Starting phenix.real_space_refine on Fri Oct 30 04:09:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n30_9335/10_2026/6n30_9335.cif" } resolution = 3.2 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= 0.009 sd= 0.171 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 22180 2.51 5 N 6069 2.21 5 O 6490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34851 Number of models: 1 Model: "" Number of chains: 28 Chain: "b2" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 770 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 1, 'TRANS': 132} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 22, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 186 Chain: "b2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 84 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 18 Chain: "b1" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 889 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 14, 'GLU:plan': 27, 'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 238 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3736 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3794 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3780 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 475} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3610 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3581 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3614 Classifications: {'peptide': 471} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2196 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 273} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 924 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "I" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1188 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ASP:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.58, per 1000 atoms: 0.22 Number of scatterers: 34851 At special positions: 0 Unit cell: (127.2, 138.86, 226.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 Mg 4 11.99 O 6490 8.00 N 6069 7.00 C 22180 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8580 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 28 sheets defined 59.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'b2' and resid 10 through 29 Processing helix chain 'b2' and resid 29 through 123 removed outlier: 4.342A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILEb2 48 " --> pdb=" O ILEb2 44 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASPb2 49 " --> pdb=" O ALAb2 45 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLNb2 50 " --> pdb=" O ASNb2 46 " (cutoff:3.500A) Processing helix chain 'b2' and resid 124 through 140 Processing helix chain 'b2' and resid 601 through 616 Processing helix chain 'b1' and resid 9 through 143 removed outlier: 3.608A pdb=" N TYRb1 13 " --> pdb=" O GLYb1 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix removed outlier: 3.743A pdb=" N ALAb1 45 " --> pdb=" O GLUb1 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASNb1 46 " --> pdb=" O GLUb1 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLUb1 47 " --> pdb=" O HISb1 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLUb1 59 " --> pdb=" O ARGb1 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYSb1 60 " --> pdb=" O GLNb1 56 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEUb1 61 " --> pdb=" O GLUb1 57 " (cutoff:3.500A) Processing helix chain 'b1' and resid 145 through 163 Processing helix chain 'a' and resid 16 through 38 removed outlier: 3.582A pdb=" N MET a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 68 through 73 Processing helix chain 'a' and resid 75 through 92 removed outlier: 3.745A pdb=" N THR a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 130 Processing helix chain 'a' and resid 153 through 191 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 234 removed outlier: 4.262A pdb=" N MET a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'c3' and resid 3 through 37 Processing helix chain 'c3' and resid 40 through 72 removed outlier: 4.001A pdb=" N THRc3 47 " --> pdb=" O VALc3 43 " (cutoff:3.500A) Proline residue: c3 59 - end of helix removed outlier: 3.924A pdb=" N PHEc3 67 " --> pdb=" O VALc3 63 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILEc3 68 " --> pdb=" O VALc3 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGc3 72 " --> pdb=" O ILEc3 68 " (cutoff:3.500A) Processing helix chain 'c4' and resid 3 through 37 Processing helix chain 'c4' and resid 40 through 72 removed outlier: 4.525A pdb=" N LEUc4 58 " --> pdb=" O LEUc4 54 " (cutoff:3.500A) Proline residue: c4 59 - end of helix Processing helix chain 'c5' and resid 3 through 37 Processing helix chain 'c5' and resid 40 through 56 Processing helix chain 'c5' and resid 56 through 72 Processing helix chain 'c6' and resid 3 through 37 Processing helix chain 'c6' and resid 40 through 71 Proline residue: c6 59 - end of helix Processing helix chain 'c7' and resid 3 through 37 Processing helix chain 'c7' and resid 40 through 56 Processing helix chain 'c7' and resid 56 through 72 removed outlier: 4.031A pdb=" N ILEc7 68 " --> pdb=" O VALc7 64 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 37 Processing helix chain 'c8' and resid 40 through 72 removed outlier: 4.290A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 3 through 37 Processing helix chain 'c9' and resid 40 through 72 removed outlier: 4.373A pdb=" N LEUc9 58 " --> pdb=" O LEUc9 54 " (cutoff:3.500A) Proline residue: c9 59 - end of helix removed outlier: 3.635A pdb=" N GLYc9 71 " --> pdb=" O PHEc9 67 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARGc9 72 " --> pdb=" O ILEc9 68 " (cutoff:3.500A) Processing helix chain 'c0' and resid 3 through 37 Processing helix chain 'c0' and resid 40 through 56 removed outlier: 3.666A pdb=" N LEUc0 44 " --> pdb=" O LEUc0 40 " (cutoff:3.500A) Processing helix chain 'c0' and resid 56 through 72 removed outlier: 3.504A pdb=" N ILEc0 60 " --> pdb=" O GLUc0 56 " (cutoff:3.500A) Processing helix chain 'c1' and resid 3 through 37 Processing helix chain 'c1' and resid 40 through 71 removed outlier: 4.938A pdb=" N LEUc1 58 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) Proline residue: c1 59 - end of helix Processing helix chain 'c2' and resid 3 through 37 removed outlier: 3.526A pdb=" N GLNc2 37 " --> pdb=" O GLYc2 33 " (cutoff:3.500A) Processing helix chain 'c2' and resid 40 through 71 removed outlier: 3.827A pdb=" N THRc2 47 " --> pdb=" O VALc2 43 " (cutoff:3.500A) Proline residue: c2 59 - end of helix Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.785A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.673A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.803A pdb=" N HIS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.576A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 Proline residue: C 239 - end of helix removed outlier: 4.301A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.864A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.650A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 420 removed outlier: 3.696A pdb=" N LEU C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.601A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.523A pdb=" N LEU C 487 " --> pdb=" O ASN C 483 