3.91 % Allowed : 17.45 % Favored : 78.64 % 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 are not related in a simple way. whole: -0.57 (0.14), residues: 3246 helix: 0.47 (0.14), residues: 1354 sheet: -1.13 (0.22), residues: 437 loop : -0.84 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 45 TYR 0.030 0.002 TYR F 234 PHE 0.014 0.002 PHE C 276 TRP 0.029 0.002 TRP C 132 HIS 0.012 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (28437) covalent geometry : angle 0.80994 / 0.39 (39035) hydrogen bonds : bond 0.04759 / 3.26 ( 1333) hydrogen bonds : angle 5.45428 / 3.87 ( 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 451 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 348 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: -0.2541 (OUTLIER) cc_final: -0.3083 (mpt-90) REVERT: B 8 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6175 (mp10) REVERT: B 158 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6181 (tt0) REVERT: B 208 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.5810 (m90) REVERT: B 222 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7042 (pt0) REVERT: C 107 LEU cc_start: 0.6278 (mm) cc_final: 0.5897 (pp) REVERT: C 427 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: C 431 ARG cc_start: 0.8177 (ptt90) cc_final: 0.7150 (mtm110) REVERT: D 14 TYR cc_start: 0.8830 (t80) cc_final: 0.8582 (t80) REVERT: D 33 LYS cc_start: 0.8962 (mttm) cc_final: 0.8579 (mtmt) REVERT: D 216 HIS cc_start: 0.7235 (m-70) cc_final: 0.6748 (m90) REVERT: E 92 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8434 (tm) REVERT: F 250 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7820 (tm-30) REVERT: G 118 TYR cc_start: 0.8795 (t80) cc_final: 0.8544 (t80) REVERT: G 316 GLN cc_start: 0.8635 (tp40) cc_final: 0.8371 (tp40) REVERT: G 340 VAL cc_start: 0.9330 (p) cc_final: 0.9089 (t) REVERT: H 92 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8792 (mt) REVERT: H 136 ASP cc_start: 0.8101 (p0) cc_final: 0.7408 (p0) REVERT: H 140 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8396 (mmtm) REVERT: H 173 MET cc_start: 0.8236 (ttt) cc_final: 0.6825 (ttt) REVERT: I 9 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8523 (tt) REVERT: I 119 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8654 (pp) REVERT: J 41 ASP cc_start: 0.7908 (t70) cc_final: 0.7348 (t70) REVERT: N 141 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8236 (ppp80) outliers start: 103 outliers final: 56 residues processed: 416 average time/residue: 0.1673 time to fit residues: 114.9972 Evaluate side-chains 356 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 31 LEU 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 208 HIS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 170 ASP 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 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 437 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 22 LEU 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 264 LEU 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 210 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 9 ILE 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 I residue 320 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 82 LYS 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 203 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: 10.0000 chunk 121 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN G 18 ASN H 18 ASN H 316 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN I 316 GLN ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN ** N 201 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.124164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088967 restraints weight = 55757.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087980 restraints weight = 35884.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088160 restraints weight = 29315.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088427 restraints weight = 25856.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088641 restraints weight = 24084.942| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 28437 Z= 0.322 Angle : 0.857 11.581 39035 Z= 0.422 Chirality : 0.059 0.583 4425 Planarity : 0.006 0.075 4775 Dihedral : 14.371 157.006 4742 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.04 % Favored : 95.81 % Rotamer: Outliers : 5.31 % Allowed : 17.83 % Favored : 76.86 % 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 are not related in a simple way. whole: -0.56 (0.14), residues: 3246 helix: 0.51 (0.14), residues: 1358 sheet: -1.01 (0.23), residues: 443 loop : -0.92 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 292 TYR 0.038 0.002 TYR C 519 PHE 0.031 0.002 PHE C 123 TRP 0.044 0.002 TRP C 249 HIS 0.010 0.002 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.32 (28437) covalent geometry : angle 0.85743 / 0.42 (39035) hydrogen bonds : bond 0.04979 / 3.38 ( 1333) hydrogen bonds : angle 5.48041 / 3.88 ( 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 453 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 313 time to evaluate : 1.033 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: B 20 LEU cc_start: 0.7466 (mm) cc_final: 0.7065 (mt) REVERT: B 45 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7463 (tt) REVERT: B 158 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: B 187 GLN cc_start: 0.6291 (mm-40) cc_final: 0.5871 (mm110) REVERT: C 132 TRP cc_start: 0.8418 (t-100) cc_final: 0.8201 (t-100) REVERT: