Starting phenix.real_space_refine on Tue Aug 26 21:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694.map" model { file = "/net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imn_60694/08_2025/9imn_60694_neut.cif" } resolution = 2.97 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= 0.001 sd= 0.034 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 14 5.49 5 Mg 70 5.21 5 S 148 5.16 5 C 29270 2.51 5 N 6078 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42392 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2388 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "C" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3444 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Chain: "D" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2686 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "G" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1464 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "H" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "I" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 210 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "V" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 216 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "W" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 156 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "X" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 214 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "a" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2388 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "b" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "c" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3444 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Chain: "d" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2686 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "e" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "f" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "g" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1464 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "h" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "i" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "k" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "l" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "m" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 210 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "t" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "v" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 216 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "w" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 156 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "x" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 214 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 477 Unusual residues: {'BCR': 1, 'CLA': 4, 'FE2': 1, 'LHG': 2, 'LMG': 1, 'PHO': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1235 Unusual residues: {'BCR': 2, 'CLA': 16, 'LHG': 2, 'LMG': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1263 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "D" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 342 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 2, 'LHG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'HEM': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 431 Unusual residues: {'BCR': 1, 'CLA': 4, 'FE2': 1, 'LHG': 2, 'PHO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1191 Unusual residues: {'BCR': 2, 'CLA': 16, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1309 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "d" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 386 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 2, 'LHG': 2, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "e" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "h" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "k" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.17, per 1000 atoms: 0.19 Number of scatterers: 42392 At special positions: 0 Unit cell: (142.04, 190.8, 136.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 148 16.00 P 14 15.00 Mg 70 11.99 O 6808 8.00 N 6078 7.00 C 29270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=57, symmetry=0 Number of additional bonds: simple=57, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8048 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 18 sheets defined 69.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 33 through 54 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 138 removed outlier: 3.940A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.545A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.649A pdb=" N ASP A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.895A pdb=" N ARG A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 removed outlier: 3.736A pdb=" N GLU A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 removed outlier: 4.161A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 14 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.616A pdb=" N MET B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.882A pdb=" N ASP B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.153A pdb=" N ILE B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 234 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.658A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 removed outlier: 3.565A pdb=" N GLY B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 318 through 322 removed outlier: 4.128A pdb=" N GLY B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.093A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.998A pdb=" N LEU B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.989A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 5.306A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 removed outlier: 3.839A pdb=" N LEU C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.874A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.549A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 169 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.805A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.667A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.514A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 314 Processing helix chain 'C' and resid 341 through 347 removed outlier: 3.955A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.526A pdb=" N HIS C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.127A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.482A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.554A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 221 removed outlier: 3.740A pdb=" N GLY D 203 " --> pdb=" O MET D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 257 removed outlier: 3.509A pdb=" N PHE D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 290 removed outlier: 3.979A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.497A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 9 through 16 removed outlier: 3.581A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.782A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 47 removed outlier: 3.557A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.967A pdb=" N TYR E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE E 56 " --> pdb=" O ASN E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 56' Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 41 Proline residue: F 28 - end of helix removed outlier: 4.049A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 3.651A pdb=" N ALA G 138 " --> pdb=" O GLN G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'G' and resid 170 through 178 Processing helix chain 'G' and resid 183 through 216 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.564A pdb=" N ALA G 222 " --> pdb=" O ASP G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 263 removed outlier: 4.144A pdb=" N LYS G 250 " --> pdb=" O THR G 246 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 280 Processing helix chain 'G' and resid 284 through 290 removed outlier: 3.973A pdb=" N ARG G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 299 removed outlier: 3.925A pdb=" N ASN G 299 " --> pdb=" O LYS G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 310 removed outlier: 4.176A pdb=" N GLN G 303 " --> pdb=" O ASN G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 325 Processing helix chain 'H' and resid 24 through 31 Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 removed outlier: 3.739A pdb=" N LEU H 84 " --> pdb=" O TRP H 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 85 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.617A pdb=" N ASN I 26 " --> pdb=" O GLY I 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 26 through 29 Proline residue: K 29 - end of helix No H-bonds generated for 'chain 'K' and resid 26 through 29' Processing helix chain 'K' and resid 30 through 44 removed outlier: 4.098A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.753A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 30 Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 4 through 30 removed outlier: 3.934A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix removed outlier: 3.755A pdb=" N VAL V 23 " --> pdb=" O GLY V 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 97 Processing helix chain 'X' and resid 66 through 95 Processing helix chain 'Z' and resid 2 through 29 removed outlier: 3.657A pdb=" N VAL Z 21 " --> pdb=" O PHE Z 17 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 61 Processing helix chain 'a' and resid 12 through 22 Processing helix chain 'a' and resid 33 through 54 Proline residue: a 39 - end of