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.592A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.564A pdb=" N HIS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.602A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 220 " --> pdb=" O ALA A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.573A pdb=" N LEU A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 4.021A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.822A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.807A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.684A pdb=" N GLY A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.525A pdb=" N THR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 373 through 380 removed outlier: 4.198A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.534A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.728A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 20 through 23 removed outlier: 3.603A pdb=" N ILE B 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.536A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.575A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.651A pdb=" N HIS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 3.557A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.910A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.866A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.607A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.807A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.698A pdb=" N SER B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.844A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.531A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 467 removed outlier: 3.612A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.645A pdb=" N LEU B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 179 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 4.939A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 removed outlier: 3.824A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.583A pdb=" N GLU F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 315 through 323 Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.652A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 396 through 410 removed outlier: 3.609A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 443 removed outlier: 3.571A pdb=" N GLY F 443 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 removed outlier: 3.987A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.737A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.773A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.764A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.628A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 380 Processing helix chain 'D' and resid 380 through 388 Processing helix chain 'D' and resid 394 through 410 removed outlier: 4.302A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.786A pdb=" N LYS D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 3.525A pdb=" N ALA E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 176 Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.629A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'E' and resid 221 through 243 removed outlier: 3.593A pdb=" N ARG E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.978A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.601A pdb=" N TYR E 277 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.834A pdb=" N MET E 285 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 312 Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.592A pdb=" N LEU E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 5.010A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 removed outlier: 3.878A pdb=" N GLU E 391 " --> pdb=" O GLY E 388 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 392 " --> pdb=" O MET E 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 388 through 392' Processing helix chain 'E' and resid 395 through 410 removed outlier: 4.202A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 removed outlier: 3.691A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 453 removed outlier: 3.545A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'G' and resid 3 through 42 Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.866A pdb=" N LYS G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.751A pdb=" N ASN G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.838A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 89 through 131 removed outlier: 3.884A pdb=" N ALA H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 22 removed outlier: 3.503A pdb=" N TYR I 10 " --> pdb=" O ILE I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 41 removed outlier: 3.658A pdb=" N ASP I 30 " --> pdb=" O ARG I 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.010A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 66 Processing helix chain 'I' and resid 70 through 83 Processing helix chain 'I' and resid 85 through 87 No H-bonds generated for 'chain 'I' and resid 85 through 87' Processing helix chain 'I' and resid 88 through 105 removed outlier: 3.746A pdb=" N ASP I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 134 Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.732A pdb=" N LEU I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.675A pdb=" N THR C 91 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 removed outlier: 6.848A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 4 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 106 through 108 removed outlier: 6.396A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.568A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY A 61 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 14 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.235A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER A 227 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLN A 341 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLY A 360 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.506A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.661A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.126A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.569A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 319 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.566A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.073A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.390A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.383A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB9, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.160A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 216 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.271A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.690A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR E 307 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 306 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU E 156 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.200A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 135 through 136 removed outlier: 4.080A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.480A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 19 removed outlier: 6.058A pdb=" N HIS H 5 " --> pdb=" O VAL H 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AC9, first strand: chain 'H' and resid 48 through 51 removed outlier: 3.602A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 62 " --> pdb=" O GLU H 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 138 through 143 removed outlier: 3.837A pdb=" N SER I 113 " --> pdb=" O ILE I 143 " (cutoff:3.500A) 2195 hydrogen bonds defined for protein. 