C 164 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8012 (pp) REVERT: C 315 TYR cc_start: 0.8220 (m-80) cc_final: 0.7965 (m-80) REVERT: C 427 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5782 (pm20) REVERT: C 431 ARG cc_start: 0.8125 (ptt90) cc_final: 0.6991 (mtm110) REVERT: D 33 LYS cc_start: 0.9009 (mttm) cc_final: 0.8578 (mtmt) REVERT: D 173 MET cc_start: 0.8045 (mmm) cc_final: 0.7763 (mmm) REVERT: D 216 HIS cc_start: 0.7392 (m-70) cc_final: 0.6803 (m90) REVERT: D 250 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8020 (mm-40) REVERT: E 41 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: E 92 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8607 (tm) REVERT: F 250 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 316 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6911 (tm-30) REVERT: G 18 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8785 (p0) REVERT: G 34 GLU cc_start: 0.8218 (pp20) cc_final: 0.7920 (pp20) REVERT: G 118 TYR cc_start: 0.9008 (t80) cc_final: 0.8758 (t80) REVERT: G 173 MET cc_start: 0.8963 (ttp) cc_final: 0.8665 (ttp) REVERT: G 221 MET cc_start: 0.7096 (tpp) cc_final: 0.6797 (tpp) REVERT: G 316 GLN cc_start: 0.8714 (tp40) cc_final: 0.8442 (tp40) REVERT: H 114 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.7998 (m) REVERT: H 173 MET cc_start: 0.8504 (ttt) cc_final: 0.6996 (ttt) REVERT: I 109 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.3993 (pm20) REVERT: I 119 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8775 (pp) REVERT: I 161 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8666 (ttmm) REVERT: I 169 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (mp) REVERT: J 158 GLU cc_start: 0.8102 (tp30) cc_final: 0.7548 (tp30) REVERT: J 194 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8094 (tp) outliers start: 140 outliers final: 96 residues processed: 413 average time/residue: 0.1758 time to fit residues: 118.3319 Evaluate side-chains 386 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 277 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 45 LEU 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 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 125 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 169 HIS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 292 VAL 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 437 CYS Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 18 ASN 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 115 VAL 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 264 LEU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 6 ILE 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 210 ILE 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 18 ASN Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 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 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 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 186 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS 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 38 VAL Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 LYS 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 J residue 31 LEU 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 183 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 82 LYS 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 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 28 optimal weight: 0.0870 chunk 40 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 297 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 222 HIS C 235 ASN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 236 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 ** N 201 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.127597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093432 restraints weight = 54754.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093790 restraints weight = 37023.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094033 restraints weight = 31966.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094403 restraints weight = 25524.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094570 restraints weight = 22726.293| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28437 Z= 0.153 Angle : 0.775 16.053 39035 Z= 0.374 Chirality : 0.053 0.487 4425 Planarity : 0.005 0.062 4775 Dihedral : 14.215 156.544 4736 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.49 % Rotamer: Outliers : 4.44 % Allowed : 19.61 % Favored : 75.95 % 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 are not related in a simple way. whole: -0.40 (0.14), residues: 3246 helix: 0.70 (0.14), residues: 1357 sheet: -1.11 (0.22), residues: 453 loop : -0.83 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.034 0.002 TYR E 234 PHE 0.017 0.002 PHE C 123 TRP 0.026 0.002 TRP C 132 HIS 0.010 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (28437) covalent geometry : angle 0.77496 / 0.37 (39035) hydrogen bonds : bond 0.04488 / 3.07 ( 1333) hydrogen bonds : angle 5.24863 / 3.73 ( 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 441 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 324 time to evaluate : 1.057 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 20 LEU cc_start: 0.7635 (mm) cc_final: 0.7158 (mt) REVERT: B 24 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5430 (tm-30) REVERT: B 45 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6909 (tt) REVERT: B 