helix Processing helix chain 'a' and resid 95 through 99 Processing helix chain 'a' and resid 101 through 108 Processing helix chain 'a' and resid 109 through 138 removed outlier: 4.122A pdb=" N GLN a 113 " --> pdb=" O GLY a 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP a 131 " --> pdb=" O MET a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 159 removed outlier: 3.510A pdb=" N ALA a 146 " --> pdb=" O TRP a 142 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA a 149 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Proline residue: a 150 - end of helix Processing helix chain 'a' and resid 159 through 166 Processing helix chain 'a' and resid 167 through 171 removed outlier: 3.711A pdb=" N ASP a 170 " --> pdb=" O SER a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 190 removed outlier: 3.515A pdb=" N PHE a 180 " --> pdb=" O ILE a 176 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 223 Processing helix chain 'a' and resid 248 through 259 removed outlier: 3.569A pdb=" N ILE a 259 " --> pdb=" O PHE a 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 294 removed outlier: 3.584A pdb=" N PHE a 273 " --> pdb=" O ARG a 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA a 276 " --> pdb=" O HIS a 272 " (cutoff:3.500A) Proline residue: a 279 - end of helix Processing helix chain 'a' and resid 308 through 312 removed outlier: 3.824A pdb=" N ARG a 312 " --> pdb=" O SER a 309 " (cutoff:3.500A) Processing helix chain 'a' and resid 316 through 333 removed outlier: 3.537A pdb=" N MET a 331 " --> pdb=" O GLY a 327 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS a 332 " --> pdb=" O MET a 328 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU a 333 " --> pdb=" O GLU a 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 13 removed outlier: 4.026A pdb=" N VAL b 11 " --> pdb=" O VAL b 8 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL b 12 " --> pdb=" O HIS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 43 removed outlier: 3.572A pdb=" N SER b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 59 removed outlier: 3.911A pdb=" N GLY b 59 " --> pdb=" O TRP b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 69 removed outlier: 3.771A pdb=" N LEU b 69 " --> pdb=" O PHE b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 117 Processing helix chain 'b' and resid 120 through 124 Processing helix chain 'b' and resid 134 through 157 removed outlier: 3.555A pdb=" N GLY b 140 " --> pdb=" O PRO b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 191 removed outlier: 3.833A pdb=" N ASP b 191 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 194 through 219 removed outlier: 4.310A pdb=" N ILE b 198 " --> pdb=" O ASN b 194 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA b 199 " --> pdb=" O PRO b 195 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 229 Processing helix chain 'b' and resid 234 through 259 Processing helix chain 'b' and resid 264 through 269 Processing helix chain 'b' and resid 271 through 277 removed outlier: 4.028A pdb=" N TRP b 275 " --> pdb=" O THR b 271 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 294 Processing helix chain 'b' and resid 297 through 304 removed outlier: 3.559A pdb=" N TRP b 302 " --> pdb=" O LEU b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 306 through 313 removed outlier: 3.564A pdb=" N ASP b 313 " --> pdb=" O LEU b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 322 removed outlier: 4.168A pdb=" N GLY b 322 " --> pdb=" O PRO b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 330 through 335 removed outlier: 3.992A pdb=" N ASP b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 391 through 396 Processing helix chain 'b' and resid 413 through 425 removed outlier: 3.547A pdb=" N LYS b 423 " --> pdb=" O LYS b 419 " (cutoff:3.500A) Processing helix chain 'b' and resid 446 through 475 Processing helix chain 'b' and resid 475 through 481 Processing helix chain 'c' and resid 15 through 20 Processing helix chain 'c' and resid 22 through 31 removed outlier: 5.273A pdb=" N ASN c 27 " --> pdb=" O TRP c 24 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE c 31 " --> pdb=" O ALA c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 61 removed outlier: 3.664A pdb=" N LEU c 37 " --> pdb=" O LEU c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 72 removed outlier: 4.099A pdb=" N GLN c 72 " --> pdb=" O MET c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 84 removed outlier: 3.533A pdb=" N LEU c 83 " --> pdb=" O HIS c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 92 removed outlier: 3.874A pdb=" N GLU c 92 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 123 removed outlier: 3.619A pdb=" N ALA c 111 " --> pdb=" O LEU c 107 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL c 112 " --> pdb=" O ILE c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 142 through 169 removed outlier: 3.549A pdb=" N ASN c 147 " --> pdb=" O ASN c 143 " (cutoff:3.500A) Processing helix chain 'c' and resid 193 through 203 removed outlier: 3.672A pdb=" N TYR c 200 " --> pdb=" O VAL c 196 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU c 201 " --> pdb=" O ILE c 197 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL c 202 " --> pdb=" O PHE c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 removed outlier: 3.674A pdb=" N SER c 214 " --> pdb=" O TRP c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 217 through 241 removed outlier: 3.641A pdb=" N ILE c 221 " --> pdb=" O ASN c 217 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP c 227 " --> pdb=" O GLY c 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 245 through 250 Processing helix chain 'c' and resid 255 through 281 removed outlier: 3.687A pdb=" N PHE c 272 " --> pdb=" O GLY c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 286 through 291 Processing helix chain 'c' and resid 293 through 314 removed outlier: 3.668A pdb=" N SER c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 341 through 347 removed outlier: 3.936A pdb=" N ARG c 345 " --> pdb=" O GLU c 342 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP c 347 " --> pdb=" O MET c 344 " (cutoff:3.500A) Processing helix chain 'c' and resid 354 through 356 No H-bonds generated for 'chain 'c' and resid 354 through 356' Processing helix chain 'c' and resid 364 through 371 removed outlier: 3.783A pdb=" N ASN c 370 " --> pdb=" O ASN c 366 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 386 removed outlier: 3.675A pdb=" N THR c 385 " --> pdb=" O ALA c 381 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS c 386 " --> pdb=" O GLU c 382 " (cutoff:3.500A) Processing helix chain 'c' and resid 409 through 442 Processing helix chain 'c' and resid 453 through 457 Processing helix chain 'd' and resid 13 through 23 Processing helix chain 'd' and resid 33 through 54 Proline residue: d 39 - end of helix Processing helix chain 'd' and resid 82 through 86 Processing helix chain 'd' and resid 100 through 107 Processing helix chain 'd' and resid 108 through 137 removed outlier: 4.315A pdb=" N ALA d 112 " --> pdb=" O GLY d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 146 Processing helix chain 'd' and resid 146 through 158 removed outlier: 3.533A pdb=" N ILE d 150 " --> pdb=" O PHE d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 164 Processing helix chain 'd' and resid 166 through 170 removed outlier: 3.633A pdb=" N PHE d 169 " --> pdb=" O GLY d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 190 removed outlier: 3.555A pdb=" N GLN d 186 " --> pdb=" O ILE d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 193 No H-bonds generated for 'chain 'd' and resid 191 through 193' Processing helix chain 'd' and resid 194 through 221 removed outlier: 3.843A pdb=" N GLY d 203 " --> pdb=" O MET d 199 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 257 Processing helix chain 'd' and resid 263 through 291 removed outlier: 4.070A pdb=" N LEU d 272 " --> pdb=" O HIS d 268 " (cutoff:3.500A) Proline residue: d 275 - end of helix removed outlier: 3.833A pdb=" N LEU d 291 " --> pdb=" O VAL d 287 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 Processing helix chain 'd' and resid 313 through 334 removed outlier: 4.244A pdb=" N ALA d 331 " --> pdb=" O ALA d 327 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN d 332 " --> pdb=" O TRP d 328 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 338 Processing helix chain 'd' and resid 348 through 352 Processing helix chain 'e' and resid 9 through 16 removed outlier: 3.580A pdb=" N ILE e 13 " --> pdb=" O PRO e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 40 removed outlier: 3.709A pdb=" N TRP e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Proline residue: e 28 - end of helix removed outlier: 3.567A pdb=" N VAL e 38 " --> pdb=" O GLY e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 47 removed outlier: 3.719A pdb=" N ASP e 45 " --> pdb=" O GLY e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 56 removed outlier: 3.880A pdb=" N TYR e 55 " --> pdb=" O PRO e 52 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE e 56 " --> pdb=" O ASN e 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 52 through 56' Processing helix chain 'e' and resid 71 through 80 removed outlier: 3.570A pdb=" N LYS e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 39 Proline residue: f 28 - end of helix Processing helix chain 'g' and resid 132 through 142 Processing helix chain 'g' and resid 167 through 169 No H-bonds generated for 'chain 'g' and resid 167 through 169' Processing helix chain 'g' and resid 170 through 178 Processing helix chain 'g' and resid 183 through 216 Processing helix chain 'g' and resid 218 through 232 