6444 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: 7.40 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5895 1.29 - 1.42: 8214 1.42 - 1.55: 20938 1.55 - 1.68: 150 1.68 - 1.81: 191 Bond restraints: 35388 Sorted by residual: bond pdb=" N SERb1 130 " pdb=" CA SERb1 130 " ideal model delta sigma weight residual 1.459 1.338 0.121 1.21e-02 6.83e+03 1.01e+02 bond pdb=" CA SERb1 137 " pdb=" C SERb1 137 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.30e-02 5.92e+03 6.75e+01 bond pdb=" N ALAb1 109 " pdb=" CA ALAb1 109 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.19e-02 7.06e+03 6.54e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 ... (remaining 35383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 47270 4.15 - 8.30: 743 8.30 - 12.46: 77 12.46 - 16.61: 9 16.61 - 20.76: 2 Bond angle restraints: 48101 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 119.11 20.76 1.00e+00 1.00e+00 4.31e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.72 20.15 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 125.24 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 48096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 20224 17.42 - 34.85: 858 34.85 - 52.27: 140 52.27 - 69.70: 21 69.70 - 87.12: 13 Dihedral angle restraints: 21256 sinusoidal: 7873 harmonic: 13383 Sorted by residual: dihedral pdb=" CA LEU G 189 " pdb=" C LEU G 189 " pdb=" N PRO G 190 " pdb=" CA PRO G 190 " ideal model delta harmonic sigma weight residual 180.00 104.78 75.22 0 5.00e+00 4.00e-02 2.26e+02 dihedral pdb=" CA PRO B 482 " pdb=" C PRO B 482 " pdb=" N ASN B 483 " pdb=" CA ASN B 483 " ideal model delta harmonic sigma weight residual 180.00 145.34 34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA VAL B 366 " pdb=" C VAL B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual -180.00 -149.82 -30.18 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 21253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5350 0.128 - 0.257: 373 0.257 - 0.385: 44 0.385 - 0.513: 5 0.513 - 0.641: 2 Chirality restraints: 5774 Sorted by residual: chirality pdb=" CA SERb1 130 " pdb=" N SERb1 130 " pdb=" C SERb1 130 " pdb=" CB SERb1 130 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA GLUb2 67 " pdb=" N GLUb2 67 " pdb=" C GLUb2 67 " pdb=" CB GLUb2 67 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA LYSb1 60 " pdb=" N LYSb1 60 " pdb=" C LYSb1 60 " pdb=" CB LYSb1 60 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 5771 not shown) Planarity restraints: 6223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 189 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO G 190 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO G 190 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO G 190 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEUb1 68 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C LEUb1 68 " 0.057 2.00e-02 2.50e+03 pdb=" O LEUb1 68 " -0.021 2.00e-02 2.50e+03 pdb=" N METb1 69 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAb2 58 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ALAb2 58 " -0.056 2.00e-02 2.50e+03 pdb=" O ALAb2 58 " 0.022 2.00e-02 2.50e+03 pdb=" N GLUb2 59 " 0.017 2.00e-02 2.50e+03 ... (remaining 6220 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.45: 5 1.45 - 2.31: 64 2.31 - 3.18: 29325 3.18 - 4.04: 91332 4.04 - 4.90: 168836 Warning: very small nonbonded interaction distances. Nonbonded interactions: 289562 Sorted by model distance: nonbonded pdb=" C ALAc3 35 " pdb=" OE2 GLU H 31 " model vdw 0.590 3.270 nonbonded pdb=" O ALAc3 35 " pdb=" OE2 GLU H 31 " model vdw 0.858 3.040 nonbonded pdb=" C ARGc3 36 " pdb=" OE1 GLU H 31 " model vdw 0.901 3.270 nonbonded pdb=" O ARGc3 36 " pdb=" OE1 GLU H 31 " model vdw 1.223 3.040 nonbonded pdb=" O ALAc3 35 " pdb=" CD GLU H 31 " model vdw 1.242 3.270 ... (remaining 289557 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 8 through 20 and (name N or name CA or name C or name O o \ r name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name CB )) or resid 40 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 through 392 or (resid 393 and (name \ N or name CA or name C or name O or name CB )) or (resid 394 and (name N or name \ CA or name C or name CB )) or resid 395 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 466 through 601)) selection = (chain 'B' and ((resid 8 through 20 and (name N or name CA or name C or name O o \ r name CB )) or resid 21 through 22 or (resid 23 through 24 and (name N or name \ CA or name C or name O or name CB )) or resid 25 through 38 or (resid 39 and (na \ me N or name CA or name C or name CB )) or resid 40 through 352 or (resid 353 an \ d (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 354 \ through 392 or (resid 393 and (name N or name CA or name C or name O or name CB \ )) or (resid 394 and (name N or name CA or name C or name CB )) or resid 395 th \ rough 396 or (resid 397 through 398 and (name N or name CA or name C or name O o \ r name CB )) or resid 399 through 402 or (resid 403 through 406 and (name N or n \ ame CA or name C or name O or name CB )) or resid 407 through 450 or (resid 451 \ and (name N or name CA or name C or name O or name CB )) or resid 452 through 48 \ 4 or (resid 485 and (name N or name CA or name C or name O or name CB )) or resi \ d 486 through 488 or (resid 489 through 490 and (name N or name CA or name C or \ name O or name CB )) or resid 491 through 495 or (resid 496 and (name N or name \ CA or name C or name O or name CB )) or resid 497 through 601)) selection = (chain 'C' and (resid 8 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 187 or (resid 188 and (n \ ame N or name CA or name C or name O or name CB )) or resid 189 through 352 or ( \ resid 353 and (name N or name CA or name C or name CB or name CG1 or name CG2)) \ or resid 354 through 396 or (resid 397 through 398 and (name N or name CA or nam \ e C or name O or name CB )) or resid 399 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 450 or (resid 4 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 452 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or r \ esid 466 through 484 or (resid 485 and (name N or name CA or name C or name O or \ name CB )) or resid 486 through 488 or (resid 489 through 490 and (name N or na \ me CA or name C or name O or name CB )) or resid 491 through 495 or (resid 496 a \ nd (name N or name CA or name C or name O or name CB )) or resid 497 through 601 \ )) } ncs_group { reference = (chain 'D' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 195 or (res \ id 196 and (name N or name CA or name C or name CB or name CG or name OD1 or nam \ e ND2)) or resid 197 through 208 or (resid 209 and (name N or name CA or name C \ or name CB or name OG )) or resid 210 through 296 or (resid 297 