158 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6177 (tt0) REVERT: B 183 LEU cc_start: 0.8506 (tp) cc_final: 0.8168 (tt) REVERT: B 187 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6480 (mm110) REVERT: B 208 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.5874 (m90) REVERT: B 222 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6763 (pt0) REVERT: C 107 LEU cc_start: 0.6503 (mm) cc_final: 0.6217 (pp) REVERT: C 132 TRP cc_start: 0.8176 (t-100) cc_final: 0.7967 (t-100) REVERT: C 164 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 315 TYR cc_start: 0.8017 (m-80) cc_final: 0.7746 (m-10) REVERT: C 388 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7799 (ttpp) REVERT: C 427 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6152 (pm20) REVERT: D 14 TYR cc_start: 0.8859 (t80) cc_final: 0.8645 (t80) REVERT: D 33 LYS cc_start: 0.8998 (mttm) cc_final: 0.8627 (mtmt) REVERT: D 216 HIS cc_start: 0.7323 (m-70) cc_final: 0.6818 (m90) REVERT: D 250 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7904 (mm-40) REVERT: D 260 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9320 (mm) REVERT: E 7 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8746 (m-70) REVERT: E 92 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8629 (tm) REVERT: E 109 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5549 (pm20) REVERT: E 216 HIS cc_start: 0.4032 (OUTLIER) cc_final: 0.3543 (p-80) REVERT: F 250 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7851 (tm-30) REVERT: G 34 GLU cc_start: 0.8207 (pp20) cc_final: 0.7851 (pp20) REVERT: G 41 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: G 118 TYR cc_start: 0.8900 (t80) cc_final: 0.8693 (t80) REVERT: G 173 MET cc_start: 0.8921 (ttp) cc_final: 0.8566 (ttp) REVERT: G 221 MET cc_start: 0.7237 (tpp) cc_final: 0.6837 (tpp) REVERT: G 316 GLN cc_start: 0.8722 (tp40) cc_final: 0.8439 (tp40) REVERT: H 114 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7994 (m) REVERT: H 140 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8438 (mmtm) REVERT: H 173 MET cc_start: 0.8368 (ttt) cc_final: 0.6845 (ttt) REVERT: I 109 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3678 (pm20) REVERT: I 119 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8771 (pp) REVERT: I 161 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (ttmm) REVERT: I 169 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8951 (mp) REVERT: N 141 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.8247 (ppp80) REVERT: N 181 LEU cc_start: 0.8300 (mt) cc_final: 0.8043 (mt) outliers start: 117 outliers final: 72 residues processed: 403 average time/residue: 0.1805 time to fit residues: 118.3199 Evaluate side-chains 390 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 300 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 LEU 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 208 HIS Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 164 LEU 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 235 ASN Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE 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 497 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 18 ASN 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 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 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 210 ILE Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU 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 230 THR Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ILE 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 203 VAL Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 140 optimal weight: 6.9990 chunk 327 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 332 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 309 optimal weight: 40.0000 chunk 270 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 222 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN E 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN H 18 ASN ** H 316 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.124809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091164 restraints weight = 55260.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091074 restraints weight = 40384.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091462 restraints weight = 37340.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091789 restraints weight = 28653.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092043 restraints weight = 25344.163| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 28437 Z= 0.250 Angle : 0.798 13.342 39035 Z= 0.391 Chirality : 0.054 0.542 4425 Planarity : 0.005 0.066 4775 Dihedral : 14.171 158.952 4736 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 5.12 % Allowed : 19.80 % Favored : 75.08 % 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 are not related in a simple way. whole: -0.38 (0.14), residues: 3246 helix: 0.70 (0.14), residues: 1361 sheet: -1.04 (0.22), residues: 453 loop : -0.83 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 43 TYR 0.027 0.002 TYR E 234 PHE 0.015 0.002 PHE J 148 TRP 0.023 0.002 TRP C 390 HIS 0.009 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (28437) covalent geometry : angle 0.79837 / 0.39 (39035) hydrogen bonds : bond 0.04584 / 3.13 ( 1333) hydrogen bonds : angle 5.24998 / 3.72 ( 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 438 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 303 time to evaluate : 1.006 