Starting phenix.real_space_refine on Thu Mar 5 00:06:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x40_22038/03_2026/6x40_22038.map" } resolution = 2.86 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= 0.004 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11240 2.51 5 N 2829 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17411 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'RI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.17, per 1000 atoms: 0.24 Number of scatterers: 17411 At special positions: 0 Unit cell: (129.525, 139.425, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3245 8.00 N 2829 7.00 C 11240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 846.9 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 28 sheets defined 31.4% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.614A pdb=" N SER A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.522A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 238 removed outlier: 3.914A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.686A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 340 removed outlier: 4.146A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 removed outlier: 4.005A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.684A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.998A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.816A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 310 Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.813A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.674A pdb=" N LEU B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.900A pdb=" N VAL C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.194A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.151A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 268 removed outlier: 4.311A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 4.036A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.776A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 275 Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.731A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 99 through 106 removed outlier: 4.120A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.128A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.627A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.660A pdb=" N THR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 4.348A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 removed outlier: 3.564A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 357 removed outlier: 3.942A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.953A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.717A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.704A pdb=" N THR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.513A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.758A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.700A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.134A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.176A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.088A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.692A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.924A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.683A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.472A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.308A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.822A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.822A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 208 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.686A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.686A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N SER E 61 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.682A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.197A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.774A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.949A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.590A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.590A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.676A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.244A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3478 1.33 - 1.45: 5299 1.45 - 1.58: 8905 1.58 - 1.71: 0 1.71 - 1.84: 167 Bond restraints: 17849 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.334 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.334 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N SER E 286 " pdb=" CA SER E 286 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.17e-02 7.31e+03 9.18e+00 bond pdb=" N ASN A 100 " pdb=" CA ASN A 100 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.28e+00 bond pdb=" N LYS E 184 " pdb=" CA LYS E 184 " ideal model delta sigma weight residual 1.452 1.488 -0.037 1.30e-02 5.92e+03 7.97e+00 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 23969 3.89 - 7.78: 277 7.78 - 11.67: 31 11.67 - 15.56: 5 15.56 - 19.45: 2 Bond angle restraints: 24284 Sorted by residual: angle pdb=" CA LEU K 11 " pdb=" CB LEU K 11 " pdb=" CG LEU K 11 " ideal model delta sigma weight residual 116.30 135.75 -19.45 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU B 277 " pdb=" CB LEU B 277 " pdb=" CG LEU B 277 " ideal model delta sigma weight residual 116.30 135.13 -18.83 3.50e+00 8.16e-02 2.89e+01 angle pdb=" CA MET C 227 " pdb=" CB MET C 227 " pdb=" CG MET C 227 " ideal model delta sigma weight residual 114.10 123.90 -9.80 2.00e+00 2.50e-01 2.40e+01 angle pdb=" CB MET I 11 " pdb=" CG MET I 11 " pdb=" SD MET I 11 " ideal model delta sigma weight residual 112.70 99.06 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CA MET A 227 " pdb=" CB MET A 227 " pdb=" CG MET A 227 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.02e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 