and (name N or n \ ame CA or name C or name CB or name CG or name CD or name CE or name NZ )) or re \ sid 298 through 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 through 420 or (resid 421 and (name N or name CA or name \ C or name CB or name OG1 or name CG2)) or (resid 422 and (name N or name CA or \ name C )) or resid 423 through 469)) selection = (chain 'E' and (resid 2 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 381 or (resid 38 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 383 through \ 388 or (resid 389 through 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name C o \ r name O or name CB )) or resid 396 or (resid 397 and (name N or name CA or name \ C or name O or name CB )) or resid 398 through 430 or (resid 431 and (name N or \ name CA or name C or name O or name CB )) or resid 432 through 468 or (resid 46 \ 9 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 130 or (res \ id 131 and (name N or name CA or name C or name O or name CB )) or resid 132 thr \ ough 195 or (resid 196 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2)) or resid 197 through 208 or (resid 209 and (name N or na \ me CA or name C or name CB or name OG )) or resid 210 through 296 or (resid 297 \ and (name N or name CA or name C or name CB or name CG or name CD or name CE or \ name NZ )) or resid 298 through 381 or (resid 382 and (name N or name CA or name \ C or name O or name CB )) or resid 383 through 388 or (resid 389 through 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 39 \ 4 through 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or re \ sid 398 through 420 or (resid 421 and (name N or name CA or name C or name CB or \ name OG1 or name CG2)) or (resid 422 and (name N or name CA or name C )) or res \ id 423 through 468 or (resid 469 and (name N or name CA or name C or name O or n \ ame CB )))) } ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 through 139 and \ (name N or name CA or name C or name O or name CB )) or (resid 140 and (name N o \ r name CA or name C or name CB )))) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 140)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } 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: 3.410 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.330 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.451 35394 Z= 0.692 Angle : 1.268 20.760 48101 Z= 0.776 Chirality : 0.075 0.641 5774 Planarity : 0.008 0.108 6223 Dihedral : 10.681 87.122 12676 Min Nonbonded Distance : 0.590 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 0.78 % Allowed : 5.83 % Favored : 93.39 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.11), residues: 4646 helix: -1.52 (0.09), residues: 2495 sheet: -1.55 (0.21), residues: 546 loop : -2.02 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 271 TYR 0.035 0.003 TYRc3 69 PHE 0.043 0.004 PHEc9 65 TRP 0.023 0.002 TRP a 206 HIS 0.031 0.003 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.01057 / 0.59 (35388) covalent geometry : angle 1.26812 / 0.78 (48101) hydrogen bonds : bond 0.15632 / 11.32 ( 2195) hydrogen bonds : angle 6.96096 / 5.12 ( 6444) Misc. bond : bond 0.28066 / 13.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 691 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 184 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4978 (mt) REVERT: a 223 MET cc_start: 0.7704 (tmm) cc_final: 0.7482 (tmm) REVERT: C 354 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8021 (mtt90) REVERT: C 363 VAL cc_start: 0.8420 (p) cc_final: 0.8087 (m) REVERT: C 458 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7537 (tttm) REVERT: C 489 LYS cc_start: 0.8307 (mmtm) cc_final: 0.8031 (mmtm) REVERT: A 54 GLU cc_start: 0.7853 (tt0) cc_final: 0.7624 (tt0) REVERT: A 326 ILE cc_start: 0.9014 (tt) cc_final: 0.8745 (tt) REVERT: A 363 VAL cc_start: 0.8664 (t) cc_final: 0.8393 (m) REVERT: A 393 GLU cc_start: 0.7212 (pp20) cc_final: 0.6966 (pp20) REVERT: A 436 ILE cc_start: 0.7954 (mm) cc_final: 0.7698 (tp) REVERT: A 458 LYS cc_start: 0.7989 (ttpm) cc_final: 0.7762 (ttpt) REVERT: A 463 PHE cc_start: 0.8590 (t80) cc_final: 0.8164 (t80) REVERT: B 60 MET cc_start: 0.8898 (mmt) cc_final: 0.8254 (mmt) REVERT: B 129 ILE cc_start: 0.9151 (tt) cc_final: 0.8921 (tt) REVERT: B 157 VAL cc_start: 0.9254 (t) cc_final: 0.9003 (t) REVERT: B 262 ASP cc_start: 0.8238 (m-30) cc_final: 0.8014 (m-30) REVERT: B 289 ASP cc_start: 0.8766 (p0) cc_final: 0.8492 (p0) REVERT: B 384 LEU cc_start: 0.8311 (mt) cc_final: 0.8101 (mt) REVERT: B 440 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8839 (tp) REVERT: B 489 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8170 (ttmm) REVERT: F 10 MET cc_start: 0.7401 (mtp) cc_final: 0.7128 (mtm) REVERT: F 17 LYS cc_start: 0.8462 (tttt) cc_final: 0.8081 (ttmt) REVERT: F 74 MET cc_start: 0.8747 (mtt) cc_final: 0.8509 (mtt) REVERT: F 307 TYR cc_start: 0.7763 (t80) cc_final: 0.7556 (t80) REVERT: F 375 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8132 (tp40) REVERT: F 381 GLN cc_start: 0.8116 (tt0) cc_final: 0.7757 (tp-100) REVERT: D 44 ILE cc_start: 0.8392 (mt) cc_final: 0.8155 (tp) REVERT: D 62 ILE cc_start: 0.8897 (tp) cc_final: 0.8571 (pt) REVERT: D 143 ASP cc_start: 0.8255 (m-30) cc_final: 0.7579 (m-30) REVERT: D 168 ILE cc_start: 0.8627 (mt) cc_final: 0.8349 (mm) REVERT: D 175 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.7766 (mp) REVERT: D 420 PHE cc_start: 0.8950 (m-10) cc_final: 0.8746 (m-10) REVERT: E 7 ILE cc_start: 0.9149 (mt) cc_final: 0.8928 (mm) REVERT: E 39 GLU cc_start: 0.7811 (pm20) cc_final: 0.7549 (pm20) REVERT: E 454 ARG cc_start: 0.8857 (mtt-85) cc_final: 0.8448 (mtt-85) REVERT: G 84 ASP cc_start: 0.8018 (t0) cc_final: 0.7689 (t0) REVERT: G 120 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7416 (mtm-85) REVERT: G 168 LEU cc_start: 0.7991 (pt) cc_final: 0.7742 (pt) REVERT: G 204 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7162 (tm-30) REVERT: H 112 ASP cc_start: 0.7670 (m-30) cc_final: 0.7276 (m-30) REVERT: I 3 GLN cc_start: 0.7307 (tm-30) cc_final: 0.6891 (tm-30) REVERT: I 57 GLN cc_start: 0.8685 (mm110) cc_final: 0.8419 (mm-40) REVERT: I 69 VAL cc_start: 0.8368 (m) cc_final: 0.8030 (t) REVERT: I 88 LEU cc_start: 0.7772 (tt) cc_final: 0.7023 (mm) REVERT: I 110 VAL cc_start: 0.8268 (t) cc_final: 0.8059 (p) REVERT: I 175 GLN cc_start: 0.7991 (tt0) cc_final: 0.7719 (tt0) outliers start: 27 outliers final: 9 residues processed: 714 average time/residue: 0.2296 time to fit residues: 261.7955 Evaluate side-chains 493 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 481 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [432, 197, 388, 455, 215, 20, 132, 261, 248, 207, 401] chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 16 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 HIS ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 37 GLN c8 23 ASN c0 23 ASN C 186 GLN C 422 GLN C 425 HIS A 186 GLN A 322 GLN A 422 GLN A 425 HIS A 467 ASN B 186 GLN B 215 HIS B 425 HIS F 169 GLN F 179 HIS F 217 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 330 ASN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 28 ASN E 34 HIS E 289 GLN E 324 HIS G 55 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123439 