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: B 20 LEU cc_start: 0.7771 (mm) cc_final: 0.7273 (mt) REVERT: B 24 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5587 (tm-30) REVERT: B 45 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6729 (tt) REVERT: B 158 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5927 (tt0) REVERT: B 183 LEU cc_start: 0.8547 (tp) cc_final: 0.8212 (tt) REVERT: B 187 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6668 (mm110) REVERT: B 208 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.5767 (m90) REVERT: C 97 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6909 (ttp-110) REVERT: C 164 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 277 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8595 (ttm170) REVERT: C 427 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: D 33 LYS cc_start: 0.8988 (mttm) cc_final: 0.8692 (mtmt) REVERT: D 187 GLN cc_start: 0.8810 (tt0) cc_final: 0.8391 (tt0) REVERT: D 216 HIS cc_start: 0.7315 (m-70) cc_final: 0.6829 (m90) REVERT: E 41 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: E 92 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8675 (tm) REVERT: E 109 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5544 (pm20) REVERT: E 216 HIS cc_start: 0.3986 (OUTLIER) cc_final: 0.3496 (p-80) REVERT: F 250 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7792 (tm-30) REVERT: F 316 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6762 (tm-30) REVERT: G 21 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (p0) REVERT: G 34 GLU cc_start: 0.8201 (pp20) cc_final: 0.7905 (pp20) REVERT: G 41 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: G 118 TYR cc_start: 0.9016 (t80) cc_final: 0.8794 (t80) REVERT: G 173 MET cc_start: 0.8961 (ttp) cc_final: 0.8551 (ttp) REVERT: G 221 MET cc_start: 0.7306 (tpp) cc_final: 0.6976 (tpp) REVERT: G 316 GLN cc_start: 0.8600 (tp40) cc_final: 0.8358 (tp40) REVERT: H 114 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8271 (m) REVERT: H 155 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8058 (ttp80) REVERT: H 173 MET cc_start: 0.8541 (ttt) cc_final: 0.6940 (ttt) REVERT: H 341 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: I 109 GLU cc_start: 0.4344 (OUTLIER) cc_final: 0.3757 (pm20) REVERT: I 119 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8727 (pp) REVERT: I 169 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (mp) REVERT: J 41 ASP cc_start: 0.7794 (t70) cc_final: 0.7193 (t70) REVERT: N 181 LEU cc_start: 0.8361 (mt) cc_final: 0.8093 (mt) outliers start: 135 outliers final: 94 residues processed: 398 average time/residue: 0.1804 time to fit residues: 116.8445 Evaluate side-chains 401 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 288 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 LEU 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 208 HIS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 97 ARG 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 169 HIS 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 277 ARG Chi-restraints excluded: chain C residue 292 VAL 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 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 11 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 18 ASN 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 109 GLU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 VAL 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 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 210 ILE Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN 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 205 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 G residue 344 THR 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 216 HIS 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 109 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL 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 316 GLN 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 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 183 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 50 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN G 7 HIS ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN G 285 HIS ** H 316 GLN ** 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** ** N 201 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.127208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092582 restraints weight = 54951.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091480 restraints weight = 35532.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091630 restraints weight = 31758.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092088 restraints weight = 26949.