10216 21.86 - 43.72: 545 43.72 - 65.58: 54 65.58 - 87.44: 40 87.44 - 109.29: 16 Dihedral angle restraints: 10871 sinusoidal: 4615 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -8.68 -77.32 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual -86.00 -9.99 -76.01 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -11.23 -74.77 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 10868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.761: 2809 0.761 - 1.521: 2 1.521 - 2.282: 0 2.282 - 3.043: 1 3.043 - 3.803: 2 Chirality restraints: 2814 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 1.40 -3.80 2.00e-02 2.50e+03 3.62e+04 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 0.85 -3.25 2.00e-02 2.50e+03 2.63e+04 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 0.08 -2.48 2.00e-02 2.50e+03 1.54e+04 ... (remaining 2811 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.196 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" C7 NAG N 1 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.270 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.192 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C7 NAG N 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3029 2.77 - 3.30: 15334 3.30 - 3.83: 29873 3.83 - 4.37: 36165 4.37 - 4.90: 62936 Nonbonded interactions: 147337 Sorted by model distance: nonbonded pdb=" OE1 GLN C 224 " pdb=" OG1 THR C 225 " model vdw 2.233 3.040 nonbonded pdb=" O ALA C 252 " pdb=" OG1 THR C 256 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 247 " pdb=" OG SER B 251 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.294 3.040 ... (remaining 147332 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.008 0.087 17881 Z= 0.376 Angle : 1.357 61.750 24371 Z= 0.641 Chirality : 0.131 3.803 2814 Planarity : 0.008 0.166 2985 Dihedral : 14.332 109.295 6824 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.42 % Allowed : 6.27 % Favored : 93.31 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.03 (0.16), residues: 2103 helix: -0.26 (0.20), residues: 564 sheet: -0.88 (0.18), residues: 627 loop : -2.36 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 98 TYR 0.039 0.003 TYR C 157 PHE 0.060 0.003 PHE B 258 TRP 0.025 0.002 TRP C 336 HIS 0.008 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00761 (17849) covalent geometry : angle 1.12350 (24284) SS BOND : bond 0.00402 ( 9) SS BOND : angle 3.38167 ( 18) hydrogen bonds : bond 0.14853 ( 806) hydrogen bonds : angle 6.14665 ( 2592) link_ALPHA1-2 : bond 0.02224 ( 3) link_ALPHA1-2 : angle 7.83044 ( 9) link_ALPHA1-3 : bond 0.00483 ( 2) link_ALPHA1-3 : angle 4.18798 ( 6) link_ALPHA1-6 : bond 0.00714 ( 2) link_ALPHA1-6 : angle 2.59829 ( 6) link_BETA1-4 : bond 0.05327 ( 9) link_BETA1-4 : angle 21.17903 ( 27) link_NAG-ASN : bond 0.02985 ( 7) link_NAG-ASN : angle 7.66335 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 452 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7199 (ptp) cc_final: 0.6693 (pp-130) REVERT: A 153 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 138 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 209 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 236 MET cc_start: 0.6708 (mmp) cc_final: 0.6390 (mmp) REVERT: C 43 ASP cc_start: 0.7897 (m-30) cc_final: 0.7573 (m-30) REVERT: C 163 ASP cc_start: 0.8277 (m-30) cc_final: 0.7971 (m-30) REVERT: C 227 MET cc_start: 0.6835 (mmm) cc_final: 0.6270 (ptm) REVERT: D 123 GLU cc_start: 0.7607 (pt0) cc_final: 0.7330 (pm20) REVERT: D 192 ASP cc_start: 0.7641 (t0) cc_final: 0.7441 (t0) REVERT: E 68 ILE cc_start: 0.8856 (mt) cc_final: 0.8572 (mm) REVERT: L 11 MET cc_start: 0.6305 (ptp) cc_final: 0.6039 (ptm) REVERT: K 46 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6797 (mt-10) outliers start: 8 outliers final: 4 residues processed: 457 average time/residue: 0.5729 time to fit residues: 292.2347 Evaluate side-chains 354 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 55 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 185 GLN A 224 GLN A 265 ASN B 68 GLN B 229 GLN B 275 ASN B 308 ASN B 346 ASN C 65 GLN C 185 GLN C 265 ASN C 267 HIS C 303 ASN D 68 GLN D 102 HIS D 189 ASN D 190 GLN D 275 ASN D 314 GLN E 69 ASN E 128 ASN E 163 HIS I 53 ASN J 6 GLN L 53 ASN K 6 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106422 restraints weight = 21448.485| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.13 r_work: 0.3133 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17881 Z= 0.151 Angle : 0.641 11.142 24371 Z= 0.319 Chirality : 0.045 0.269 2814 Planarity : 0.004 0.063 2985 Dihedral : 8.618 78.785 2891 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.09 % Allowed : 15.14 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.30 (0.17), residues: 2103 helix: 0.33 (0.21), residues: 561 sheet: -0.64 (0.19), residues: 634 loop : -1.74 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.015 0.001 TYR C 157 PHE 0.011 0.001 PHE C 212 TRP 0.011 0.001 TRP K 103 HIS 0.006 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00311 (17849) covalent geometry : angle 0.62893 (24284) SS BOND : bond 0.00246 ( 9) SS BOND : angle 2.64608 ( 18) hydrogen bonds : bond 0.03891 ( 806) hydrogen bonds : angle 4.86608 ( 2592) link_ALPHA1-2 : bond 0.00732 ( 3) link_ALPHA1-2 : angle 1.64518 ( 9) link_ALPHA1-3 : bond 0.01553 ( 2) link_ALPHA1-3 : angle 1.22299 ( 6) link_ALPHA1-6 : bond 0.00820 ( 2) link_ALPHA1-6 : angle 1.48462 ( 6) link_BETA1-4 : bond 0.00635 ( 9) link_BETA1-4 : angle 2.36369 ( 27) link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.94128 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8221 (ptp) cc_final: 0.6784 (pp-130) REVERT: A 294 MET cc_start: 0.8250 (tpp) cc_final: 0.7846 (mmp) REVERT: B 15 PHE cc_start: 0.7857 (m-80) cc_final: 0.7613 (m-80) REVERT: B 90 MET cc_start: 0.8435 (tpt) cc_final: 0.8006 (tpt) REVERT: B 138 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 236 MET cc_start: 0.6907 (mmp) cc_final: 0.6618 (mmp) REVERT: B 258 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7536 (t80) REVERT: C 43 ASP cc_start: 0.8692 (m-30) cc_final: 0.8472 (m-30) REVERT: C 185 GLN cc_start: 0.8194 (tt0) cc_final: 0.7844 (tp40) REVERT: C 227 MET cc_start: 0.7282 (mmm) cc_final: 0.6345 (ttt) REVERT: C 303 ASN cc_start: 0.7501 (t0) cc_final: 0.7181 (t0) REVERT: D 42 LYS cc_start: 0.8681 (mttt) cc_final: 0.8334 (mtmt) REVERT: D 123 GLU cc_start: 0.8487 (pt0) cc_final: 0.7693 (pm20) REVERT: D 192 ASP cc_start: 0.8274 (t0) cc_final: 0.8010 (t0) REVERT: D 249 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7442 (mtm110) REVERT: E 56 ASP cc_start: 0.8161 (m-30) cc_final: 0.7666 (m-30) REVERT: E 232 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6810 (ptm-80) REVERT: E 236 PHE cc_start: 0.7567 (m-80) cc_final: 0.7281 (m-80) REVERT: E 334 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: E 355 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7297 (mp) REVERT: I 13 MET cc_start: 0.5550 (ppp) cc_final: 0.5285 (pp-130) REVERT: I 102 LYS cc_start: 0.8411 (tptm) cc_final: 0.8201 (tptp) REVERT: L 11 MET cc_start: 0.6502 (ptp) cc_final: 0.6194 (ptm) REVERT: K 46 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7352 (mt-10) outliers start: 77 outliers final: 32 residues processed: 400 average time/residue: 0.5554 time to fit residues: 249.9649 Evaluate side-chains 379 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 145 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 GLN D 314 GLN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102422 restraints weight = 21751.432| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.09 r_work: 0.3065 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17881 Z= 0.207 Angle : 0.631 13.360 24371 Z= 0.313 Chirality : 0.046 0.319 2814 Planarity : 0.004 0.061 2985 Dihedral : 6.848 66.564 2887 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.62 % Allowed : 17.58 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.89 (0.17), residues: 2103 helix: 0.58 (0.21), residues: 583 sheet: -0.53 (0.19), residues: 630 loop : -1.35 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 250 TYR 0.028 0.002 TYR C 299 PHE 0.017 0.002 PHE E 338 TRP 0.012 0.001 TRP A 237 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00466 (17849) covalent geometry : angle 0.62008 (24284) SS BOND : bond 0.00217 ( 9) SS BOND : angle 2.55741 ( 18) hydrogen bonds : bond 0.03417 ( 806) hydrogen bonds : angle 4.64111 ( 2592) link_ALPHA1-2 : bond 0.00485 ( 3) link_ALPHA1-2 : angle 1.62562 ( 9) link_ALPHA1-3 : bond 0.01358 ( 2) link_ALPHA1-3 : angle 1.23224 ( 6) link_ALPHA1-6 : bond 0.00499 ( 2) link_ALPHA1-6 : angle 1.76157 ( 6) link_BETA1-4 : bond 0.00352 ( 9) link_BETA1-4 : angle 2.12740 ( 27) link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 1.73584 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8180 (ptp) cc_final: 0.6732 (pp-130) REVERT: A 224 GLN cc_start: 0.8610 (tp40) cc_final: 0.8195 (tp-100) REVERT: B 15 PHE cc_start: 0.7894 (m-80) cc_final: 0.7664 (m-80) REVERT: B 90 MET cc_start: 0.8467 (tpt) cc_final: 0.8058 (tpt) REVERT: B 138 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 141 MET cc_start: 0.8879 (mtt) cc_final: 0.8612 (mtt) REVERT: B 229 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7416 (tp-100) REVERT: B 258 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7771 (t80) REVERT: C 43 ASP cc_start: 0.8743 (m-30) cc_final: 0.8457 (m-30) REVERT: C 185 GLN cc_start: 0.8112 (tt0) cc_final: 0.7853 (tp40) REVERT: C 214 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 227 MET cc_start: 0.7472 (mmm) cc_final: 0.6499 (ttt) REVERT: C 303 ASN cc_start: 0.7614 (t0) cc_final: 0.7309 (t0) REVERT: D 42 LYS cc_start: 0.8736 (mttt) cc_final: 0.8381 (mtmt) REVERT: D 123 GLU cc_start: 0.8520 (pt0) cc_final: 0.7718 (pm20) REVERT: D 249 ARG cc_start: 0.7645 (mtm110) cc_final: 0.6969 (mtp-110) REVERT: E 68 ILE cc_start: 0.9014 (mt) cc_final: 0.8682 (mm) REVERT: E 232 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6860 (ptm-80) REVERT: E 331 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6577 (ttp) REVERT: E 334 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6296 (m-10) REVERT: I 13 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5273 (pp-130) REVERT: J 46 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: L 11 MET cc_start: 0.6927 (ptp) cc_final: 0.6647 (ptm) REVERT: L 42 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: K 19 LYS cc_start: 0.8517 (tttt) cc_final: 0.8132 (tptm) REVERT: K 46 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7525 (mt-10) REVERT: K 77 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7443 (t0) REVERT: K 110 GLN cc_start: 0.8403 (pt0) cc_final: 0.8091 (pm20) outliers start: 87 outliers final: 50 residues processed: 391 average time/residue: 0.5672 time to fit residues: 248.5047 Evaluate side-chains 398 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 265 ASN D 314 GLN E 347 ASN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104874 restraints weight = 21720.999| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.07 r_work: 0.3158 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17881 Z= 0.133 Angle : 0.573 10.094 24371 Z= 0.286 Chirality : 0.043 0.207 2814 Planarity : 0.004 0.057 2985 Dihedral : 6.192 60.481 2887 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.41 % Allowed : 19.22 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.52 (0.18), residues: 2103 helix: 0.89 (0.21), residues: 584 sheet: -0.27 (0.20), residues: 605 loop : -1.15 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 250 TYR 0.039 0.001 TYR E 