Processing helix chain 'g' and resid 246 through 263 removed outlier: 3.942A pdb=" N LYS g 250 " --> pdb=" O THR g 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL g 251 " --> pdb=" O PRO g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 266 through 280 removed outlier: 3.762A pdb=" N LYS g 271 " --> pdb=" O GLU g 267 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 292 No H-bonds generated for 'chain 'g' and resid 290 through 292' Processing helix chain 'g' and resid 293 through 299 removed outlier: 4.067A pdb=" N ASN g 299 " --> pdb=" O LYS g 295 " (cutoff:3.500A) Processing helix chain 'g' and resid 299 through 310 removed outlier: 4.301A pdb=" N GLN g 303 " --> pdb=" O ASN g 299 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA g 304 " --> pdb=" O PRO g 300 " (cutoff:3.500A) Processing helix chain 'g' and resid 315 through 325 Processing helix chain 'h' and resid 24 through 31 Processing helix chain 'h' and resid 46 through 69 Processing helix chain 'h' and resid 80 through 85 removed outlier: 3.590A pdb=" N LEU h 84 " --> pdb=" O TRP h 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 26 removed outlier: 3.680A pdb=" N ASN i 26 " --> pdb=" O GLY i 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 17 Proline residue: k 17 - end of helix Processing helix chain 'k' and resid 18 through 25 removed outlier: 3.848A pdb=" N VAL k 24 " --> pdb=" O PRO k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 44 removed outlier: 3.719A pdb=" N PHE k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE k 33 " --> pdb=" O PRO k 29 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE k 37 " --> pdb=" O ILE k 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 38 removed outlier: 4.636A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 30 Proline residue: m 18 - end of helix Processing helix chain 't' and resid 2 through 23 Processing helix chain 'v' and resid 4 through 30 removed outlier: 4.205A pdb=" N GLY v 19 " --> pdb=" O VAL v 15 " (cutoff:3.500A) Proline residue: v 20 - end of helix Processing helix chain 'w' and resid 80 through 97 Processing helix chain 'x' and resid 66 through 95 Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.548A pdb=" N VAL z 21 " --> pdb=" O PHE z 17 " (cutoff:3.500A) Proline residue: z 24 - end of helix Processing helix chain 'z' and resid 36 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA2, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 3.940A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.503A pdb=" N VAL B 377 " --> pdb=" O ASP B 372 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 372 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'a' and resid 297 through 298 Processing sheet with id=AB2, first strand: chain 'b' and resid 166 through 169 Processing sheet with id=AB3, first strand: chain 'b' and resid 336 through 340 removed outlier: 3.922A pdb=" N GLU b 431 " --> pdb=" O VAL b 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 377 through 380 removed outlier: 6.965A pdb=" N LEU b 370 " --> pdb=" O ARG b 378 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE b 346 " --> pdb=" O LEU b 354 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL b 356 " --> pdb=" O ALA b 344 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N ALA b 344 " --> pdb=" O VAL b 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 173 through 175 Processing sheet with id=AB6, first strand: chain 'c' and resid 329 through 331 Processing sheet with id=AB7, first strand: chain 'c' and resid 358 through 359 Processing sheet with id=AB8, first strand: chain 'd' and resid 3 through 5 removed outlier: 3.708A pdb=" N TYR d 8 " --> pdb=" O ILE d 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 77 through 78 2149 hydrogen bonds defined for protein. 6183 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: 7.67 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 16635 1.39 - 1.56: 26846 1.56 - 1.74: 37 1.74 - 1.92: 254 1.92 - 2.10: 288 Bond restraints: 44060 Sorted by residual: bond pdb=" C6 SQD C 501 " pdb=" S SQD C 501 " ideal model delta sigma weight residual 1.840 1.663 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C6 SQD c 501 " pdb=" S SQD c 501 " ideal model delta sigma weight residual 1.840 1.664 0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C7 LHG A 410 " pdb=" O7 LHG A 410 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C7 LHG a 409 " pdb=" O7 LHG a 409 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C7 LHG b 520 " pdb=" O7 LHG b 520 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 44055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 59539 3.60 - 7.19: 910 7.19 - 10.79: 107 10.79 - 14.39: 69 14.39 - 17.99: 65 Bond angle restraints: 60690 Sorted by residual: angle pdb=" NB CLA B 504 " pdb="MG CLA B 504 " pdb=" ND CLA B 504 " ideal model delta sigma weight residual 176.90 158.91 17.99 3.00e+00 1.11e-01 3.59e+01 angle pdb=" NB CLA C 504 " pdb="MG CLA C 504 " pdb=" ND CLA C 504 " ideal model delta sigma weight residual 176.90 159.26 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" NB CLA b 504 " pdb="MG CLA b 504 " pdb=" ND CLA b 504 " ideal model delta sigma weight residual 176.90 159.42 17.48 3.00e+00 1.11e-01 3.39e+01 angle pdb=" NB CLA c 505 " pdb="MG CLA c 505 " pdb=" ND CLA c 505 " ideal model delta sigma weight residual 176.90 159.54 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" NB CLA C 513 " pdb="MG CLA C 513 " pdb=" ND CLA C 513 " ideal model delta sigma weight residual 176.90 159.69 17.21 3.00e+00 1.11e-01 3.29e+01 ... (remaining 60685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.25: 22411 29.25 - 58.50: 1239 58.50 - 87.75: 139 87.75 - 117.00: 53 117.00 - 146.25: 22 Dihedral angle restraints: 23864 sinusoidal: 11258 harmonic: 12606 Sorted by residual: dihedral pdb=" C3A DGD c 519 " pdb=" C1A DGD c 519 " pdb=" C2A DGD c 519 " pdb=" O1A DGD c 519 " ideal model delta sinusoidal sigma weight residual -24.22 122.03 -146.25 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3A DGD C 518 " pdb=" C1A DGD C 518 " pdb=" C2A DGD C 518 " pdb=" O1A DGD C 518 " ideal model delta sinusoidal sigma weight residual -24.22 120.78 -145.00 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C27 BCR k 101 " pdb=" C28 BCR k 101 " pdb=" C29 BCR k 101 " pdb=" C30 BCR k 101 " ideal model delta sinusoidal sigma weight residual -60.81 64.29 -125.10 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 23861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4640 0.046 - 0.091: 975 0.091 - 0.137: 234 0.137 - 0.183: 29 0.183 - 0.228: 20 Chirality restraints: 5898 Sorted by residual: chirality pdb=" C2 LHG A 409 " pdb=" C1 LHG A 409 " pdb=" C3 LHG A 409 " pdb=" O2 LHG A 409 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C2 LHG a 408 " pdb=" C1 LHG a 408 " pdb=" C3 LHG a 408 " pdb=" O2 LHG a 408 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE W 95 " pdb=" N ILE W 95 " pdb=" C ILE W 95 " pdb=" CB ILE W 95 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 5895 not shown) Planarity restraints: 7514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO a 405 " -0.115 2.00e-02 2.50e+03 1.25e-01 1.26e+03 pdb=" ND PHO a 405 " -0.137 2.00e-02 2.50e+03 pdb=" C1A PHO a 405 " -0.012 2.00e-02 2.50e+03 pdb=" C1B PHO a 405 " -0.044 2.00e-02 2.50e+03 pdb=" C1C PHO a 405 " -0.027 2.00e-02 2.50e+03 pdb=" C1D PHO a 405 " -0.013 2.00e-02 2.50e+03 pdb=" C2A PHO a 405 " 0.071 2.00e-02 2.50e+03 pdb=" C2B PHO a 405 " 0.130 2.00e-02 2.50e+03 pdb=" C2C PHO a 405 " -0.071 2.00e-02 2.50e+03 pdb=" C2D PHO a 405 " 0.043 2.00e-02 2.50e+03 pdb=" C3A PHO a 405 " -0.316 2.00e-02 2.50e+03 pdb=" C3B PHO a 405 " 0.151 2.00e-02 2.50e+03 pdb=" C3C PHO a 405 " -0.046 2.00e-02 2.50e+03 pdb=" C3D PHO a 405 " 0.051 2.00e-02 2.50e+03 pdb=" C4A PHO a 405 " -0.200 2.00e-02 2.50e+03 pdb=" C4B PHO a 405 " -0.013 2.00e-02 2.50e+03 pdb=" C4C PHO a 405 " 0.018 2.00e-02 2.50e+03 pdb=" C4D PHO a 405 " -0.017 2.00e-02 2.50e+03 pdb=" CAB PHO a 405 " 0.281 2.00e-02 2.50e+03 pdb=" CAC PHO a 405 " -0.074 2.00e-02 2.50e+03 pdb=" CAD PHO a 405 " 0.096 2.00e-02 2.50e+03 pdb=" CBD PHO a 405 " 0.168 2.00e-02 2.50e+03 pdb=" CHA PHO a 405 " 0.043 2.00e-02 2.50e+03 pdb=" CHB PHO a 405 " -0.133 2.00e-02 2.50e+03 pdb=" CHC PHO a 405 " -0.050 2.00e-02 2.50e+03 pdb=" CHD PHO a 405 " 0.065 2.00e-02 2.50e+03 pdb=" CMB PHO a 405 " 0.238 2.00e-02 2.50e+03 pdb=" CMC PHO a 405 " -0.135 2.00e-02 2.50e+03 pdb=" CMD PHO a 405 " 0.097 2.00e-02 2.50e+03 pdb=" NA PHO a 405 " -0.173 2.00e-02 2.50e+03 pdb=" NC PHO a 405 " 0.030 2.00e-02 2.50e+03 pdb=" OBD PHO a 405 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 405 " 0.113 2.00e-02 2.50e+03 1.24e-01 1.23e+03 pdb=" ND PHO A 405 " 0.108 2.00e-02 2.50e+03 pdb=" C1A PHO A 405 " 0.011 2.00e-02 2.50e+03 pdb=" C1B PHO A 405 " 0.044 2.00e-02 2.50e+03 pdb=" C1C PHO A 405 " 0.024 2.00e-02 2.50e+03 pdb=" C1D PHO A 405 " 0.007 2.00e-02 2.50e+03 pdb=" C2A PHO A 405 " -0.082 2.00e-02 2.50e+03 pdb=" C2B PHO A 405 " -0.128 2.00e-02 2.50e+03 pdb=" C2C PHO A 405 " 0.069 2.00e-02 2.50e+03 pdb=" C2D PHO A 405 " -0.041 2.00e-02 2.50e+03 pdb=" C3A PHO A 405 " 0.320 2.00e-02 2.50e+03 pdb=" C3B PHO A 405 " -0.150 2.00e-02 2.50e+03 pdb=" C3C PHO A 405 " 0.049 2.00e-02 2.50e+03 pdb=" C3D PHO A 405 " -0.053 2.00e-02 2.50e+03 pdb=" C4A PHO A 405 " 0.204 2.00e-02 2.50e+03 pdb=" C4B PHO A 405 " 0.011 2.00e-02 2.50e+03 pdb=" C4C PHO A 405 " -0.013 2.00e-02 2.50e+03 pdb=" C4D PHO A 405 " 0.006 2.00e-02 2.50e+03 pdb=" CAB PHO A 405 " -0.280 2.00e-02 2.50e+03 pdb=" CAC PHO A 405 " 0.079 2.00e-02 2.50e+03 pdb=" CAD PHO A 405 " -0.095 2.00e-02 2.50e+03 pdb=" CBD PHO A 405 " -0.146 2.00e-02 2.50e+03 pdb=" CHA PHO A 405 " -0.041 2.00e-02 2.50e+03 pdb=" CHB PHO A 405 " 0.134 2.00e-02 2.50e+03 pdb=" CHC PHO A 405 " 0.046 2.00e-02 2.50e+03 pdb=" CHD PHO A 405 " -0.054 2.00e-02 2.50e+03 pdb=" CMB PHO A 405 " -0.235 2.00e-02 2.50e+03 pdb=" CMC PHO A 405 " 0.129 2.00e-02 2.50e+03 pdb=" CMD PHO A 405 " -0.086 2.00e-02 2.50e+03 pdb=" NA PHO A 405 " 0.180 2.00e-02 2.50e+03 pdb=" NC PHO A 405 " -0.028 2.00e-02 2.50e+03 pdb=" OBD PHO A 405 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 401 " 0.012 2.00e-02 2.50e+03 7.31e-02 4.28e+02 pdb=" ND PHO D 401 " -0.087 2.00e-02 2.50e+03 pdb=" C1A PHO D 401 " 0.022 2.00e-02 2.50e+03 pdb=" C1B PHO D 401 " 0.003 2.00e-02 2.50e+03 pdb=" C1C PHO D 401 " 0.032 2.00e-02 2.50e+03 pdb=" C1D PHO D 401 " 0.017 2.00e-02 2.50e+03 pdb=" C2A PHO D 401 " 0.178 2.00e-02 2.50e+03 pdb=" C2B PHO D 401 " 0.035 2.00e-02 2.50e+03 pdb=" C2C PHO D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C2D PHO D 401 " 0.034 2.00e-02 2.50e+03 pdb=" C3A PHO D 401 " -0.161 2.00e-02 2.50e+03 pdb=" C3B PHO D 401 " 0.048 2.00e-02 2.50e+03 pdb=" C3C PHO D 401 " -0.026 2.00e-02 2.50e+03 pdb=" C3D PHO D 401 " 0.003 2.00e-02 2.50e+03 pdb=" C4A PHO D 401 " -0.110 2.00e-02 2.50e+03 pdb=" C4B PHO D 401 " 0.030 2.00e-02 2.50e+03 pdb=" C4C PHO D 401 " 0.055 2.00e-02 2.50e+03 pdb=" C4D PHO D 401 " -0.019 2.00e-02 2.50e+03 pdb=" CAB PHO D 401 " 0.050 2.00e-02 2.50e+03 pdb=" CAC PHO D 401 " -0.086 2.00e-02 2.50e+03 pdb=" CAD PHO D 401 " -0.012 2.00e-02 2.50e+03 pdb=" CBD PHO D 401 " 0.097 2.00e-02 2.50e+03 pdb=" CHA PHO D 401 " 0.031 2.00e-02 2.50e+03 pdb=" CHB PHO D 401 " -0.040 2.00e-02 2.50e+03 pdb=" CHC PHO D 401 " 0.007 2.00e-02 2.50e+03 pdb=" CHD PHO D 401 " 0.085 2.00e-02 2.50e+03 pdb=" CMB PHO D 401 " 0.024 2.00e-02 2.50e+03 pdb=" CMC PHO D 401 " -0.108 2.00e-02 2.50e+03 pdb=" CMD PHO D 401 " 0.060 2.00e-02 2.50e+03 pdb=" NA PHO D 401 " -0.138 2.00e-02 2.50e+03 pdb=" NC PHO D 401 " 0.089 2.00e-02 2.50e+03 pdb=" OBD PHO D 401 " -0.094 2.00e-02 2.50e+03 ... (remaining 7511 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 275 2.54 - 3.13: 32719 3.13 - 3.72: 63686 3.72 - 4.31: 93880 4.31 - 4.90: 159966 Nonbonded interactions: 350526 Sorted by model distance: nonbonded pdb=" OE2 GLU C 452 " pdb=" OG1 THR D 248 " model vdw 1.952 3.040 nonbonded pdb=" OE2 GLU B 350 " pdb=" NH1 ARG B 352 " model vdw 2.090 3.120 nonbonded pdb=" NE2 HIS f 23 " pdb="FE HEM e 101 " model vdw 2.113 3.080 nonbonded pdb=" NE2 HIS F 23 " pdb="FE HEM F 102 " model vdw 2.120 3.080 nonbonded pdb=" OG1 THR a 286 " pdb=" O1D CLA a 402 " model vdw 2.135 3.040 ... (remaining 350521 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' and (resid 10 through 407 or resid 409)) selection = (chain 'a' and (resid 10 through 407 or (resid 409 and (name C1 or name C10 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C4 or name C5 or name C6 or na \ me C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name O3 or name \ O4 or name O5 or name O6 or name O7 or name O8 or name O9 or name P )))) } ncs_group { reference = (chain 'B' and resid 2 through 520) selection = (chain 'b' and (resid 2 through 519 or (resid 520 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name \ O3 or name O4 or name O5 or name O6 or name O7 or name O8 or name O9 or name P \ )))) } ncs_group { reference = (chain 'C' and (resid 12 through 501 or resid 503 through 514 or resid 516 throu \ gh 517 or (resid 519 through 520 and (name C1A or name C1B or name C1D or name C \ 1E or name C1G or name C2A or name C2B or name C2D or name C2E or name C2G or na \ me C3A or name C3B or name C3D or name C3E or name C3G or name C4B or name C4D o \ r name C4E or name C5B or name C5D or name C5E or name C6B or name C6D or name C \ 6E or name C7B or name C8B or name C9B or name CAB or name CBB or name CCB or na \ me CDB or name CEB or name CFB or name CGB or name O1A or name O1B or name O1G o \ r name O2D or name O2E or name O2G or name O3D or name O3E or name O3G or name O \ 4D or name O4E or name O5D or name O5E or name O6D or name O6E)))) selection = (chain 'c' and (resid 12 through 501 or resid 503 through 514 or resid 516 throu \ gh 517 or (resid 519 through 520 and (name C1A or name C1B or name C1D or name C \ 1E or name C1G or name C2A or name C2B or name C2D or name C2E or name C2G or na \ me C3A or name C3B or name C3D or name C3E or name C3G or name C4B or name C4D o \ r name C4E or name C5B or name C5D or name C5E or name C6B or name C6D or name C \ 6E or name C7B or name C8B or name C9B or name CAB or name CBB or name CCB or na \ me CDB or name CEB or name CFB or name CGB or name O1A or name O1B or name O1G o \ r name O2D or name O2E or name O2G or name O3D or name O3E or name O3G or name O \ 4D or name O4E or name O5D or name O5E or name O6D or name O6E)))) } ncs_group { reference = (chain 'D' and (resid 2 through 406 or (resid 407 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name \ O3 or name O4 or name O5 or name O6 or name O7 or name O8 or name O9 or name P \ )))) selection = (chain 'd' and resid 2 through 407) } ncs_group { reference = chain 'E' selection = (chain 'e' and resid 8 through 82) } ncs_group { reference = (chain 'F' and resid 14 through 101) selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'K' selection = (chain 'k' and resid 10 through 46) } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = (chain 'V' and resid 3 through 33) selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.730 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 0.177 44117 Z= 0.468 Angle : 1.165 17.985 60690 Z= 0.438 Chirality : 0.042 0.228 5898 Planarity : 0.014 0.146 7514 Dihedral : 18.165 146.251 15816 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.13), residues: 4374 helix: 1.88 (0.10), residues: 2758 sheet: 0.42 (0.75), residues: 50 loop : -0.45 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 338 TYR 0.016 0.001 TYR L 35 PHE 0.035 0.001 PHE B 246 TRP 0.021 0.001 TRP W 93 HIS 0.006 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00731 (44060) covalent geometry : angle 1.16494 (60690) hydrogen bonds : bond 0.19862 ( 2149) hydrogen bonds : angle 6.50723 ( 6183) Misc. bond : bond 0.08717 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 1.300 Fit side-chains REVERT: A 25 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8822 (mt-10) REVERT: B 121 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7601 (mp0) REVERT: C 373 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8352 (mm110) REVERT: D 9 GLN cc_start: 0.7740 (tt0) cc_final: 0.7482 (tt0) REVERT: E 25 ILE cc_start: 0.8886 (tp) cc_final: 0.8542 (tt) REVERT: G 132 PHE cc_start: 0.8387 (t80) cc_final: 0.8140 (t80) REVERT: H 34 ASN cc_start: 0.9367 (t0) cc_final: 0.9042 (t0) REVERT: L 1 MET cc_start: 0.5018 (ppp) cc_final: 0.4693 (ppp) REVERT: L 12 GLU cc_start: 0.8189 (pm20) cc_final: 0.7900 (pm20) REVERT: Z 36 ASN cc_start: 0.7892 (m-40) cc_final: 0.7574 (m110) REVERT: b 440 ASP cc_start: 0.8843 (m-30) cc_final: 0.8602 (m-30) REVERT: d 45 LEU cc_start: 0.9111 (mm) cc_final: 0.8890 (mm) REVERT: e 15 THR cc_start: 0.7625 (m) cc_final: 0.7308 (p) REVERT: e 25 ILE cc_start: 0.8977 (tp) cc_final: 0.8743 (pp) REVERT: e 74 GLU cc_start: 0.8852 (tp30) cc_final: 0.8642 (tp30) REVERT: g 262 MET cc_start: 0.7149 (mpp) cc_final: 0.6809 (mpp) REVERT: l 3 ARG cc_start: 0.6514 (mtp-110) cc_final: 0.5889 (mtp180) REVERT: l 12 GLU cc_start: 0.8930 (pp20) cc_final: 0.8378 (pp20) REVERT: z 33 TRP cc_start: 0.6668 (t60) cc_final: 0.6232 (t-100) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.5232 time to fit residues: 339.1142 Evaluate side-chains 451 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 100 HIS C 299 GLN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN Z 58 ASN a 191 ASN b 14 ASN b 349 GLN c 56 ASN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084467 restraints weight = 65992.416| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.91 r_work: 0.2888 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 44117 Z= 0.162 Angle : 0.640 12.847 60690 Z= 0.294 Chirality : 0.042 0.278 5898 Planarity : 0.005 0.053 7514 Dihedral : 16.629 121.461 8248 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.16 % Allowed : 7.45 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.13), residues: 4374 helix: 2.15 (0.10), residues: 2774 sheet: -0.03 (0.73), residues: 50 loop : -0.38 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 224 TYR 0.020 0.001 TYR L 35 PHE 0.028 0.001 PHE B 246 TRP 0.019 0.001 TRP c 165 HIS 0.007 0.001 HIS a 272 Details of bonding type rmsd covalent geometry : bond 0.00365 (44060) covalent geometry : angle 0.63982 (60690) hydrogen bonds : bond 0.05660 ( 2149) hydrogen bonds : angle 4.58343 ( 6183) Misc. bond : bond 0.05550 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 497 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9150 (mt-10) REVERT: B 63 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8659 (mp) REVERT: B 362 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: D 9 GLN cc_start: 0.7592 (tt0) cc_final: 0.7337 (tt0) REVERT: D 281 MET cc_start: 0.9139 (mmp) cc_final: 0.8904 (mmp) REVERT: E 25 ILE cc_start: 0.8895 (tp) cc_final: 0.8509 (tt) REVERT: G 132 PHE cc_start: 0.8277 (t80) cc_final: 0.8000 (t80) REVERT: H 34 ASN cc_start: 0.9374 (t0) cc_final: 0.9069 (t0) REVERT: L 1 MET cc_start: 0.4879 (ppp) cc_final: 0.4451 (ppp) REVERT: L 12 GLU cc_start: 0.8351 (pm20) cc_final: 0.7753 (pm20) REVERT: Z 60 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: a 70 SER cc_start: 0.9038 (m) cc_final: 0.8788 (p) REVERT: e 25 ILE cc_start: 0.8868 (tp) cc_final: 0.8494 (tt) REVERT: e 26 THR cc_start: 0.8724 (t) cc_final: 0.8449 (t) REVERT: e 74 GLU cc_start: 0.8943 (tp30) cc_final: 0.8591 (tp30) REVERT: g 286 GLN cc_start: 0.7744 (mp10) cc_final: 0.7430 (mp10) REVERT: g 306 LEU cc_start: 0.8165 (tp) cc_final: 0.7933 (tm) REVERT: l 3 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.6007 (mtp180) REVERT: l 12 GLU cc_start: 0.8935 (pp20) cc_final: 0.8238 (pp20) REVERT: t 25 ASP cc_start: 0.8235 (t0) cc_final: 0.8031 (t0) REVERT: t 29 MET cc_start: 0.5165 (pmm) cc_final: 0.4889 (pmm) REVERT: v 4 GLU cc_start: 0.8165 (pm20) cc_final: 0.7341 (mm-30) REVERT: z 33 TRP cc_start: 0.6567 (t60) cc_final: 0.6216 (t-100) outliers start: 42 outliers final: 17 residues processed: 513 average time/residue: 0.5280 time to fit residues: 340.7870 Evaluate side-chains 474 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 454 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain i residue 3 THR Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain m residue 28 LYS Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain z residue 41 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 122 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 398 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN D 332 GLN G 195 GLN b 14 ASN f 40 GLN g 195 GLN z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088453 restraints weight = 67077.453| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.13 r_work: 0.2907 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 44117 Z= 0.166 Angle : 0.597 12.636 60690 Z= 0.275 Chirality : 0.042 0.283 5898 Planarity : 0.005 0.054 7514 Dihedral : 15.411 120.475 8248 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.52 % Allowed : 11.19 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.13), residues: 4374 helix: 2.20 (0.10), residues: 2764 sheet: -0.40 (0.68), residues: 54 loop : -0.33 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 338 TYR 0.022 0.001 TYR L 35 PHE 0.028 0.001 PHE a 260 TRP 0.022 0.001 TRP c 165 HIS 0.007 0.001 HIS a 195 Details of bonding type rmsd covalent geometry : bond 0.00385 (44060) covalent geometry : angle 0.59669 (60690) hydrogen bonds : bond 0.05017 ( 2149) hydrogen bonds : angle 4.30017 ( 6183) Misc. bond : bond 0.03755 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 476 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9120 (mt-10) REVERT: B 63 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 121 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: B 362 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: D 9 GLN cc_start: 0.7562 (tt0) cc_final: 0.7346 (tt0) REVERT: D 265 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8594 (mtp85) REVERT: D 281 MET cc_start: 0.9191 (mmp) cc_final: 0.8980 (mmp) REVERT: E 25 ILE cc_start: 0.8880 (tp) cc_final: 0.8505 (tt) REVERT: F 18 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7477 (tmm-80) REVERT: G 132 PHE cc_start: 0.8223 (t80) cc_final: 0.7972 (t80) REVERT: G 281 PHE cc_start: 0.8103 (t80) cc_final: 0.7893 (t80) REVERT: L 1 MET cc_start: 0.5266 (ppp) cc_final: 0.4926 (ppp) REVERT: L 12 GLU cc_start: 0.8362 (pm20) cc_final: 0.7760 (pm20) REVERT: L 35 TYR cc_start: 0.9286 (m-80) cc_final: 0.9083 (m-80) REVERT: T 29 MET cc_start: 0.5459 (ppp) cc_final: 0.5234 (pmm) REVERT: Z 60 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: b 362 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: c 277 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: e 25 ILE cc_start: 0.8811 (tp) cc_final: 0.8465 (tt) REVERT: e 26 THR cc_start: 0.8707 (t) cc_final: 0.8414 (t) REVERT: e 74 GLU cc_start: 0.9001 (tp30) cc_final: 0.8671 (tp30) REVERT: g 132 PHE cc_start: 0.7498 (t80) cc_final: 0.7292 (t80) REVERT: g 263 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7968 (tt) REVERT: l 1 MET cc_start: 0.4696 (tmt) cc_final: 0.4312 (tmt) REVERT: l 12 GLU cc_start: 0.8951 (pp20) cc_final: 0.8232 (pp20) REVERT: t 29 MET cc_start: 0.5167 (pmm) cc_final: 0.4904 (pmm) REVERT: z 1 MET cc_start: 0.8015 (ttt) cc_final: 0.7342 (tmm) REVERT: z 33 TRP cc_start: 0.6736 (t60) cc_final: 0.6486 (t-100) REVERT: z 60 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8021 (m-10) outliers start: 55 outliers final: 23 residues processed: 490 average time/residue: 0.5364 time to fit residues: 331.1687 Evaluate side-chains 479 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 448 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain Z residue 41 PHE Chi-restraints excluded: chain Z residue 52 PHE Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain g residue 246 THR Chi-restraints excluded: chain g residue 263 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain m residue 28 LYS Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain z residue 41 PHE Chi-restraints excluded: chain z residue 60 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 414 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN E 61 GLN E 71 ASN G 195 GLN Z 58 ASN b 14 ASN g 195 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087901 restraints weight = 66993.867| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.10 r_work: 0.2898 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 44117 Z= 0.174 Angle : 0.590 15.215 60690 Z= 0.272 Chirality : 0.042 0.270 5898 Planarity : 0.005 0.055 7514 Dihedral : 15.203 120.095 8248 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.30 % Allowed : 12.47 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.13), residues: 4374 helix: 2.16 (0.10), residues: 2774 sheet: -0.49 (0.69), residues: 54 loop : -0.33 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 338 TYR 0.025 0.001 TYR l 35 PHE 0.022 0.001 PHE B 246 TRP 0.024 0.001 TRP c 165 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00408 (44060) covalent geometry : angle 0.59045 (60690) hydrogen bonds : bond 0.04824 ( 2149) hydrogen bonds : angle 4.20096 ( 6183) Misc. bond : bond 0.03854 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 470 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9132 (mt-10) REVERT: B 63 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 121 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 338 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8790 (m) REVERT: B 362 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: D 281 MET cc_start: 0.9203 (mmp) cc_final: 0.8995 (mmp) REVERT: E 25 ILE cc_start: 0.8938 (tp) cc_final: 0.8733 (tp) REVERT: F 18 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7651 (tmm-80) REVERT: F 39 MET cc_start: 0.9089 (mtm) cc_final: 0.8606 (mtp) REVERT: G 132 PHE cc_start: 0.8174 (t80) cc_final: 0.7924 (t80) REVERT: G 286 GLN cc_start: 0.7766 (pm20) cc_final: 0.7524 (pm20) REVERT: L 1 MET cc_start: 0.5158 (ppp) cc_final: 0.4810 (ppp) REVERT: L 12 GLU cc_start: 0.8339 (pm20) cc_final: 0.7536 (pm20) REVERT: W 96 TRP cc_start: 0.7277 (t-100) cc_final: 0.6916 (t60) REVERT: Z 60 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: a 13 LEU cc_start: 0.8137 (pt) cc_final: 0.7864 (mm) REVERT: b 177 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8074 (pmt170) REVERT: b 338 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8783 (m) REVERT: b 362 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: c 277 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8573 (tpp) REVERT: e 15 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.7070 (p) REVERT: e 25 ILE cc_start: 0.8747 (tp) cc_final: 0.8434 (tt) REVERT: e 26 THR cc_start: 0.8698 (t) cc_final: 0.8401 (t) REVERT: e 74 GLU cc_start: 0.9006 (tp30) cc_final: 0.8622 (tp30) REVERT: g 132 PHE cc_start: 0.7668 (t80) cc_final: 0.7356 (t80) REVERT: g 263 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7898 (tt) REVERT: g 281 PHE cc_start: 0.8405 (t80) cc_final: 0.8006 (t80) REVERT: g 286 GLN cc_start: 0.7831 (pm20) cc_final: 0.7608 (pm20) REVERT: l 12 GLU cc_start: 0.8929 (pp20) cc_final: 0.8118 (pp20) REVERT: t 29 MET cc_start: 0.5187 (pmm) cc_final: 0.4861 (pmm) REVERT: w 96 TRP cc_start: 0.7259 (t-100) cc_final: 0.6881 (t60) REVERT: z 1 MET cc_start: 0.8076 (ttt) cc_final: 0.7427 (tmm) REVERT: z 33 TRP cc_start: 0.6913 (t60) cc_final: 0.6652 (t-100) outliers start: 83 outliers final: 28 residues processed: 499 average time/residue: 0.5458 time to fit residues: 344.6114 Evaluate side-chains 485 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 446 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain Z residue 41 PHE Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain g residue 246 THR Chi-restraints excluded: chain g residue 263 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain i residue 3 THR Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 41 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 5.9990 chunk 295 optimal weight: 40.0000 chunk 346 optimal weight: 2.9990 chunk 401 optimal weight: 3.9990 chunk 276 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN D 9 GLN G 195 GLN Z 58 ASN a 190 HIS b 14 ASN b 349 GLN d 332 GLN e 71 ASN g 195 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 58 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089223 restraints weight = 66920.121| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.18 r_work: 0.2909 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 44117 Z= 0.140 Angle : 0.559 14.622 60690 Z= 0.259 Chirality : 0.040 0.260 5898 Planarity : 0.004 0.058 7514 Dihedral : 15.030 119.599 8248 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.13 % Allowed : 13.66 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.13), residues: 4374 helix: 2.21 (0.10), residues: 2774 sheet: -0.40 (0.71), residues: 54 loop : -0.28 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 31 TYR 0.025 0.001 TYR l 35 PHE 0.021 0.001 PHE a 260 TRP 0.025 0.001 TRP c 165 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00320 (44060) covalent geometry : angle 0.55890 (60690) hydrogen