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092273 restraints weight = 23109.385| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28437 Z= 0.150 Angle : 0.760 15.074 39035 Z= 0.369 Chirality : 0.051 0.463 4425 Planarity : 0.005 0.055 4775 Dihedral : 14.088 158.063 4736 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.33 % Rotamer: Outliers : 4.93 % Allowed : 20.03 % Favored : 75.04 % 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 are not related in a simple way. whole: -0.29 (0.14), residues: 3246 helix: 0.78 (0.14), residues: 1360 sheet: -1.07 (0.23), residues: 436 loop : -0.77 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 135 TYR 0.027 0.002 TYR D 14 PHE 0.023 0.001 PHE N 21 TRP 0.019 0.002 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (28437) covalent geometry : angle 0.75962 / 0.37 (39035) hydrogen bonds : bond 0.04331 / 2.96 ( 1333) hydrogen bonds : angle 5.13264 / 3.65 ( 3812) *********************** REFINEMENT MACRO_CYCLE 8 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 447 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 317 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: B 8 GLN cc_start: 0.6288 (mm-40) cc_final: 0.5722 (mp10) REVERT: B 20 LEU cc_start: 0.7480 (mm) cc_final: 0.7024 (mt) REVERT: B 24 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5460 (tm-30) REVERT: B 45 LEU cc_start: 0.7570 (mp) cc_final: 0.7342 (tt) REVERT: B 158 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: B 183 LEU cc_start: 0.8455 (tp) cc_final: 0.8124 (tt) REVERT: B 187 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6478 (mm110) REVERT: B 208 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.5713 (m90) REVERT: B 222 GLU cc_start: 0.7719 (mm-30) cc_final: 0.6799 (pt0) REVERT: C 164 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8020 (pp) REVERT: C 277 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8535 (ttm170) REVERT: C 427 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6023 (pm20) REVERT: C 519 TYR cc_start: 0.8344 (m-80) cc_final: 0.7884 (m-80) REVERT: D 33 LYS cc_start: 0.9004 (mttm) cc_final: 0.8649 (mtmt) REVERT: D 187 GLN cc_start: 0.8788 (tt0) cc_final: 0.8377 (tt0) REVERT: D 205 THR cc_start: 0.9099 (m) cc_final: 0.8742 (m) REVERT: D 216 HIS cc_start: 0.7282 (m-70) cc_final: 0.6735 (m90) REVERT: E 92 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8729 (tm) REVERT: E 109 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5520 (pm20) REVERT: E 216 HIS cc_start: 0.3971 (OUTLIER) cc_final: 0.3378 (p-80) REVERT: E 317 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7512 (mm-30) REVERT: F 250 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7783 (tm-30) REVERT: G 21 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7580 (p0) REVERT: G 34 GLU cc_start: 0.8185 (pp20) cc_final: 0.7789 (pp20) REVERT: G 41 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (pt0) REVERT: G 118 TYR cc_start: 0.8944 (t80) cc_final: 0.8743 (t80) REVERT: G 173 MET cc_start: 0.8954 (ttp) cc_final: 0.8698 (ttp) REVERT: G 221 MET cc_start: 0.7293 (tpp) cc_final: 0.6914 (tpp) REVERT: H 114 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8167 (m) REVERT: H 140 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8539 (mmtm) REVERT: H 155 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8035 (ttp80) REVERT: I 109 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.4034 (pm20) REVERT: I 119 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8811 (pp) REVERT: I 169 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8853 (mp) REVERT: N 141 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.8545 (ppp80) REVERT: N 181 LEU cc_start: 0.8416 (mt) cc_final: 0.8157 (mt) outliers start: 130 outliers final: 86 residues processed: 408 average time/residue: 0.1779 time to fit residues: 119.0881 Evaluate side-chains 395 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 293 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 218 THR 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 277 ARG Chi-restraints excluded: chain C residue 292 VAL 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 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 11 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 22 LEU 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 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 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 210 ILE Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN 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 205 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 G residue 363 MET 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 177 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 316 GLN Chi-restraints excluded: chain J residue 13 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 181 LEU Chi-restraints excluded: chain J residue 190 ILE 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 203 VAL Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 323 optimal weight: 0.6980 chunk 329 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN F 18 ASN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093278 restraints weight = 55109.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092150 restraints weight = 34406.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.092541 restraints weight = 28360.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092819 restraints weight = 24442.