314 PHE 0.016 0.001 PHE D 258 TRP 0.016 0.001 TRP A 237 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00288 (17849) covalent geometry : angle 0.56458 (24284) SS BOND : bond 0.00115 ( 9) SS BOND : angle 2.25470 ( 18) hydrogen bonds : bond 0.03145 ( 806) hydrogen bonds : angle 4.45701 ( 2592) link_ALPHA1-2 : bond 0.00475 ( 3) link_ALPHA1-2 : angle 1.48501 ( 9) link_ALPHA1-3 : bond 0.01330 ( 2) link_ALPHA1-3 : angle 1.18795 ( 6) link_ALPHA1-6 : bond 0.00495 ( 2) link_ALPHA1-6 : angle 1.62093 ( 6) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 1.81275 ( 27) link_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 1.53141 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 354 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8154 (ptp) cc_final: 0.6589 (pp-130) REVERT: A 224 GLN cc_start: 0.8578 (tp40) cc_final: 0.8180 (tp-100) REVERT: B 15 PHE cc_start: 0.7792 (m-80) cc_final: 0.7574 (m-80) REVERT: B 138 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 141 MET cc_start: 0.8844 (mtt) cc_final: 0.8534 (mtt) REVERT: B 229 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7318 (tp-100) REVERT: B 236 MET cc_start: 0.7158 (mmp) cc_final: 0.6704 (mmp) REVERT: B 258 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7786 (t80) REVERT: C 43 ASP cc_start: 0.8661 (m-30) cc_final: 0.8344 (m-30) REVERT: C 185 GLN cc_start: 0.7999 (tt0) cc_final: 0.7739 (tp40) REVERT: C 214 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8710 (mt) REVERT: C 227 MET cc_start: 0.7401 (mmm) cc_final: 0.6395 (ttt) REVERT: C 303 ASN cc_start: 0.7531 (t0) cc_final: 0.7246 (t0) REVERT: D 42 LYS cc_start: 0.8692 (mttt) cc_final: 0.8312 (mtmt) REVERT: D 57 ASP cc_start: 0.8267 (m-30) cc_final: 0.8022 (m-30) REVERT: D 90 MET cc_start: 0.9057 (tpt) cc_final: 0.8793 (tpp) REVERT: D 123 GLU cc_start: 0.8495 (pt0) cc_final: 0.7624 (pm20) REVERT: D 190 GLN cc_start: 0.8430 (tt0) cc_final: 0.8222 (tt0) REVERT: D 314 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: E 68 ILE cc_start: 0.8999 (mt) cc_final: 0.8660 (mm) REVERT: E 197 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7650 (mtp180) REVERT: E 331 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6613 (ttp) REVERT: E 334 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: E 355 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7333 (mp) REVERT: I 13 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5055 (pp-130) REVERT: J 46 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: L 11 MET cc_start: 0.7023 (ptp) cc_final: 0.6767 (ptm) REVERT: L 42 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: K 19 LYS cc_start: 0.8474 (tttt) cc_final: 0.8040 (tptm) REVERT: K 46 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7525 (mt-10) REVERT: K 77 ASN cc_start: 0.7696 (m110) cc_final: 0.7395 (t0) REVERT: K 110 GLN cc_start: 0.8387 (pt0) cc_final: 0.8083 (pm20) outliers start: 83 outliers final: 42 residues processed: 394 average time/residue: 0.5286 time to fit residues: 234.6061 Evaluate side-chains 390 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 130 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN E 182 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104099 restraints weight = 21542.459| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.05 r_work: 0.3148 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17881 Z= 0.156 Angle : 0.576 8.927 24371 Z= 0.289 Chirality : 0.044 0.210 2814 Planarity : 0.004 0.055 2985 Dihedral : 5.950 57.216 2886 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.67 % Allowed : 20.18 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.35 (0.18), residues: 2103 helix: 1.04 (0.21), residues: 584 sheet: -0.23 (0.20), residues: 598 loop : -1.00 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.039 0.001 TYR E 314 PHE 0.019 0.001 PHE E 338 TRP 0.016 0.001 TRP A 237 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00348 (17849) covalent geometry : angle 0.56710 (24284) SS BOND : bond 0.00128 ( 9) SS BOND : angle 2.19607 ( 18) hydrogen bonds : bond 0.03130 ( 806) hydrogen bonds : angle 4.41766 ( 2592) link_ALPHA1-2 : bond 0.00430 ( 3) link_ALPHA1-2 : angle 1.51965 ( 9) link_ALPHA1-3 : bond 0.01273 ( 2) link_ALPHA1-3 : angle 1.20796 ( 6) link_ALPHA1-6 : bond 0.00413 ( 2) link_ALPHA1-6 : angle 1.75201 ( 6) link_BETA1-4 : bond 0.00343 ( 9) link_BETA1-4 : angle 1.74788 ( 27) link_NAG-ASN : bond 0.00307 ( 7) link_NAG-ASN : angle 1.57133 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 350 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8179 (ptp) cc_final: 0.6648 (pp-130) REVERT: A 224 GLN cc_start: 0.8605 (tp40) cc_final: 0.8170 (tp-100) REVERT: A 275 ILE cc_start: 0.8864 (pp) cc_final: 0.8583 (pp) REVERT: B 15 PHE cc_start: 0.7817 (m-80) cc_final: 0.7595 (m-80) REVERT: B 90 MET cc_start: 0.8456 (tpt) cc_final: 0.8072 (tpt) REVERT: B 138 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 141 MET cc_start: 0.8899 (mtt) cc_final: 0.8612 (mtt) REVERT: B 229 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7234 (tp40) REVERT: B 236 MET cc_start: 0.7260 (mmp) cc_final: 0.6803 (mmp) REVERT: B 258 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 9 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: C 43 ASP cc_start: 0.8671 (m-30) cc_final: 0.8363 (m-30) REVERT: C 185 GLN cc_start: 0.8019 (tt0) cc_final: 0.7770 (tp40) REVERT: C 214 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 227 MET cc_start: 0.7443 (mmm) cc_final: 0.6449 (ttt) REVERT: C 303 ASN cc_start: 0.7541 (t0) cc_final: 0.7286 (t0) REVERT: D 42 LYS cc_start: 0.8743 (mttt) cc_final: 0.8354 (mtmt) REVERT: D 57 ASP cc_start: 0.8262 (m-30) cc_final: 0.7875 (m-30) REVERT: D 90 MET cc_start: 0.9052 (tpt) cc_final: 0.8833 (tpp) REVERT: D 123 GLU cc_start: 0.8492 (pt0) cc_final: 0.7665 (pm20) REVERT: D 190 GLN cc_start: 