bonds : bond 0.04499 ( 2149) hydrogen bonds : angle 4.10341 ( 6183) Misc. bond : bond 0.03387 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 473 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9121 (mt-10) REVERT: B 63 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 121 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: B 338 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (m) REVERT: B 362 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: C 211 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.8113 (t60) REVERT: D 265 ARG cc_start: 0.8791 (ttm170) cc_final: 0.8587 (mtp180) REVERT: D 281 MET cc_start: 0.9182 (mmp) cc_final: 0.8916 (mmp) REVERT: E 25 ILE cc_start: 0.8943 (tp) cc_final: 0.8729 (tp) REVERT: F 18 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7637 (tmm-80) REVERT: F 39 MET cc_start: 0.9095 (mtm) cc_final: 0.8555 (mtp) REVERT: G 132 PHE cc_start: 0.8181 (t80) cc_final: 0.7924 (t80) REVERT: L 1 MET cc_start: 0.5055 (ppp) cc_final: 0.4639 (ppp) REVERT: L 12 GLU cc_start: 0.8348 (pm20) cc_final: 0.7753 (pm20) REVERT: W 96 TRP cc_start: 0.7304 (t-100) cc_final: 0.6967 (t60) REVERT: X 69 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8256 (tm) REVERT: Z 33 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.6921 (t-100) REVERT: Z 60 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: a 13 LEU cc_start: 0.8107 (pt) cc_final: 0.7827 (mm) REVERT: b 177 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8080 (pmt170) REVERT: b 246 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8471 (p90) REVERT: b 338 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8782 (m) REVERT: b 362 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: c 211 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.8130 (t60) REVERT: c 277 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8568 (tpp) REVERT: d 11 LYS cc_start: 0.8371 (tppt) cc_final: 0.8166 (tptp) REVERT: d 281 MET cc_start: 0.9165 (mmp) cc_final: 0.8958 (mmp) REVERT: e 15 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.7073 (p) REVERT: e 25 ILE cc_start: 0.8735 (tp) cc_final: 0.8417 (tt) REVERT: e 26 THR cc_start: 0.8706 (t) cc_final: 0.8403 (t) REVERT: e 74 GLU cc_start: 0.8997 (tp30) cc_final: 0.8579 (tp30) REVERT: g 132 PHE cc_start: 0.7785 (t80) cc_final: 0.7464 (t80) REVERT: g 281 PHE cc_start: 0.8339 (t80) cc_final: 0.7984 (t80) REVERT: g 306 LEU cc_start: 0.8142 (tp) cc_final: 0.7871 (tm) REVERT: l 12 GLU cc_start: 0.8890 (pp20) cc_final: 0.8117 (pp20) REVERT: l 35 TYR cc_start: 0.9247 (m-80) cc_final: 0.9019 (m-80) REVERT: t 29 MET cc_start: 0.5268 (pmm) cc_final: 0.4912 (pmm) REVERT: w 96 TRP cc_start: 0.7252 (t-100) cc_final: 0.6877 (t60) REVERT: z 1 MET cc_start: 0.8057 (ttt) cc_final: 0.7516 (tmm) REVERT: z 33 TRP cc_start: 0.6911 (t60) cc_final: 0.6672 (t-100) REVERT: z 60 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8035 (m-10) outliers start: 77 outliers final: 27 residues processed: 509 average time/residue: 0.5265 time to fit residues: 339.8460 Evaluate side-chains 492 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 449 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 33 TRP Chi-restraints excluded: chain Z residue 41 PHE Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain g residue 246 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 41 PHE Chi-restraints excluded: chain z residue 60 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 341 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 0.0070 chunk 119 optimal weight: 3.9990 chunk 422 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN D 9 GLN Z 58 ASN a 190 HIS b 14 ASN d 142 ASN g 195 GLN z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089180 restraints weight = 66862.703| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.09 r_work: 0.2918 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 44117 Z= 0.141 Angle : 0.560 13.395 60690 Z= 0.258 Chirality : 0.040 0.250 5898 Planarity : 0.004 0.058 7514 Dihedral : 14.842 119.588 8248 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.11 % Allowed : 14.76 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.13), residues: 4374 helix: 2.25 (0.10), residues: 2774 sheet: -0.40 (0.71), residues: 54 loop : -0.25 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.025 0.001 TYR L 35 PHE 0.019 0.001 PHE B 246 TRP 0.027 0.001 TRP c 165 HIS 0.004 0.001 HIS a 272 Details of bonding type rmsd covalent geometry : bond 0.00325 (44060) covalent geometry : angle 0.55957 (60690) hydrogen bonds : bond 0.04411 ( 2149) hydrogen bonds : angle 4.06732 ( 6183) Misc. bond : bond 0.03222 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 468 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9088 (mt-10) REVERT: B 63 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 121 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 338 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8799 (m) REVERT: B 362 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: C 211 TRP cc_start: 0.9309 (OUTLIER) cc_final: 0.8123 (t60) REVERT: D 100 ASP cc_start: 0.8821 (t0) cc_final: 0.8285 (t0) REVERT: D 265 ARG cc_start: 0.8763 (ttm170) cc_final: 0.8558 (mtp180) REVERT: D 281 MET cc_start: 0.9185 (mmp) cc_final: 0.8909 (mmp) REVERT: D 302 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8394 (mm-30) REVERT: E 25 ILE cc_start: 0.8938 (tp) cc_final: 0.8734 (tp) REVERT: F 18 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7660 (tmm-80) REVERT: F 39 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8515 (mtp) REVERT: G 132 PHE cc_start: 0.8138 (t80) cc_final: 0.7912 (t80) REVERT: G 286 GLN cc_start: 0.7890 (pm20) cc_final: 0.7661 (pm20) REVERT: L 1 MET cc_start: 0.5144 (ppp) cc_final: 0.4721 (ppp) REVERT: L 12 GLU cc_start: 0.8366 (pm20) cc_final: 0.7754 (pm20) REVERT: W 96 TRP cc_start: 0.7279 (t-100) cc_final: 0.6927 (t60) REVERT: Z 60 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: a 13 LEU cc_start: 0.8087 (pt) cc_final: 0.7826 (mm) REVERT: b 177 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8075 (pmt170) REVERT: b 246 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8456 (p90) REVERT: b 338 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8782 (m) REVERT: b 362 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: b 380 ASP cc_start: 0.8508 (m-30) cc_final: 0.8291 (m-30) REVERT: c 211 TRP cc_start: 0.9309 (OUTLIER) cc_final: 0.8138 (t60) REVERT: c 277 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8598 (tpp) REVERT: d 281 MET cc_start: 0.9175 (mmp) cc_final: 0.8901 (mmp) REVERT: e 15 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7125 (p) REVERT: e 25 ILE cc_start: 0.8759 (tp) cc_final: 0.8450 (tt) REVERT: e 26 THR cc_start: 0.8684 (t) cc_final: 0.8378 (t) REVERT: e 74 GLU cc_start: 0.9012 (tp30) cc_final: 0.8597 (tp30) REVERT: g 132 PHE cc_start: 0.7833 (t80) cc_final: 0.7498 (t80) REVERT: g 194 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8694 (m) REVERT: g 286 GLN cc_start: 0.7806 (pm20) cc_final: 0.7501 (pm20) REVERT: g 306 LEU cc_start: 0.8101 (tp) cc_final: 0.7831 (tm) REVERT: l 12 GLU cc_start: 0.8880 (pp20) cc_final: 0.8087 (pp20) REVERT: t 29 MET cc_start: 0.5286 (pmm) cc_final: 0.4926 (pmm) REVERT: w 96 TRP cc_start: 0.7241 (t-100) cc_final: 0.6874 (t60) REVERT: z 1 MET cc_start: 0.8035 (ttt) cc_final: 0.7517 (tmm) REVERT: z 33 TRP cc_start: 0.6993 (t60) cc_final: 0.6770 (t-100) outliers start: 76 outliers final: 28 residues processed: 502 average time/residue: 0.5468 time to fit residues: 347.6120 Evaluate side-chains 499 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 456 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 310 GLN Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain g residue 246 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 41 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 357 optimal weight: 0.9990 chunk 426 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 360 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN G 195 GLN G 245 ASN Z 58 ASN a 190 HIS b 14 ASN d 142 ASN g 195 GLN z 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088469 restraints weight = 66975.727| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.09 r_work: 0.2907 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 44117 Z= 0.161 Angle : 0.583 14.302 60690 Z= 0.268 Chirality : 0.041 0.251 5898 Planarity : 0.004 0.059 7514 Dihedral : 14.706 119.379 8248 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.33 % Allowed : 15.40 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.13), residues: 4374 helix: 2.26 (0.10), residues: 2762 sheet: -0.42 (0.71), residues: 54 loop : -0.29 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.028 0.001 TYR L 35 PHE 0.020 0.001 PHE B 246 TRP 0.028 0.001 TRP c 165 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00378 (44060) covalent geometry : angle 0.58255 (60690) hydrogen bonds : bond 0.04519 ( 2149) hydrogen bonds : angle 4.06838 ( 6183) Misc. bond : bond 0.03090 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 461 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9093 (mt-10) REVERT: B 63 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8663 (mp) REVERT: B 121 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: B 246 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8444 (p90) REVERT: B 338 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8810 (m) REVERT: B 362 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: B 476 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7838 (ptp90) REVERT: C 211 TRP cc_start: 0.9308 (OUTLIER) cc_final: 0.8117 (t60) REVERT: D 100 ASP cc_start: 0.8819 (t0) cc_final: 0.8302 (t0) REVERT: D 265 