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093020 restraints weight = 22634.177| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28437 Z= 0.148 Angle : 0.752 15.150 39035 Z= 0.366 Chirality : 0.051 0.454 4425 Planarity : 0.005 0.054 4775 Dihedral : 14.034 158.398 4734 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 4.40 % Allowed : 20.90 % Favored : 74.70 % 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 are not related in a simple way. whole: -0.26 (0.14), residues: 3246 helix: 0.80 (0.14), residues: 1362 sheet: -1.02 (0.23), residues: 436 loop : -0.76 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 43 TYR 0.028 0.002 TYR F 234 PHE 0.015 0.001 PHE C 276 TRP 0.021 0.002 TRP C 249 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (28437) covalent geometry : angle 0.75151 / 0.37 (39035) hydrogen bonds : bond 0.04286 / 2.94 ( 1333) hydrogen bonds : angle 5.08035 / 3.61 ( 3812) *********************** REFINEMENT MACRO_CYCLE 9 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 422 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 306 time to evaluate : 1.075 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: 0.6514 (mm-40) cc_final: 0.6063 (mp10) REVERT: B 20 LEU cc_start: 0.7413 (mm) cc_final: 0.7001 (mt) REVERT: B 24 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5442 (tm-30) REVERT: B 45 LEU cc_start: 0.7562 (mp) cc_final: 0.7361 (tt) REVERT: B 158 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6201 (tt0) REVERT: B 183 LEU cc_start: 0.8475 (tp) cc_final: 0.8154 (tt) REVERT: B 187 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6522 (mm110) REVERT: B 208 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.5707 (m90) REVERT: B 222 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6760 (pt0) REVERT: C 107 LEU cc_start: 0.6798 (mm) cc_final: 0.6277 (pp) REVERT: C 164 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8098 (pp) REVERT: C 277 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8559 (ttm170) REVERT: C 427 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5968 (pm20) REVERT: C 519 TYR cc_start: 0.8291 (m-80) cc_final: 0.7871 (m-80) REVERT: D 33 LYS cc_start: 0.8984 (mttm) cc_final: 0.8652 (mtmt) REVERT: D 187 GLN cc_start: 0.8800 (tt0) cc_final: 0.8375 (tt0) REVERT: D 205 THR cc_start: 0.9151 (m) cc_final: 0.8781 (m) REVERT: D 216 HIS cc_start: 0.7235 (m-70) cc_final: 0.6686 (m90) REVERT: D 260 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9184 (mm) REVERT: E 7 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.8544 (m-70) REVERT: E 92 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8727 (tm) REVERT: E 109 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: E 317 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7523 (mm-30) REVERT: F 250 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7676 (tm-30) REVERT: G 28 VAL cc_start: 0.9639 (t) cc_final: 0.9345 (p) REVERT: G 34 GLU cc_start: 0.8151 (pp20) cc_final: 0.7796 (pp20) REVERT: G 41 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: G 118 TYR cc_start: 0.8923 (t80) cc_final: 0.8715 (t80) REVERT: G 221 MET cc_start: 0.7434 (tpp) cc_final: 0.7081 (tpp) REVERT: G 341 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: H 114 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8190 (m) REVERT: H 140 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8496 (mmtm) REVERT: H 155 ARG cc_start: 0.8342 (mtp180) cc_final: 0.8032 (ttp80) REVERT: H 173 MET cc_start: 0.8273 (ttt) cc_final: 0.7535 (ttm) REVERT: I 109 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4038 (pm20) REVERT: I 119 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8827 (pp) REVERT: I 169 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8835 (mp) REVERT: N 141 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8310 (ppp80) REVERT: N 181 LEU cc_start: 0.8451 (mt) cc_final: 0.8170 (mt) outliers start: 116 outliers final: 83 residues processed: 384 average time/residue: 0.1683 time to fit residues: 107.0855 Evaluate side-chains 394 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 294 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 218 THR 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 277 ARG Chi-restraints excluded: chain C residue 292 VAL 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 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 11 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 22 LEU 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 264 LEU 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 210 ILE Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 205 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 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 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 150 ILE 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 I residue 6 ILE Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 288 VAL 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 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 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 219 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 302 optimal weight: 10.0000 chunk 253 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN F 18 ASN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 316 GLN I 7 HIS ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092656 restraints weight = 55009.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091408 restraints weight = 34409.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091759 restraints weight = 28791.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092077 restraints weight = 24840.