0.8456 (tt0) cc_final: 0.8247 (tt0) REVERT: D 192 ASP cc_start: 0.8350 (t0) cc_final: 0.8096 (m-30) REVERT: E 68 ILE cc_start: 0.9033 (mt) cc_final: 0.8700 (mm) REVERT: E 232 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6755 (ptm-80) REVERT: E 306 PHE cc_start: 0.7276 (m-10) cc_final: 0.7046 (m-80) REVERT: E 331 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6536 (ttp) REVERT: E 355 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7319 (mp) REVERT: I 10 SER cc_start: 0.8350 (t) cc_final: 0.8116 (p) REVERT: I 13 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.5107 (pp-130) REVERT: I 61 ARG cc_start: 0.8001 (ptt-90) cc_final: 0.7697 (ptt90) REVERT: J 34 MET cc_start: 0.9301 (mmm) cc_final: 0.8963 (mmt) REVERT: J 46 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: J 82 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: J 90 ASP cc_start: 0.7873 (m-30) cc_final: 0.7644 (m-30) REVERT: J 98 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8287 (ttt90) REVERT: L 11 MET cc_start: 0.7088 (ptp) cc_final: 0.6816 (ptm) REVERT: K 19 LYS cc_start: 0.8463 (tttt) cc_final: 0.8177 (tptm) REVERT: K 46 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7567 (mt-10) REVERT: K 77 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7470 (t0) REVERT: K 110 GLN cc_start: 0.8383 (pt0) cc_final: 0.8113 (pm20) outliers start: 88 outliers final: 55 residues processed: 393 average time/residue: 0.5389 time to fit residues: 238.5042 Evaluate side-chains 398 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 190 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 201 optimal weight: 0.0070 chunk 4 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 204 GLN C 265 ASN D 314 GLN D 337 ASN E 182 GLN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102092 restraints weight = 21557.339| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.04 r_work: 0.3118 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17881 Z= 0.200 Angle : 0.610 9.654 24371 Z= 0.305 Chirality : 0.045 0.215 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.958 59.146 2886 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.31 % Allowed : 20.18 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.28 (0.18), residues: 2103 helix: 1.05 (0.21), residues: 586 sheet: -0.25 (0.20), residues: 599 loop : -0.88 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 265 TYR 0.039 0.002 TYR E 314 PHE 0.021 0.002 PHE E 338 TRP 0.013 0.001 TRP A 237 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00454 (17849) covalent geometry : angle 0.60069 (24284) SS BOND : bond 0.00180 ( 9) SS BOND : angle 2.40263 ( 18) hydrogen bonds : bond 0.03238 ( 806) hydrogen bonds : angle 4.50192 ( 2592) link_ALPHA1-2 : bond 0.00409 ( 3) link_ALPHA1-2 : angle 1.61328 ( 9) link_ALPHA1-3 : bond 0.01220 ( 2) link_ALPHA1-3 : angle 1.26543 ( 6) link_ALPHA1-6 : bond 0.00369 ( 2) link_ALPHA1-6 : angle 1.91174 ( 6) link_BETA1-4 : bond 0.00338 ( 9) link_BETA1-4 : angle 1.75822 ( 27) link_NAG-ASN : bond 0.00403 ( 7) link_NAG-ASN : angle 1.69543 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 347 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8186 (ptp) cc_final: 0.6633 (pp-130) REVERT: A 224 GLN cc_start: 0.8589 (tp40) cc_final: 0.8160 (tp-100) REVERT: A 275 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 294 MET cc_start: 0.8317 (tpp) cc_final: 0.8003 (mmt) REVERT: A 303 ASN cc_start: 0.7084 (t0) cc_final: 0.6830 (t0) REVERT: B 15 PHE cc_start: 0.7785 (m-80) cc_final: 0.7525 (m-80) REVERT: B 138 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 141 MET cc_start: 0.8912 (mtt) cc_final: 0.8695 (mtt) REVERT: B 229 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7242 (tp-100) REVERT: B 258 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7767 (t80) REVERT: C 9 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7770 (tpp) REVERT: C 43 ASP cc_start: 0.8683 (m-30) cc_final: 0.8359 (m-30) REVERT: C 185 GLN cc_start: 0.8015 (tt0) cc_final: 0.7734 (tp40) REVERT: C 227 MET cc_start: 0.7543 (mmm) cc_final: 0.6518 (ttt) REVERT: C 303 ASN cc_start: 0.7470 (t0) cc_final: 0.7225 (t0) REVERT: D 42 LYS cc_start: 0.8747 (mttt) cc_final: 0.8372 (mtmt) REVERT: D 57 ASP cc_start: 0.8284 (m-30) cc_final: 0.7858 (m-30) REVERT: D 58 MET cc_start: 0.8212 (mmm) cc_final: 0.7772 (mtm) REVERT: D 123 GLU cc_start: 0.8556 (pt0) cc_final: 0.7690 (pm20) REVERT: D 124 ASP cc_start: 0.8738 (p0) cc_final: 0.8465 (p0) REVERT: D 192 ASP cc_start: 0.8342 (t0) cc_final: 0.8068 (m-30) REVERT: E 68 ILE cc_start: 0.9065 (mt) cc_final: 0.8736 (mm) REVERT: E 232 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6810 (ptm-80) REVERT: E 331 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6544 (ttp) REVERT: I 10 SER cc_start: 0.8401 (t) cc_final: 0.8148 (p) REVERT: I 13 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5351 (pp-130) REVERT: I 37 GLN cc_start: 0.9037 (tt0) cc_final: 0.8825 (tt0) REVERT: J 46 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: J 82 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: J 90 ASP cc_start: 0.7910 (m-30) cc_final: 0.7611 (m-30) REVERT: J 98 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8291 (ttt90) REVERT: L 45 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8602 (mmtm) REVERT: K 19 LYS cc_start: 0.8421 (tttt) cc_final: 0.8124 (tptm) REVERT: K 46 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7664 (mt-10) REVERT: K 77 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7400 (t0) REVERT: K 110 GLN cc_start: 0.8452 (pt0) cc_final: 0.8132 (pm20) outliers start: 100 outliers final: 60 residues processed: 398 average time/residue: 0.5486 time to fit residues: 245.7670 Evaluate side-chains 399 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 190 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 