restraints weight = 39607.913| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.65 r_work: 0.3044 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 35394 Z= 0.166 Angle : 0.696 14.356 48101 Z= 0.354 Chirality : 0.046 0.211 5774 Planarity : 0.006 0.109 6223 Dihedral : 6.059 86.256 5090 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.52 % Allowed : 10.18 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4646 helix: 0.09 (0.10), residues: 2507 sheet: -1.35 (0.21), residues: 539 loop : -1.50 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGc3 36 TYR 0.044 0.002 TYRc9 69 PHE 0.039 0.002 PHE a 87 TRP 0.030 0.003 TRP a 206 HIS 0.009 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (35388) covalent geometry : angle 0.69633 / 0.35 (48101) hydrogen bonds : bond 0.05154 / 3.68 ( 2195) hydrogen bonds : angle 5.02426 / 3.70 ( 6444) Misc. bond : bond 0.00324 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 527 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 15 LEU cc_start: 0.7828 (tp) cc_final: 0.7557 (pp) REVERT: a 91 MET cc_start: 0.7316 (mtm) cc_final: 0.6861 (mtm) REVERT: a 122 MET cc_start: 0.8422 (tmm) cc_final: 0.7803 (tmm) REVERT: a 223 MET cc_start: 0.9214 (tmm) cc_final: 0.8651 (tmm) REVERT: a 226 MET cc_start: 0.9291 (mmm) cc_final: 0.8232 (tpt) REVERT: C 166 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8912 (tp) REVERT: C 402 LEU cc_start: 0.6547 (mp) cc_final: 0.6137 (tp) REVERT: C 458 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7982 (tttm) REVERT: C 462 LEU cc_start: 0.8166 (mm) cc_final: 0.7962 (mt) REVERT: C 489 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8071 (mmtm) REVERT: A 15 GLN cc_start: 0.8106 (mt0) cc_final: 0.7880 (mt0) REVERT: A 54 GLU cc_start: 0.8741 (tt0) cc_final: 0.8497 (tt0) REVERT: A 83 LYS cc_start: 0.8722 (mttm) cc_final: 0.8449 (mttp) REVERT: A 125 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 273 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9167 (tm) REVERT: A 326 ILE cc_start: 0.9073 (tt) cc_final: 0.8779 (tt) REVERT: A 393 GLU cc_start: 0.6881 (pp20) cc_final: 0.6660 (pp20) REVERT: A 463 PHE cc_start: 0.8555 (t80) cc_final: 0.8346 (t80) REVERT: B 60 MET cc_start: 0.9179 (mmt) cc_final: 0.8640 (mmt) REVERT: B 289 ASP cc_start: 0.8980 (p0) cc_final: 0.8682 (p0) REVERT: F 17 LYS cc_start: 0.8751 (tttt) cc_final: 0.8358 (ttmt) REVERT: F 42 VAL cc_start: 0.8247 (t) cc_final: 0.7861 (m) REVERT: F 77 ILE cc_start: 0.8936 (mt) cc_final: 0.8684 (mp) REVERT: F 273 SER cc_start: 0.8943 (t) cc_final: 0.8643 (t) REVERT: F 375 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8260 (tp40) REVERT: F 381 GLN cc_start: 0.8371 (tt0) cc_final: 0.7855 (tp40) REVERT: D 10 MET cc_start: 0.8658 (mtp) cc_final: 0.8379 (mtm) REVERT: D 44 ILE cc_start: 0.8298 (mt) cc_final: 0.8067 (tp) REVERT: D 62 ILE cc_start: 0.9004 (tp) cc_final: 0.8746 (pt) REVERT: D 143 ASP cc_start: 0.8547 (m-30) cc_final: 0.8142 (m-30) REVERT: D 144 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8389 (tm) REVERT: D 168 ILE cc_start: 0.8807 (mt) cc_final: 0.8596 (mm) REVERT: D 364 TYR cc_start: 0.8940 (t80) cc_final: 0.8731 (t80) REVERT: D 378 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8325 (tppt) REVERT: D 420 PHE cc_start: 0.8995 (m-10) cc_final: 0.8701 (m-10) REVERT: E 39 GLU cc_start: 0.8305 (pm20) cc_final: 0.8023 (pm20) REVERT: E 454 ARG cc_start: 0.9077 (mtt-85) cc_final: 0.8693 (mtt-85) REVERT: G 84 ASP cc_start: 0.8510 (t0) cc_final: 0.8277 (t0) REVERT: G 127 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.7495 (mtt-85) REVERT: G 204 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 4 ILE cc_start: 0.5740 (OUTLIER) cc_final: 0.5120 (pp) REVERT: H 35 LEU cc_start: 0.8638 (mm) cc_final: 0.8423 (mm) REVERT: H 112 ASP cc_start: 0.8166 (m-30) cc_final: 0.7785 (m-30) REVERT: H 126 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7315 (mtm-85) REVERT: I 88 LEU cc_start: 0.7310 (tt) cc_final: 0.7022 (mm) REVERT: I 110 VAL cc_start: 0.7970 (t) cc_final: 0.7512 (p) REVERT: I 175 GLN cc_start: 0.8061 (tt0) cc_final: 0.7717 (tt0) outliers start: 87 outliers final: 30 residues processed: 588 average time/residue: 0.1975 time to fit residues: 193.2021 Evaluate side-chains 492 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 458 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [413, 433, 239, 120, 461, 198, 441, 385, 269, 330, 350] chunk 413 optimal weight: 4.9990 chunk 433 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 461 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 441 optimal weight: 9.9990 chunk 385 optimal weight: 0.6980 chunk 269 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS B 488 ASN F 33 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS G 174 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120432 restraints weight = 39629.902| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.66 r_work: 0.2997 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 35394 Z= 0.192 Angle : 0.697 17.580 48101 Z= 0.345 Chirality : 0.048 0.374 5774 Planarity : 0.005 0.092 6223 Dihedral : 5.737 85.370 5081 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 3.28 % Allowed : 11.45 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.12), residues: 4646 helix: 0.71 (0.10), residues: 2520 sheet: -1.18 (0.20), residues: 551 loop : -1.31 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 154 TYR 0.029 0.002 TYRc9 69 PHE 0.028 0.002 PHE a 87 TRP 0.031 0.003 TRP a 206 HIS 0.009 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (35388) covalent geometry : angle 0.69696 / 0.35 (48101) hydrogen bonds : bond 0.04761 / 3.39 ( 2195) hydrogen bonds : angle 4.71311 / 3.47 ( 6444) Misc. bond : bond 0.00392 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 478 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 122 MET cc_start: 0.8470 (tmm) cc_final: 0.7987 (tmm) REVERT: a 223 MET cc_start: 0.9213 (tmm) cc_final: 0.8687 (tmm) REVERT: a 225 THR cc_start: 0.8869 (m) cc_final: 0.8444 (m) REVERT: a 226 MET cc_start: 0.9325 (mmm) cc_final: 0.8186 (tpt) REVERT: C 402 LEU cc_start: 0.6524 (mp) cc_final: 0.6123 (tp) REVERT: C 407 GLN cc_start: 0.7412 (mt0) cc_final: 0.7184 (mt0) REVERT: C 458 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7872 (tttm) REVERT: A 83 LYS cc_start: 0.8763 (mttm) cc_final: 0.8508 (mttp) REVERT: A 125 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 326 ILE cc_start: 0.9126 (tt) cc_final: 0.8836 (tt) REVERT: A 393 GLU cc_start: 0.7312 (pp20) cc_final: 0.7110 (pp20) REVERT: B 60 MET cc_start: 0.9219 (mmt) cc_final: 0.8926 (mmt) REVERT: B 289 ASP cc_start: 0.8979 (p0) cc_final: 0.8686 (p0) REVERT: B 489 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8215 (ttmm) REVERT: F 17 LYS cc_start: 0.8833 (tttt) cc_final: 0.8424 (ttmt) REVERT: F 77 ILE cc_start: 0.9016 (mt) cc_final: 0.8751 (mp) REVERT: F 273 SER cc_start: 0.8985 (t) cc_final: 0.8605 (t) REVERT: F 381 GLN cc_start: 0.8409 (tt0) cc_final: 0.7867 (tp40) REVERT: D 10 MET cc_start: 0.8702 (mtp) cc_final: 0.8401 (mtm) REVERT: D 44 ILE cc_start: 0.8367 (mt) cc_final: 0.8166 (tp) REVERT: D 144 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (tm) REVERT: D 168 ILE cc_start: 0.8831 (mt) cc_final: 0.8625 (mm) REVERT: D 378 