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092279 restraints weight = 22618.094| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28437 Z= 0.168 Angle : 0.758 15.363 39035 Z= 0.372 Chirality : 0.051 0.459 4425 Planarity : 0.005 0.058 4775 Dihedral : 13.996 158.602 4734 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 4.40 % Allowed : 21.21 % Favored : 74.39 % 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 are not related in a simple way. whole: -0.20 (0.14), residues: 3246 helix: 0.85 (0.14), residues: 1360 sheet: -0.92 (0.23), residues: 436 loop : -0.74 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 43 TYR 0.026 0.002 TYR F 234 PHE 0.015 0.001 PHE C 276 TRP 0.023 0.002 TRP C 249 HIS 0.008 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (28437) covalent geometry : angle 0.75776 / 0.37 (39035) hydrogen bonds : bond 0.04289 / 2.94 ( 1333) hydrogen bonds : angle 5.06100 / 3.61 ( 3812) ********************** REFINEMENT MACRO_CYCLE 10 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 410 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 294 time to evaluate : 1.126 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: 0.6654 (mm-40) cc_final: 0.6254 (mp10) REVERT: B 20 LEU cc_start: 0.7484 (mm) cc_final: 0.7069 (mt) REVERT: B 24 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: B 45 LEU cc_start: 0.7579 (mp) cc_final: 0.7361 (tt) REVERT: B 158 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: B 183 LEU cc_start: 0.8457 (tp) cc_final: 0.8131 (tt) REVERT: B 187 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5883 (mm-40) REVERT: B 208 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.5770 (m90) REVERT: C 97 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6991 (ttp-110) REVERT: C 164 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8183 (pp) REVERT: C 277 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8634 (ttm170) REVERT: C 439 GLU cc_start: 0.8382 (tt0) cc_final: 0.7779 (tt0) REVERT: C 519 TYR cc_start: 0.8385 (m-80) cc_final: 0.7982 (m-80) REVERT: D 33 LYS cc_start: 0.9008 (mttm) cc_final: 0.8671 (mtmt) REVERT: D 187 GLN cc_start: 0.8819 (tt0) cc_final: 0.8409 (tt0) REVERT: D 205 THR cc_start: 0.9161 (m) cc_final: 0.8859 (m) REVERT: D 216 HIS cc_start: 0.7285 (m-70) cc_final: 0.6690 (m90) REVERT: D 260 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9185 (mm) REVERT: E 7 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8575 (m-70) REVERT: E 92 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8724 (tm) REVERT: E 109 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5488 (pm20) REVERT: E 317 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 250 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7693 (tm-30) REVERT: G 34 GLU cc_start: 0.8173 (pp20) cc_final: 0.7782 (pp20) REVERT: G 41 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: G 118 TYR cc_start: 0.8978 (t80) cc_final: 0.8766 (t80) REVERT: G 221 MET cc_start: 0.7436 (tpp) cc_final: 0.7065 (tpp) REVERT: G 341 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: H 114 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8184 (m) REVERT: H 155 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7972 (ttp80) REVERT: I 169 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8784 (mp) REVERT: I 173 MET cc_start: 0.8405 (tmm) cc_final: 0.7976 (ppp) REVERT: N 141 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.8323 (ppp80) REVERT: N 181 LEU cc_start: 0.8477 (mt) cc_final: 0.8210 (mt) outliers start: 116 outliers final: 85 residues processed: 377 average time/residue: 0.1783 time to fit residues: 110.0939 Evaluate side-chains 392 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 292 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 164 LEU 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 277 ARG Chi-restraints excluded: chain C residue 292 VAL 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 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 11 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 7 HIS 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 264 LEU 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 210 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 205 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 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 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 230 THR Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 288 VAL 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 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 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 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 143 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093426 restraints weight = 55033.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.092681 restraints weight = 39479.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093090 restraints weight = 39665.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093551 restraints weight = 29164.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093832 restraints weight = 25689.586| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.418 28437 Z= 0.315 Angle : 0.955 59.200 39035 Z= 0.520 Chirality : 0.051 0.502 4425 Planarity : 0.005 0.058 4775 Dihedral : 14.000 158.602 4734 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 4.25 % Allowed : 21.13 % Favored : 74.62 % Cbeta Deviations : 0.06 % 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 are not related in a simple way. whole: -0.20 (0.14), residues: 3246 helix: 0.84 (0.14), residues: 1360 sheet: -0.92 (0.23), residues: 436 loop : -0.74 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 43 TYR 0.024 0.001 TYR F 234 PHE 0.027 0.001 PHE N 21 TRP 0.024 0.002 TRP B 213 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.31 (28437) covalent geometry : angle 0.95508 / 0.52 (39035) hydrogen bonds : bond 0.04282 / 2.94 ( 1333) hydrogen bonds : angle 5.06617 / 3.61 ( 3812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.96 seconds wall clock time: 75 minutes 35.05 seconds (4535.05 seconds total)