204 GLN D 314 GLN E 182 GLN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103559 restraints weight = 21629.541| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.05 r_work: 0.3139 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17881 Z= 0.151 Angle : 0.580 9.207 24371 Z= 0.290 Chirality : 0.044 0.203 2814 Planarity : 0.004 0.051 2985 Dihedral : 5.796 58.497 2886 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.15 % Allowed : 20.50 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.16 (0.18), residues: 2103 helix: 1.19 (0.22), residues: 584 sheet: -0.24 (0.20), residues: 599 loop : -0.79 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.041 0.001 TYR E 314 PHE 0.023 0.001 PHE C 306 TRP 0.019 0.001 TRP A 319 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00338 (17849) covalent geometry : angle 0.57137 (24284) SS BOND : bond 0.00110 ( 9) SS BOND : angle 2.31002 ( 18) hydrogen bonds : bond 0.03087 ( 806) hydrogen bonds : angle 4.40484 ( 2592) link_ALPHA1-2 : bond 0.00468 ( 3) link_ALPHA1-2 : angle 1.46245 ( 9) link_ALPHA1-3 : bond 0.01179 ( 2) link_ALPHA1-3 : angle 1.18303 ( 6) link_ALPHA1-6 : bond 0.00336 ( 2) link_ALPHA1-6 : angle 1.77512 ( 6) link_BETA1-4 : bond 0.00363 ( 9) link_BETA1-4 : angle 1.64012 ( 27) link_NAG-ASN : bond 0.00392 ( 7) link_NAG-ASN : angle 1.63634 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8185 (ptp) cc_final: 0.6659 (pp-130) REVERT: A 275 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8674 (pp) REVERT: B 15 PHE cc_start: 0.7806 (m-80) cc_final: 0.7560 (m-80) REVERT: B 81 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7155 (ttt) REVERT: B 138 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 141 MET cc_start: 0.8928 (mtt) cc_final: 0.8678 (mtt) REVERT: B 229 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7302 (tp-100) REVERT: B 258 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7832 (t80) REVERT: C 43 ASP cc_start: 0.8671 (m-30) cc_final: 0.8353 (m-30) REVERT: C 185 GLN cc_start: 0.7966 (tt0) cc_final: 0.7741 (tp40) REVERT: C 227 MET cc_start: 0.7533 (mmm) cc_final: 0.6515 (ttt) REVERT: C 303 ASN cc_start: 0.7511 (t0) cc_final: 0.7259 (t0) REVERT: D 42 LYS cc_start: 0.8737 (mttt) cc_final: 0.8359 (mtmt) REVERT: D 123 GLU cc_start: 0.8545 (pt0) cc_final: 0.7698 (pm20) REVERT: D 192 ASP cc_start: 0.8324 (t0) cc_final: 0.8071 (m-30) REVERT: D 314 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: E 68 ILE cc_start: 0.9065 (mt) cc_final: 0.8741 (mm) REVERT: E 199 TYR cc_start: 0.7819 (m-80) cc_final: 0.7412 (m-80) REVERT: E 232 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6836 (ptm-80) REVERT: E 272 THR cc_start: 0.8959 (t) cc_final: 0.8741 (m) REVERT: E 331 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6524 (ttp) REVERT: E 333 SER cc_start: 0.8346 (t) cc_final: 0.8064 (p) REVERT: I 13 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5360 (pp-130) REVERT: I 37 GLN cc_start: 0.9046 (tt0) cc_final: 0.8836 (tt0) REVERT: I 61 ARG cc_start: 0.7854 (ptt-90) cc_final: 0.7597 (ptt90) REVERT: J 46 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: J 82 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: J 90 ASP cc_start: 0.7950 (m-30) cc_final: 0.7671 (m-30) REVERT: J 98 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8308 (ttt90) REVERT: L 45 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8601 (mmtm) REVERT: K 19 LYS cc_start: 0.8386 (tttt) cc_final: 0.8079 (tptm) REVERT: K 46 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7667 (mt-10) REVERT: K 77 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7435 (t0) REVERT: K 110 GLN cc_start: 0.8423 (pt0) cc_final: 0.8143 (pm20) outliers start: 97 outliers final: 63 residues processed: 385 average time/residue: 0.5395 time to fit residues: 234.1153 Evaluate side-chains 391 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 318 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 265 ASN D 190 GLN E 182 GLN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100898 restraints weight = 21783.832| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.06 r_work: 0.3110 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17881 Z= 0.204 Angle : 0.621 9.034 24371 Z= 0.309 Chirality : 0.045 0.213 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.866 57.891 2886 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.89 % Allowed : 20.92 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.16 (0.18), residues: 2103 helix: 1.17 (0.21), residues: 575 sheet: -0.27 (0.20), residues: 589 loop : -0.73 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.044 0.002 TYR E 314 PHE 0.023 0.002 PHE E 338 TRP 0.014 0.001 TRP A 237 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00468 (17849) covalent geometry : angle 0.61177 (24284) SS BOND : bond 0.00187 ( 9) SS BOND : angle 2.45077 ( 18) hydrogen bonds : bond 0.03208 ( 806) hydrogen bonds : angle 4.49495 ( 2592) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.57498 ( 9) link_ALPHA1-3 : bond 0.01201 ( 2) link_ALPHA1-3 : angle 1.30314 ( 6) link_ALPHA1-6 : bond 0.00242 ( 2) link_ALPHA1-6 : angle 1.93856 ( 6) link_BETA1-4 : bond 0.00332 ( 9) link_BETA1-4 : angle 1.71563 ( 27) link_NAG-ASN : bond 0.00464 ( 7) link_NAG-ASN : angle 1.72444 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8197 (ptp) cc_final: 0.6643 (pp-130) REVERT: A 275 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 303 ASN cc_start: 0.6602 (t0) cc_final: 0.6370 (t0) REVERT: B 15 PHE cc_start: 0.7760 (m-80) cc_final: 0.7498 (m-80) REVERT: B 24 ASP cc_start: 0.7731 (t0) cc_final: 0.7204 (p0) REVERT: B 81 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7123 (ttt) REVERT: B 138 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8178 (mt-10) REVERT: B 141 MET cc_start: 0.8919 (mtt) cc_final: 0.8690 (mtt) REVERT: B 229 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7230 (tp-100) REVERT: B 258 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7824 (t80) REVERT: C 43 ASP cc_start: 0.8723 (m-30) cc_final: 0.8395 (m-30) REVERT: C 185 GLN cc_start: 0.8009 (tt0) cc_final: 0.7740 (tp40) REVERT: C 214 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8661 (mt) REVERT: C 227 MET cc_start: 0.7516 (mmm) cc_final: 0.6514 (ttt) REVERT: C 303 ASN cc_start: 0.7454 (t0) cc_final: 0.7191 (t0) REVERT: D 42 LYS cc_start: 0.8739 (mttt) cc_final: 0.8356 (mtmt) REVERT: D 58 MET cc_start: 0.8139 (mmm) cc_final: 0.7837 (mtm) REVERT: D 123 GLU cc_start: 0.8589 (pt0) cc_final: 0.7708 (pm20) REVERT: D 192 ASP cc_start: 0.8270 (t0) cc_final: 0.7999 (m-30) REVERT: E 68 ILE cc_start: 0.9094 (mt) cc_final: 0.8771 (mm) REVERT: E 199 TYR cc_start: 0.7762 (m-80) cc_final: 0.7367 (m-80) REVERT: E 232 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6824 (ptm-80) REVERT: E 272 THR cc_start: 0.8958 (t) cc_final: 0.8694 (m) REVERT: E 331 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6609 (ttp) REVERT: E 333 SER cc_start: 0.8349 (t) cc_final: 0.8066 (p) REVERT: I 13 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5434 (pp-130) REVERT: I 37 GLN cc_start: 0.9049 (tt0) cc_final: 0.8836 (tt0) REVERT: I 61 ARG cc_start: 0.7851 (ptt-90) cc_final: 0.7558 (ptt90) REVERT: J 30 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7747 (ttmm) REVERT: J 46 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: J 82 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: J 90 ASP cc_start: 0.7947 (m-30) cc_final: 0.7615 (m-30) REVERT: J 98 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8288 (ttt90) REVERT: L 45 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8570 (mmtm) REVERT: K 19 LYS cc_start: 0.8333 (tttt) cc_final: 0.8053 (tptm) REVERT: K 46 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7507 (mt-10) REVERT: K 77 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7416 (t0) REVERT: K 110 GLN cc_start: 0.8452 (pt0) cc_final: 0.8145 (pm20) outliers start: 92 outliers final: 64 residues processed: 370 average time/residue: 0.5586 time to fit residues: 232.5453 Evaluate side-chains 393 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 187 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN L 42 GLN K 55 ASN ** K 77 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 = 0.3668 r_free = 0.3668 target = 0.142253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100410 restraints weight = 21783.285| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.05 r_work: 0.3105 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17881 Z= 0.212 Angle : 0.628 9.183 24371 Z= 0.313 Chirality : 0.046 0.209 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.883 56.901 2884 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.51 % Allowed : 21.93 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.17 (0.18), residues: 2103 helix: 1.15 (0.21), residues: 575 sheet: -0.32 (0.20), residues: 590 loop : -0.68 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 265 TYR 0.045 0.002 TYR E 314 PHE 0.024 0.002 PHE E 338 TRP 0.030 0.001 TRP A 319 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00486 (17849) covalent geometry : angle 0.61885 (24284) SS BOND : bond 0.00194 ( 9) SS BOND : angle 2.60249 ( 18) hydrogen bonds : bond 0.03228 ( 806) hydrogen bonds : angle 4.53369 ( 2592) link_ALPHA1-2 : bond 0.00446 ( 3) link_ALPHA1-2 : angle 1.58319 ( 9) link_ALPHA1-3 : bond 0.01159 ( 2) link_ALPHA1-3 : angle 1.32414 ( 6) link_ALPHA1-6 : bond 0.00222 ( 2) link_ALPHA1-6 : angle 1.96086 ( 6) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 1.71469 ( 27) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 1.72631 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8187 (ptp) cc_final: 0.6655 (pp-130) REVERT: A 261 MET cc_start: 0.8404 (tpt) cc_final: 0.8179 (mmm) REVERT: B 24 ASP cc_start: 0.7671 (t0) cc_final: 0.7355 (p0) REVERT: B 81 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7187 (ttt) REVERT: B 138 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 141 MET cc_start: 0.8925 (mtt) cc_final: 0.8711 (mtt) REVERT: B 229 GLN cc_start: 0.7659 (tp-100) cc_final: 0.7229 (tp-100) REVERT: B 258 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7792 (t80) REVERT: C 43 ASP cc_start: 0.8723 (m-30) cc_final: 0.8402 (m-30) REVERT: C 185 GLN cc_start: 0.8005 (tt0) cc_final: 0.7730 (tp40) REVERT: C 214 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8681 (mt) REVERT: C 227 MET cc_start: 0.7556 (mmm) cc_final: 0.6509 (ttt) REVERT: C 303 ASN cc_start: 0.7471 (t0) cc_final: 0.7206 (t0) REVERT: D 42 LYS cc_start: 0.8736 (mttt) cc_final: 0.8358 (mtmt) REVERT: D 58 MET cc_start: 0.8148 (mmm) cc_final: 0.7837 (mtm) REVERT: D 123 GLU cc_start: 0.8611 (pt0) cc_final: 0.7750 (pm20) REVERT: D 192 ASP cc_start: 0.8271 (t0) cc_final: 0.8021 (m-30) REVERT: E 68 ILE cc_start: 0.9099 (mt) cc_final: 0.8784 (mm) REVERT: E 199 TYR cc_start: 0.7788 (m-80) cc_final: 0.7379 (m-80) REVERT: E 272 THR cc_start: 0.8981 (t) cc_final: 0.8708 (m) REVERT: E 331 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6704 (ttp) REVERT: E 333 SER cc_start: 0.8375 (t) cc_final: 0.8097 (p) REVERT: I 13 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5521 (pp-130) REVERT: I 37 GLN cc_start: 0.9051 (tt0) cc_final: 0.8844 (tt0) REVERT: I 61 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7562 (ptt90) REVERT: J 30 LYS cc_start: 0.8374 (mtpt) cc_final: 0.7819 (ttmm) REVERT: J 82 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: J 90 ASP cc_start: 0.7965 (m-30) cc_final: 0.7662 (m-30) REVERT: J 98 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8286 (ttt90) REVERT: L 11 MET cc_start: 0.6715 (ptm) cc_final: 0.6398 (ptp) REVERT: L 45 