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8345 (tppt) REVERT: D 420 PHE cc_start: 0.9016 (m-10) cc_final: 0.8732 (m-10) REVERT: E 39 GLU cc_start: 0.8287 (pm20) cc_final: 0.8014 (pm20) REVERT: E 170 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: E 177 GLN cc_start: 0.8269 (mt0) cc_final: 0.7715 (mp10) REVERT: E 233 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (tp) REVERT: G 22 LYS cc_start: 0.8457 (tttp) cc_final: 0.8148 (tppt) REVERT: G 127 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.7486 (mtt-85) REVERT: G 204 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7407 (tm-30) REVERT: H 4 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5235 (pp) REVERT: H 35 LEU cc_start: 0.8689 (mm) cc_final: 0.8388 (mm) REVERT: H 112 ASP cc_start: 0.8206 (m-30) cc_final: 0.7841 (m-30) REVERT: I 88 LEU cc_start: 0.7520 (tt) cc_final: 0.7263 (mm) REVERT: I 97 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8350 (mm) REVERT: I 175 GLN cc_start: 0.8077 (tt0) cc_final: 0.7714 (tt0) outliers start: 113 outliers final: 60 residues processed: 555 average time/residue: 0.2015 time to fit residues: 185.3915 Evaluate side-chains 506 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 441 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c0 residue 58 LEU Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [157, 370, 80, 304, 116, 198, 390, 246, 60, 45, 236] chunk 157 optimal weight: 6.9990 chunk 370 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 390 optimal weight: 0.6980 chunk 246 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.180942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119083 restraints weight = 39588.962| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.89 r_work: 0.3008 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35394 Z= 0.169 Angle : 0.683 18.267 48101 Z= 0.332 Chirality : 0.047 0.293 5774 Planarity : 0.005 0.080 6223 Dihedral : 5.541 84.708 5081 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 3.48 % Allowed : 12.70 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4646 helix: 1.04 (0.10), residues: 2516 sheet: -1.12 (0.20), residues: 563 loop : -1.11 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.022 0.001 TYRc9 69 PHE 0.025 0.001 PHE a 87 TRP 0.026 0.002 TRP a 206 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (35388) covalent geometry : angle 0.68303 / 0.33 (48101) hydrogen bonds : bond 0.04464 / 3.18 ( 2195) hydrogen bonds : angle 4.55644 / 3.35 ( 6444) Misc. bond : bond 0.00346 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 462 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 15 LEU cc_start: 0.7530 (tp) cc_final: 0.7264 (pp) REVERT: a 122 MET cc_start: 0.8456 (tmm) cc_final: 0.8065 (tmm) REVERT: a 223 MET cc_start: 0.9182 (tmm) cc_final: 0.8636 (tmm) REVERT: a 225 THR cc_start: 0.8956 (m) cc_final: 0.8541 (m) REVERT: a 226 MET cc_start: 0.9298 (mmm) cc_final: 0.8174 (tpt) REVERT: C 129 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.7851 (mt) REVERT: C 130 GLU cc_start: 0.8282 (tp30) cc_final: 0.7961 (tp30) REVERT: C 402 LEU cc_start: 0.6517 (mp) cc_final: 0.6100 (tp) REVERT: C 407 GLN cc_start: 0.7143 (mt0) cc_final: 0.6924 (mt0) REVERT: C 458 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7852 (tttm) REVERT: A 15 GLN cc_start: 0.8145 (mt0) cc_final: 0.7813 (mt0) REVERT: A 83 LYS cc_start: 0.8699 (mttm) cc_final: 0.8436 (mttp) REVERT: A 125 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 326 ILE cc_start: 0.9141 (tt) cc_final: 0.8857 (tt) REVERT: B 47 VAL cc_start: 0.9091 (t) cc_final: 0.8843 (p) REVERT: B 60 MET cc_start: 0.9193 (mmt) cc_final: 0.8903 (mmt) REVERT: B 289 ASP cc_start: 0.8958 (p0) cc_final: 0.8675 (p0) REVERT: B 489 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8190 (ttmm) REVERT: F 17 LYS cc_start: 0.8824 (tttt) cc_final: 0.8415 (ttmt) REVERT: F 42 VAL cc_start: 0.8289 (t) cc_final: 0.7990 (m) REVERT: F 77 ILE cc_start: 0.8986 (mt) cc_final: 0.8738 (mp) REVERT: F 365 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6180 (mp-120) REVERT: F 381 GLN cc_start: 0.8348 (tt0) cc_final: 0.7829 (tp40) REVERT: D 10 MET cc_start: 0.8678 (mtp) cc_final: 0.8348 (mtm) REVERT: D 378 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8360 (tppt) REVERT: D 420 PHE cc_start: 0.9025 (m-10) cc_final: 0.8763 (m-10) REVERT: E 3 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.7957 (mtt-85) REVERT: E 39 GLU cc_start: 0.8253 (pm20) cc_final: 0.7997 (pm20) REVERT: E 177 GLN cc_start: 0.8316 (mt0) cc_final: 0.7757 (mp10) REVERT: E 233 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8525 (tp) REVERT: G 22 LYS cc_start: 0.8438 (tttp) cc_final: 0.8119 (tppt) REVERT: G 84 ASP cc_start: 0.8854 (t0) cc_final: 0.8369 (t0) REVERT: G 120 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7831 (mtm110) REVERT: G 127 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7658 (ttm-80) REVERT: G 204 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7324 (tm-30) REVERT: H 4 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5229 (pp) REVERT: H 35 LEU cc_start: 0.8743 (mm) cc_final: 0.8434 (mm) REVERT: H 112 ASP cc_start: 0.8184 (m-30) cc_final: 0.7801 (m-30) REVERT: I 3 GLN cc_start: 0.6762 (tm-30) cc_final: 0.6465 (tm-30) REVERT: I 16 GLN cc_start: 0.8351 (mt0) cc_final: 0.8064 (mt0) REVERT: I 88 LEU cc_start: 0.7358 (tt) cc_final: 0.6902 (mm) REVERT: I 97 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8368 (mm) REVERT: I 175 GLN cc_start: 0.8104 (tt0) cc_final: 0.7735 (tt0) outliers start: 120 outliers final: 80 residues processed: 550 average time/residue: 0.1950 time to fit residues: 180.2643 Evaluate side-chains 520 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 435 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 36 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c7 residue 5 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [432, 40, 384, 454, 399, 341, 457, 216, 92, 50, 104] chunk 432 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 384 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 399 optimal weight: 0.9990 chunk 341 optimal weight: 0.6980 chunk 457 optimal weight: 0.0470 chunk 216 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b2 31 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 358 ASN A 163 GLN A 422 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120224 restraints weight = 39621.277| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.96 r_work: 0.2994 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35394 Z= 0.165 Angle : 0.663 15.226 48101 Z= 0.324 Chirality : 0.046 0.330 5774 Planarity : 0.005 0.078 6223 Dihedral : 5.398 83.437 5081 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 3.36 % Allowed : 13.77 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4646 helix: 1.26 (0.10), residues: 2519 sheet: -1.01 (0.21), residues: 554 loop : -1.00 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 93 TYR 0.021 0.001 TYR C 438 PHE 0.021 0.001 PHE a 87 TRP 0.026 0.002 TRP a 206 HIS 0.007 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (35388) covalent geometry : angle 0.66280 / 0.32 (48101) hydrogen bonds : bond 0.04287 / 3.05 ( 2195) hydrogen bonds : angle 4.43652 / 3.26 ( 6444) Misc. bond : bond 0.00325 