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8563 (mtp180) REVERT: D 281 MET cc_start: 0.9191 (mmp) cc_final: 0.8919 (mmp) REVERT: D 302 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 25 ILE cc_start: 0.8943 (tp) cc_final: 0.8718 (tp) REVERT: F 18 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7680 (tmm-80) REVERT: F 39 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: G 132 PHE cc_start: 0.8148 (t80) cc_final: 0.7935 (t80) REVERT: G 286 GLN cc_start: 0.7882 (pm20) cc_final: 0.7548 (pm20) REVERT: K 21 ILE cc_start: 0.8147 (tp) cc_final: 0.7846 (tp) REVERT: L 1 MET cc_start: 0.5165 (ppp) cc_final: 0.4742 (ppp) REVERT: L 12 GLU cc_start: 0.8389 (pm20) cc_final: 0.8087 (pp20) REVERT: W 96 TRP cc_start: 0.7268 (t-100) cc_final: 0.6929 (t60) REVERT: Z 60 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: a 13 LEU cc_start: 0.8093 (pt) cc_final: 0.7792 (mm) REVERT: b 177 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8082 (pmt170) REVERT: b 246 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8467 (p90) REVERT: b 338 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8782 (m) REVERT: b 362 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: b 380 ASP cc_start: 0.8518 (m-30) cc_final: 0.8301 (m-30) REVERT: c 211 TRP cc_start: 0.9318 (OUTLIER) cc_final: 0.8151 (t60) REVERT: c 277 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8567 (tpp) REVERT: d 11 LYS cc_start: 0.8339 (tppt) cc_final: 0.8080 (tptt) REVERT: d 281 MET cc_start: 0.9190 (mmp) cc_final: 0.8911 (mmp) REVERT: e 15 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7068 (p) REVERT: e 25 ILE cc_start: 0.8759 (tp) cc_final: 0.8453 (tt) REVERT: e 26 THR cc_start: 0.8666 (t) cc_final: 0.8363 (t) REVERT: e 74 GLU cc_start: 0.9006 (tp30) cc_final: 0.8661 (tp30) REVERT: g 132 PHE cc_start: 0.7991 (t80) cc_final: 0.7735 (t80) REVERT: g 194 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8706 (m) REVERT: g 262 MET cc_start: 0.6856 (mmt) cc_final: 0.6543 (mmp) REVERT: g 306 LEU cc_start: 0.8063 (tp) cc_final: 0.7796 (tm) REVERT: l 12 GLU cc_start: 0.8867 (pp20) cc_final: 0.8051 (pp20) REVERT: t 29 MET cc_start: 0.5135 (pmm) cc_final: 0.4669 (pmm) REVERT: w 96 TRP cc_start: 0.7257 (t-100) cc_final: 0.6901 (t60) REVERT: z 1 MET cc_start: 0.8068 (ttt) cc_final: 0.7485 (tmm) outliers start: 84 outliers final: 32 residues processed: 501 average time/residue: 0.5154 time to fit residues: 327.9413 Evaluate side-chains 503 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 455 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain a residue 260 PHE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 310 GLN Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 41 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 141 optimal weight: 0.7980 chunk 374 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 390 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 255 optimal weight: 8.9990 chunk 365 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN Z 58 ASN a 190 HIS b 14 ASN b 179 GLN z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087902 restraints weight = 67646.038| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.07 r_work: 0.2869 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 44117 Z= 0.225 Angle : 0.636 15.221 60690 Z= 0.292 Chirality : 0.043 0.262 5898 Planarity : 0.005 0.059 7514 Dihedral : 14.832 119.186 8248 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.13 % Allowed : 15.96 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.13), residues: 4374 helix: 2.11 (0.10), residues: 2774 sheet: -0.47 (0.74), residues: 50 loop : -0.33 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 334 TYR 0.032 0.001 TYR L 35 PHE 0.023 0.002 PHE a 17 TRP 0.031 0.001 TRP c 165 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00533 (44060) covalent geometry : angle 0.63569 (60690) hydrogen bonds : bond 0.05058 ( 2149) hydrogen bonds : angle 4.17965 ( 6183) Misc. bond : bond 0.03537 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 468 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9128 (mt-10) REVERT: A 260 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: B 63 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 121 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 246 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8575 (p90) REVERT: B 338 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8791 (m) REVERT: B 353 GLU cc_start: 0.8550 (pt0) cc_final: 0.8088 (pm20) REVERT: B 362 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: B 387 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8560 (mp0) REVERT: C 211 TRP cc_start: 0.9348 (OUTLIER) cc_final: 0.8163 (t60) REVERT: D 100 ASP cc_start: 0.8863 (t0) cc_final: 0.8420 (t0) REVERT: D 281 MET cc_start: 0.9203 (mmp) cc_final: 0.8947 (mmp) REVERT: E 25 ILE cc_start: 0.8941 (tp) cc_final: 0.8712 (tp) REVERT: E 65 LEU cc_start: 0.8969 (tp) cc_final: 0.8769 (tt) REVERT: F 18 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7690 (tmm-80) REVERT: F 39 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8702 (mtp) REVERT: G 132 PHE cc_start: 0.8184 (t80) cc_final: 0.7965 (t80) REVERT: G 286 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: G 294 SER cc_start: 0.8668 (p) cc_final: 0.8426 (m) REVERT: G 306 LEU cc_start: 0.7661 (tp) cc_final: 0.7369 (tm) REVERT: K 21 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7846 (tp) REVERT: L 1 MET cc_start: 0.5066 (ppp) cc_final: 0.4687 (ppp) REVERT: L 12 GLU cc_start: 0.8405 (pm20) cc_final: 0.8084 (pp20) REVERT: W 96 TRP cc_start: 0.7247 (t-100) cc_final: 0.6920 (t60) REVERT: Z 60 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: a 13 LEU cc_start: 0.8097 (pt) cc_final: 0.7798 (mm) REVERT: b 177 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8079 (pmt170) REVERT: b 246 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8478 (p90) REVERT: b 338 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8774 (m) REVERT: b 353 GLU cc_start: 0.8485 (pt0) cc_final: 0.8083 (pm20) REVERT: b 362 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: b 380 ASP cc_start: 0.8604 (m-30) cc_final: 0.8393 (m-30) REVERT: c 211 TRP cc_start: 0.9355 (OUTLIER) cc_final: 0.8199 (t60) REVERT: c 277 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: d 281 MET cc_start: 0.9222 (mmp) cc_final: 0.9009 (mmp) REVERT: e 15 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7095 (p) REVERT: e 25 ILE cc_start: 0.8779 (tp) cc_final: 0.8463 (tt) REVERT: e 26 THR cc_start: 0.8745 (t) cc_final: 0.8445 (t) REVERT: e 74 GLU cc_start: 0.9022 (tp30) cc_final: 0.8673 (tp30) REVERT: g 286 GLN cc_start: 0.7863 (pm20) cc_final: 0.7625 (pm20) REVERT: g 306 LEU cc_start: 0.8078 (tp) cc_final: 0.7862 (tm) REVERT: l 12 GLU cc_start: 0.8862 (pp20) cc_final: 0.8009 (pp20) REVERT: t 29 MET cc_start: 0.5197 (pmm) cc_final: 0.4805 (pmm) REVERT: w 96 TRP cc_start: 0.7282 (t-100) cc_final: 0.6943 (t60) REVERT: z 1 MET cc_start: 0.8079 (ttt) cc_final: 0.7504 (tmm) REVERT: z 60 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8062 (m-10) outliers start: 77 outliers final: 39 residues processed: 499 average time/residue: 0.5567 time to fit residues: 350.6578 Evaluate side-chains 512 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 454 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain a residue 260 PHE Chi-restraints excluded: chain a residue 329 GLU Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 66 MET Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 310 GLN Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 13 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain g residue 194 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain m residue 28 LYS Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 33 TRP Chi-restraints excluded: chain z residue 41 PHE Chi-restraints excluded: chain z residue 60 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 121 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 375 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 chunk 399 optimal weight: 0.7980 chunk 365 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN G 228 ASN ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN a 190 HIS b 14 ASN g 195 GLN z 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089289 restraints weight = 66887.066| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.11 r_work: 0.2925 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 44117 Z= 0.127 Angle : 0.564 14.539 60690 Z= 0.263 Chirality : 0.040 0.240 5898 Planarity : 0.004 0.056 7514 Dihedral : 14.496 118.973 8248 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.69 % Allowed : 16.76 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.13), residues: 4374 helix: 2.26 (0.10), residues: 2764 sheet: -0.29 (0.75), residues: 50 loop : -0.25 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 352 TYR 0.027 0.001 TYR l 35 PHE 0.025 0.001 PHE a 17 TRP 0.032 0.001 TRP c 165 HIS 0.005 0.001 HIS a 272 Details of bonding type rmsd covalent geometry : bond 0.00288 (44060) covalent geometry : angle 0.56400 (60690) hydrogen bonds : bond 0.04300 ( 2149) hydrogen bonds : angle 4.03358 ( 6183) Misc. bond : bond 0.03088 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 473 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9066 (mt-10) REVERT: A 260 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: A 293 MET cc_start: 0.8727 (mtt) cc_final: 0.8226 (mtt) REVERT: B 25 MET cc_start: 0.9441 (tpt) cc_final: 0.9208 (tpp) REVERT: B 63 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 121 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: B 246 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8437 (p90) REVERT: B 338 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8795 (m) REVERT: B 362 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: B 387 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8539 (mp0) REVERT: C 211 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.8144 (t60) REVERT: C 451 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7285 (p0) REVERT: D 100 ASP cc_start: 0.8809 (t0) cc_final: 0.8385 (t0) REVERT: D 265 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8577 (mtp180) REVERT: D 281 MET cc_start: 0.9170 (mmp) cc_final: 0.8895 (mmp) REVERT: E 25 ILE cc_start: 0.8938 (tp) cc_final: 0.8709 (tp) REVERT: F 18 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.7634 (tmm-80) REVERT: F 39 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8443 (mtp) REVERT: G 132 PHE cc_start: 0.8190 (t80) cc_final: 0.7975 (t80) REVERT: G 286 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: G 294 SER cc_start: 0.8710 (p) cc_final: 0.8466 (m) REVERT: G 306 LEU cc_start: 0.7576 (tp) cc_final: 0.7335 (tm) REVERT: H 35 SER cc_start: 0.9197 (p) cc_final: 0.8735 (m) REVERT: K 21 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7802 (tp) REVERT: L 1 MET cc_start: 0.5092 (ppp) cc_final: 0.4725 (ppp) REVERT: L 12 GLU cc_start: 0.8379 (pm20) cc_final: 0.7919 (pp20) REVERT: W 96 TRP cc_start: 0.7233 (t-100) cc_final: 0.6903 (t60) REVERT: Z 60 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: a 13 LEU cc_start: 0.8103 (pt) cc_final: 0.7808 (mm) REVERT: b 177 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (pmt170) REVERT: b 246 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8454 (p90) REVERT: b 338 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8797 (m) REVERT: b 353 GLU cc_start: 0.8433 (pt0) cc_final: 0.7967 (pm20) REVERT: b 362 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: b 380 ASP cc_start: 0.8480 (m-30) cc_final: 0.8254 (m-30) REVERT: c 211 TRP cc_start: 0.9302 (OUTLIER) cc_final: 0.8146 (t60) REVERT: c 277 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8523 (tpp) REVERT: d 11 LYS cc_start: 0.8347 (tppt) cc_final: 0.8024 (tptp) REVERT: e 15 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7054 (p) REVERT: e 25 ILE cc_start: 0.8774 (tp) cc_final: 0.8460 (tt) REVERT: e 26 THR cc_start: 0.8729 (t) cc_final: 0.8424 (t) REVERT: e 74 GLU cc_start: 0.9005 (tp30) cc_final: 0.8643 (tp30) REVERT: g 194 VAL cc_start: 0.8945 (p) cc_final: 0.8704 (m) REVERT: g 262 MET cc_start: 0.6993 (mmt) cc_final: 0.6740 (mmp) REVERT: g 306 LEU cc_start: 0.7941 (tp) cc_final: 0.7690 (tm) REVERT: l 12 GLU cc_start: 0.8785 (pp20) cc_final: 0.7936 (pp20) REVERT: t 29 MET cc_start: 0.5224 (pmm) cc_final: 0.4771 (pmm) REVERT: w 96 TRP cc_start: 0.7234 (t-100) cc_final: 0.6922 (t60) REVERT: z 1 MET cc_start: 0.8031 (ttt) cc_final: 0.7638 (tmm) REVERT: z 60 PHE cc_start: 0.8425 (m-80) cc_final: 0.8067 (m-10) outliers start: 61 outliers final: 25 residues processed: 505 average time/residue: 0.5141 time to fit residues: 328.8213 Evaluate side-chains 498 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 454 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain a residue 260 PHE Chi-restraints excluded: chain a residue 264 SER Chi-restraints excluded: chain a residue 329 GLU Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 420 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN a 190 HIS b 14 ASN d 142 ASN z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.089487 restraints weight = 66804.573| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.09 r_work: 0.2924 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 44117 Z= 0.135 Angle : 0.580 15.295 60690 Z= 0.270 Chirality : 0.040 0.245 5898 Planarity : 0.004 0.075 7514 Dihedral : 14.367 118.721 8248 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 17.37 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.13), residues: 4374 helix: 2.27 (0.10), residues: 2764 sheet: -0.33 (0.74), residues: 50 loop : -0.24 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.027 0.001 TYR l 35 PHE 0.018 0.001 PHE B 246 TRP 0.033 0.001 TRP c 165 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00313 (44060) covalent geometry : angle 0.57998 (60690) hydrogen bonds : bond 0.04295 ( 2149) hydrogen bonds : angle 4.02408 ( 6183) Misc. bond : bond 0.02959 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 463 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9087 (mt-10) REVERT: B 25 MET cc_start: 0.9434 (tpt) cc_final: 0.9230 (tpp) REVERT: B 63 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 121 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: B 246 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8433 (p90) REVERT: B 338 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8798 (m) REVERT: B 362 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: C 211 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.8109 (t60) REVERT: C 451 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7167 (p0) REVERT: D 100 ASP cc_start: 0.8775 (t0) cc_final: 0.8359 (t0) REVERT: D 265 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8565 (mtp180) REVERT: D 281 MET cc_start: 0.9173 (mmp) cc_final: 0.8893 (mmp) REVERT: E 25 ILE cc_start: 0.8950 (tp) cc_final: 0.8718 (tp) REVERT: F 18 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.7643 (tmm-80) REVERT: F 39 MET cc_start: 0.9073 (mtm) cc_final: 0.8450 (mtp) REVERT: G 132 PHE cc_start: 0.8203 (t80) cc_final: 0.7987 (t80) REVERT: G 286 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: G 294 SER cc_start: 0.8701 (p) cc_final: 0.8477 (m) REVERT: G 303 GLN cc_start: 0.8222 (tp40) cc_final: 0.7870 (tp-100) REVERT: G 306 LEU cc_start: 0.7552 (tp) cc_final: 0.7296 (tm) REVERT: K 21 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7838 (tp) REVERT: L 1 MET cc_start: 0.5092 (ppp) cc_final: 0.4725 (ppp) REVERT: L 12 GLU cc_start: 0.8299 (pm20) cc_final: 0.7846 (pp20) REVERT: W 96 TRP cc_start: 0.7287 (t-100) cc_final: 0.6967 (t60) REVERT: Z 60 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: a 13 LEU cc_start: 0.8128 (pt) cc_final: 0.7824 (mm) REVERT: b 177 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8091 (pmt170) REVERT: b 246 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8470 (p90) REVERT: b 338 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8801 (m) REVERT: b 353 GLU cc_start: 0.8423 (pt0) cc_final: 0.8000 (pm20) REVERT: b 362 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: b 380 ASP cc_start: 0.8471 (m-30) cc_final: 0.8264 (m-30) REVERT: c 211 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.8154 (t60) REVERT: c 277 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8563 (tpp) REVERT: d 11 LYS cc_start: 0.8356 (tppt) cc_final: 0.8094 (tptp) REVERT: d 28 VAL cc_start: 0.9122 (t) cc_final: 0.8793 (p) REVERT: e 15 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.7013 (p) REVERT: e 25 ILE cc_start: 0.8784 (tp) cc_final: 0.8476 (tt) REVERT: e 26 THR cc_start: 0.8760 (t) cc_final: 0.8456 (t) REVERT: e 74 GLU cc_start: 0.9024 (tp30) cc_final: 0.8645 (tp30) REVERT: g 286 GLN cc_start: 0.7869 (pm20) cc_final: 0.7565 (pm20) REVERT: g 303 GLN cc_start: 0.8208 (tp40) cc_final: 0.7784 (tp-100) REVERT: g 306 LEU cc_start: 0.7889 (tp) cc_final: 0.7676 (tm) REVERT: l 12 GLU cc_start: 0.8691 (pp20) cc_final: 0.7830 (pp20) REVERT: t 29 MET cc_start: 0.5260 (pmm) cc_final: 0.4799 (pmm) REVERT: w 96 TRP cc_start: 0.7273 (t-100) cc_final: 0.6950 (t60) REVERT: z 1 MET cc_start: 0.8025 (ttt) cc_final: 0.7641 (tmm) REVERT: z 60 PHE cc_start: 0.8409 (m-80) cc_final: 0.8106 (m-10) outliers start: 54 outliers final: 27 residues processed: 493 average time/residue: 0.5944 time to fit residues: 369.7870 Evaluate side-chains 502 residues out of total 3610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 458 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain a residue 260 PHE Chi-restraints excluded: chain a residue 329 GLU Chi-restraints excluded: chain b residue 177 ARG Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 338 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 211 TRP Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 365 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 26 LEU Chi-restraints excluded: chain z residue 33 TRP Chi-restraints excluded: chain z residue 56 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 156 optimal weight: 0.5980 chunk 377 optimal weight: 9.9990 chunk 116 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 411 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 14 ASN ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN a 190 HIS b 14 ASN c 310 GLN d 142 ASN z 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089036 restraints weight = 66921.884| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.05 r_work: 0.2971 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 44117 Z= 0.108 Angle : 0.553 13.849 60690 Z= 0.258 Chirality : 0.039 0.234 5898 Planarity : 0.004 0.068 7514 Dihedral : 14.116 118.713 8248 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 17.67 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.13), residues: 4374 helix: 2.34 (0.10), residues: 2766 sheet: -0.15 (0.74), residues: 50 loop : -0.21 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 334 TYR 0.017 0.001 TYR g 309 PHE 0.029 0.001 PHE a 17 TRP 0.034 0.001 TRP c 165 HIS 0.011 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00237 (44060) covalent geometry : angle 0.55260 (60690) hydrogen bonds : bond 0.03917 ( 2149) hydrogen bonds : angle 3.94234 ( 6183) Misc. bond : bond 0.02888 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12641.28 seconds wall clock time: 216 minutes 1.03 seconds (12961.03 seconds total)