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8557 (mmtm) REVERT: K 19 LYS cc_start: 0.8311 (tttt) cc_final: 0.8023 (tptm) REVERT: K 46 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7500 (mt-10) REVERT: K 77 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7393 (t0) REVERT: K 110 GLN cc_start: 0.8513 (pt0) cc_final: 0.8192 (pm20) outliers start: 85 outliers final: 63 residues processed: 365 average time/residue: 0.5543 time to fit residues: 227.5799 Evaluate side-chains 389 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 185 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 265 ASN I 53 ASN L 42 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105858 restraints weight = 21441.656| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.03 r_work: 0.3167 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17881 Z= 0.119 Angle : 0.575 9.350 24371 Z= 0.286 Chirality : 0.043 0.192 2814 Planarity : 0.004 0.050 2985 Dihedral : 5.465 54.764 2884 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.03 % Allowed : 23.79 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.02 (0.18), residues: 2103 helix: 1.25 (0.22), residues: 576 sheet: -0.13 (0.20), residues: 571 loop : -0.65 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 265 TYR 0.045 0.001 TYR E 314 PHE 0.024 0.001 PHE E 338 TRP 0.026 0.001 TRP A 319 HIS 0.002 0.000 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00258 (17849) covalent geometry : angle 0.56776 (24284) SS BOND : bond 0.00094 ( 9) SS BOND : angle 2.12802 ( 18) hydrogen bonds : bond 0.02961 ( 806) hydrogen bonds : angle 4.32766 ( 2592) link_ALPHA1-2 : bond 0.00548 ( 3) link_ALPHA1-2 : angle 1.34274 ( 9) link_ALPHA1-3 : bond 0.01288 ( 2) link_ALPHA1-3 : angle 1.14028 ( 6) link_ALPHA1-6 : bond 0.00366 ( 2) link_ALPHA1-6 : angle 1.66262 ( 6) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 1.58068 ( 27) link_NAG-ASN : bond 0.00310 ( 7) link_NAG-ASN : angle 1.37458 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8116 (ptp) cc_final: 0.6533 (pp-130) REVERT: A 84 ASP cc_start: 0.8103 (t0) cc_final: 0.7853 (t70) REVERT: A 303 ASN cc_start: 0.6804 (t0) cc_final: 0.6593 (t0) REVERT: B 24 ASP cc_start: 0.7799 (t0) cc_final: 0.7216 (p0) REVERT: B 138 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 141 MET cc_start: 0.8905 (mtt) cc_final: 0.8614 (mtt) REVERT: B 229 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7200 (tp-100) REVERT: C 43 ASP cc_start: 0.8681 (m-30) cc_final: 0.8354 (m-30) REVERT: C 185 GLN cc_start: 0.7930 (tt0) cc_final: 0.7703 (tp40) REVERT: C 227 MET cc_start: 0.7513 (mmm) cc_final: 0.6494 (ttt) REVERT: C 303 ASN cc_start: 0.7516 (t0) cc_final: 0.7278 (t0) REVERT: C 327 VAL cc_start: 0.6932 (t) cc_final: 0.6629 (p) REVERT: D 42 LYS cc_start: 0.8661 (mttt) cc_final: 0.8289 (mtmt) REVERT: D 58 MET cc_start: 0.8096 (mmm) cc_final: 0.7757 (mtm) REVERT: D 123 GLU cc_start: 0.8559 (pt0) cc_final: 0.7713 (pm20) REVERT: D 192 ASP cc_start: 0.8230 (t0) cc_final: 0.8004 (m-30) REVERT: E 68 ILE cc_start: 0.9066 (mt) cc_final: 0.8747 (mm) REVERT: E 211 GLU cc_start: 0.7898 (pt0) cc_final: 0.7679 (pt0) REVERT: E 306 PHE cc_start: 0.7136 (m-10) cc_final: 0.6884 (m-80) REVERT: E 331 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6666 (ttp) REVERT: E 333 SER cc_start: 0.8356 (t) cc_final: 0.8084 (p) REVERT: I 13 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5750 (pp-130) REVERT: J 30 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7770 (ttmm) REVERT: J 34 MET cc_start: 0.9138 (mmm) cc_final: 0.8874 (mmt) REVERT: J 69 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8519 (m) REVERT: J 82 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: J 90 ASP cc_start: 0.7907 (m-30) cc_final: 0.7629 (m-30) REVERT: J 98 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8339 (ttt90) REVERT: L 11 MET cc_start: 0.6517 (ptm) cc_final: 0.6226 (ptp) REVERT: L 45 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8532 (mmtm) REVERT: K 19 LYS cc_start: 0.8301 (tttt) cc_final: 0.8023 (tptm) REVERT: K 46 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7670 (mt-10) REVERT: K 110 GLN cc_start: 0.8440 (pt0) cc_final: 0.8219 (pm20) outliers start: 57 outliers final: 45 residues processed: 373 average time/residue: 0.5330 time to fit residues: 224.4414 Evaluate side-chains 373 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 324 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.104744 restraints weight = 21469.946| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.08 r_work: 0.3157 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17881 Z= 0.133 Angle : 0.582 9.295 24371 Z= 0.289 Chirality : 0.043 0.219 2814 Planarity : 0.004 0.061 2985 Dihedral : 5.398 53.814 2884 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.92 % Allowed : 24.22 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.06 (0.18), residues: 2103 helix: 1.29 (0.21), residues: 576 sheet: -0.09 (0.20), residues: 589 loop : -0.59 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 265 TYR 0.045 0.001 TYR E 314 PHE 0.024 0.001 PHE A 240 TRP 0.026 0.001 TRP A 319 HIS 0.002 0.000 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00298 (17849) covalent geometry : angle 0.57492 (24284) SS BOND : bond 0.00093 ( 9) SS BOND : angle 2.04514 ( 18) hydrogen bonds : bond 0.02965 ( 806) hydrogen bonds : angle 4.29888 ( 2592) link_ALPHA1-2 : bond 0.00516 ( 3) link_ALPHA1-2 : angle 1.45345 ( 9) link_ALPHA1-3 : bond 0.01119 ( 2) link_ALPHA1-3 : angle 1.21788 ( 6) link_ALPHA1-6 : bond 0.00288 ( 2) link_ALPHA1-6 : angle 1.78335 ( 6) link_BETA1-4 : bond 0.00327 ( 9) link_BETA1-4 : angle 1.60800 ( 27) link_NAG-ASN : bond 0.00381 ( 7) link_NAG-ASN : angle 1.47389 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6979.82 seconds wall clock time: 119 minutes 19.98 seconds (7159.98 seconds total)