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 468 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 15 LEU cc_start: 0.7582 (tp) cc_final: 0.7337 (pp) REVERT: a 122 MET cc_start: 0.8416 (tmm) cc_final: 0.8143 (tmm) REVERT: a 223 MET cc_start: 0.9173 (tmm) cc_final: 0.8689 (tmm) REVERT: a 225 THR cc_start: 0.8932 (m) cc_final: 0.8413 (m) REVERT: a 226 MET cc_start: 0.9247 (mmm) cc_final: 0.7950 (tpt) REVERT: C 129 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 130 GLU cc_start: 0.8355 (tp30) cc_final: 0.8139 (tp30) REVERT: C 385 ASP cc_start: 0.7909 (m-30) cc_final: 0.7702 (m-30) REVERT: C 402 LEU cc_start: 0.6449 (mp) cc_final: 0.6001 (tp) REVERT: C 407 GLN cc_start: 0.6931 (mt0) cc_final: 0.6693 (mt0) REVERT: C 458 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7856 (tttm) REVERT: A 15 GLN cc_start: 0.8136 (mt0) cc_final: 0.7722 (mt0) REVERT: A 125 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 326 ILE cc_start: 0.9160 (tt) cc_final: 0.8873 (tt) REVERT: A 393 GLU cc_start: 0.7371 (pp20) cc_final: 0.7094 (pp20) REVERT: B 289 ASP cc_start: 0.8976 (p0) cc_final: 0.8702 (p0) REVERT: B 489 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8176 (ttmm) REVERT: F 17 LYS cc_start: 0.8858 (tttt) cc_final: 0.8453 (ttmt) REVERT: F 42 VAL cc_start: 0.8595 (t) cc_final: 0.8114 (m) REVERT: F 77 ILE cc_start: 0.9000 (mt) cc_final: 0.8748 (mp) REVERT: F 365 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6304 (mp-120) REVERT: F 381 GLN cc_start: 0.8320 (tt0) cc_final: 0.7771 (tp40) REVERT: D 10 MET cc_start: 0.8734 (mtp) cc_final: 0.8384 (mtm) REVERT: D 378 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8317 (tppt) REVERT: D 420 PHE cc_start: 0.9033 (m-10) cc_final: 0.8780 (m-10) REVERT: E 39 GLU cc_start: 0.8246 (pm20) cc_final: 0.7985 (pm20) REVERT: E 170 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: E 177 GLN cc_start: 0.8395 (mt0) cc_final: 0.7851 (mp10) REVERT: E 233 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8535 (tp) REVERT: G 22 LYS cc_start: 0.8443 (tttp) cc_final: 0.8117 (tppt) REVERT: G 84 ASP cc_start: 0.8842 (t0) cc_final: 0.8408 (t0) REVERT: G 120 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: G 127 ARG cc_start: 0.8298 (mtp-110) cc_final: 0.7430 (mtt-85) REVERT: G 204 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7271 (tm-30) REVERT: H 4 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5363 (pp) REVERT: H 35 LEU cc_start: 0.8731 (mm) cc_final: 0.8453 (mm) REVERT: H 112 ASP cc_start: 0.8173 (m-30) cc_final: 0.7791 (m-30) REVERT: I 16 GLN cc_start: 0.8320 (mt0) cc_final: 0.8003 (mt0) REVERT: I 74 GLN cc_start: 0.8538 (mm110) cc_final: 0.8210 (mm-40) REVERT: I 88 LEU cc_start: 0.7372 (tt) cc_final: 0.7073 (mm) REVERT: I 97 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8341 (mm) REVERT: I 175 GLN cc_start: 0.8106 (tt0) cc_final: 0.7709 (tt0) outliers start: 116 outliers final: 80 residues processed: 550 average time/residue: 0.2005 time to fit residues: 183.6005 Evaluate side-chains 524 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 438 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c7 residue 5 VAL Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [156, 171, 305, 411, 337, 89, 270, 381, 340, 345, 108] chunk 156 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 305 optimal weight: 0.5980 chunk 411 optimal weight: 2.9990 chunk 337 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 381 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 chunk 345 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.181927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120766 restraints weight = 39540.609| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.89 r_work: 0.3021 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35394 Z= 0.141 Angle : 0.658 16.749 48101 Z= 0.317 Chirality : 0.046 0.307 5774 Planarity : 0.005 0.077 6223 Dihedral : 5.270 83.529 5080 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 3.19 % Allowed : 14.21 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 4646 helix: 1.42 (0.10), residues: 2521 sheet: -0.92 (0.21), residues: 539 loop : -0.90 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 104 TYR 0.030 0.001 TYRb2 13 PHE 0.019 0.001 PHE a 87 TRP 0.024 0.002 TRP a 206 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (35388) covalent geometry : angle 0.65787 / 0.32 (48101) hydrogen bonds : bond 0.04115 / 2.92 ( 2195) hydrogen bonds : angle 4.37277 / 3.22 ( 6444) Misc. bond : bond 0.00171 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 466 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 14 GLN cc_start: 0.2885 (mm-40) cc_final: 0.2637 (mm-40) REVERT: b2 15 LEU cc_start: 0.7640 (tp) cc_final: 0.7365 (pp) REVERT: b2 31 GLN cc_start: 0.8147 (mm110) cc_final: 0.7889 (mp10) REVERT: a 91 MET cc_start: 0.7215 (mtp) cc_final: 0.6643 (mtm) REVERT: a 122 MET cc_start: 0.8425 (tmm) cc_final: 0.8111 (tmm) REVERT: a 223 MET cc_start: 0.9084 (tmm) cc_final: 0.8650 (tmm) REVERT: C 129 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.7852 (mt) REVERT: C 130 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (tp30) REVERT: C 236 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8696 (t80) REVERT: C 339 ASP cc_start: 0.8717 (m-30) cc_final: 0.8504 (m-30) REVERT: C 385 ASP cc_start: 0.7833 (m-30) cc_final: 0.7624 (m-30) REVERT: C 402 LEU cc_start: 0.6464 (mp) cc_final: 0.6002 (tp) REVERT: C 407 GLN cc_start: 0.6975 (mt0) cc_final: 0.6734 (mt0) REVERT: A 15 GLN cc_start: 0.8237 (mt0) cc_final: 0.7772 (mt0) REVERT: A 125 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 326 ILE cc_start: 0.9169 (tt) cc_final: 0.8906 (tt) REVERT: B 289 ASP cc_start: 0.8942 (p0) cc_final: 0.8680 (p0) REVERT: B 489 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8157 (ttmm) REVERT: F 17 LYS cc_start: 0.8792 (tttt) cc_final: 0.8384 (ttmt) REVERT: F 42 VAL cc_start: 0.8561 (t) cc_final: 0.8111 (m) REVERT: F 77 ILE cc_start: 0.9007 (mt) cc_final: 0.8758 (mp) REVERT: F 365 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6340 (mp-120) REVERT: F 375 GLN cc_start: 0.8691 (tp40) cc_final: 0.8481 (tp40) REVERT: F 381 GLN cc_start: 0.8335 (tt0) cc_final: 0.7771 (tp40) REVERT: D 10 MET cc_start: 0.8672 (mtp) cc_final: 0.8319 (mtm) REVERT: D 378 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8296 (tppt) REVERT: D 420 PHE cc_start: 0.9000 (m-10) cc_final: 0.8751 (m-10) REVERT: E 39 GLU cc_start: 0.8225 (pm20) cc_final: 0.7946 (pm20) REVERT: E 170 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: E 177 GLN cc_start: 0.8374 (mt0) cc_final: 0.7812 (mp10) REVERT: E 233 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8530 (tp) REVERT: G 22 LYS cc_start: 0.8430 (tttp) cc_final: 0.8113 (tppt) REVERT: G 40 LYS cc_start: 0.8489 (ttpp) cc_final: 0.7916 (tmmt) REVERT: G 84 ASP cc_start: 0.8872 (t0) cc_final: 0.8379 (t0) REVERT: G 120 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: G 127 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7590 (ttm-80) REVERT: G 204 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7244 (tm-30) REVERT: H 4 ILE cc_start: 0.6011 (OUTLIER) cc_final: 0.5459 (pp) REVERT: H 32 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7438 (tt) REVERT: H 35 LEU cc_start: 0.8687 (mm) cc_final: 0.8447 (mm) REVERT: H 112 ASP cc_start: 0.8172 (m-30) cc_final: 0.7796 (m-30) REVERT: I 16 GLN cc_start: 0.8330 (mt0) cc_final: 0.8001 (mt0) REVERT: I 74 GLN cc_start: 0.8554 (mm110) cc_final: 0.8226 (mm-40) REVERT: I 88 LEU cc_start: 0.7384 (tt) cc_final: 0.7035 (mm) REVERT: I 97 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8361 (mm) REVERT: I 175 GLN cc_start: 0.8122 (tt0) cc_final: 0.7695 (tt0) outliers start: 110 outliers final: 72 residues processed: 542 average time/residue: 0.2010 time to fit residues: 181.9144 Evaluate side-chains 524 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 444 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c7 residue 5 VAL Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [279, 35, 93, 38, 366, 288, 431, 79, 284, 42, 157] chunk 279 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 288 optimal weight: 0.7980 chunk 431 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 284 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 157 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN F 304 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 365 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.182160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121607 restraints weight = 39468.953| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.06 r_work: 0.3019 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35394 Z= 0.138 Angle : 0.653 15.534 48101 Z= 0.315 Chirality : 0.046 0.349 5774 Planarity : 0.005 0.076 6223 Dihedral : 5.138 83.855 5078 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 3.02 % Allowed : 15.08 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4646 helix: 1.56 (0.10), residues: 2505 sheet: -0.91 (0.21), residues: 531 loop : -0.90 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.025 0.001 TYR C 438 PHE 0.026 0.001 PHE a 160 TRP 0.024 0.002 TRP a 206 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (35388) covalent geometry : angle 0.65290 / 0.32 (48101) hydrogen bonds : bond 0.04038 / 2.87 ( 2195) hydrogen bonds : angle 4.31567 / 3.18 ( 6444) Misc. bond : bond 0.00291 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 461 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 17 MET cc_start: 0.4004 (ppp) cc_final: 0.3665 (ppp) REVERT: a 91 MET cc_start: 0.7294 (mtp) cc_final: 0.6726 (mtm) REVERT: a 122 MET cc_start: 0.8419 (tmm) cc_final: 0.8073 (tmm) REVERT: a 223 MET cc_start: 0.9077 (tmm) cc_final: 0.8662 (tmm) REVERT: a 226 MET cc_start: 0.9091 (mmm) cc_final: 0.7997 (tpt) REVERT: c1 48 MET cc_start: 0.8935 (ttp) cc_final: 0.8591 (ptt) REVERT: C 129 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.7860 (mt) REVERT: C 130 GLU cc_start: 0.8236 (tp30) cc_final: 0.7993 (tp30) REVERT: C 339 ASP cc_start: 0.8710 (m-30) cc_final: 0.8474 (m-30) REVERT: C 354 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8284 (mtt90) REVERT: C 385 ASP cc_start: 0.7812 (m-30) cc_final: 0.7534 (m-30) REVERT: C 402 LEU cc_start: 0.6399 (mp) cc_final: 0.6166 (tp) REVERT: A 15 GLN cc_start: 0.8276 (mt0) cc_final: 0.7741 (mt0) REVERT: A 250 MET cc_start: 0.9121 (ttp) cc_final: 0.8862 (ttt) REVERT: A 326 ILE cc_start: 0.9175 (tt) cc_final: 0.8905 (tt) REVERT: A 393 GLU cc_start: 0.7441 (pp20) cc_final: 0.7141 (pp20) REVERT: B 60 MET cc_start: 0.9139 (mmt) cc_final: 0.8836 (mmt) REVERT: B 289 ASP cc_start: 0.8927 (p0) cc_final: 0.8662 (p0) REVERT: B 489 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8098 (ttmm) REVERT: F 17 LYS cc_start: 0.8789 (tttt) cc_final: 0.8381 (ttmt) REVERT: F 77 ILE cc_start: 0.8964 (mt) cc_final: 0.8716 (mp) REVERT: F 381 GLN cc_start: 0.8326 (tt0) cc_final: 0.7731 (tp40) REVERT: D 10 MET cc_start: 0.8683 (mtp) cc_final: 0.8328 (mtm) REVERT: D 378 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8270 (tppt) REVERT: E 39 GLU cc_start: 0.8225 (pm20) cc_final: 0.7939 (pm20) REVERT: E 170 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: E 177 GLN cc_start: 0.8398 (mt0) cc_final: 0.7826 (mp10) REVERT: G 40 LYS cc_start: 0.8484 (ttpp) cc_final: 0.7897 (tmmt) REVERT: G 84 ASP cc_start: 0.8873 (t0) cc_final: 0.8269 (t0) REVERT: G 107 HIS cc_start: 0.8119 (m-70) cc_final: 0.7315 (m-70) REVERT: G 120 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: G 127 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7601 (ttm-80) REVERT: G 204 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7173 (tm-30) REVERT: H 4 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5710 (pp) REVERT: H 32 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7489 (tt) REVERT: H 35 LEU cc_start: 0.8752 (mm) cc_final: 0.8517 (mm) REVERT: H 112 ASP cc_start: 0.8128 (m-30) cc_final: 0.7735 (m-30) REVERT: I 16 GLN cc_start: 0.8310 (mt0) cc_final: 0.7950 (mt0) REVERT: I 88 LEU cc_start: 0.7361 (tt) cc_final: 0.7138 (mm) REVERT: I 97 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (mm) REVERT: I 175 GLN cc_start: 0.8123 (tt0) cc_final: 0.7689 (tt0) outliers start: 104 outliers final: 76 residues processed: 532 average time/residue: 0.2011 time to fit residues: 178.2919 Evaluate side-chains 527 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 446 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [36, 234, 365, 405, 290, 95, 422, 201, 200, 311, 319] chunk 36 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 365 optimal weight: 0.4980 chunk 405 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 422 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 200 optimal weight: 0.1980 chunk 311 optimal weight: 0.1980 chunk 319 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 345 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124121 restraints weight = 39533.977| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.56 r_work: 0.3055 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35394 Z= 0.125 Angle : 0.651 16.387 48101 Z= 0.312 Chirality : 0.045 0.359 5774 Planarity : 0.004 0.075 6223 Dihedral : 5.024 85.294 5077 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 2.52 % Allowed : 15.60 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4646 helix: 1.70 (0.10), residues: 2494 sheet: -0.83 (0.21), residues: 526 loop : -0.84 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 454 TYR 0.025 0.001 TYR C 438 PHE 0.018 0.001 PHE a 87 TRP 0.025 0.002 TRP a 206 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (35388) covalent geometry : angle 0.65063 / 0.31 (48101) hydrogen bonds : bond 0.03881 / 2.75 ( 2195) hydrogen bonds : angle 4.25020 / 3.13 ( 6444) Misc. bond : bond 0.00254 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 482 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 15 LEU cc_start: 0.7680 (tp) cc_final: 0.7404 (pp) REVERT: b2 27 LYS cc_start: 0.6186 (mmtm) cc_final: 0.5448 (mmtp) REVERT: b2 31 GLN cc_start: 0.8273 (mm110) cc_final: 0.7939 (mp10) REVERT: a 91 MET cc_start: 0.7296 (mtp) cc_final: 0.6726 (mtm) REVERT: a 122 MET cc_start: 0.8374 (tmm) cc_final: 0.8049 (tmm) REVERT: a 223 MET cc_start: 0.9077 (tmm) cc_final: 0.8586 (tmm) REVERT: a 226 MET cc_start: 0.9143 (mmm) cc_final: 0.7929 (tpt) REVERT: c4 32 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7586 (pp20) REVERT: c1 48 MET cc_start: 0.8971 (ttp) cc_final: 0.8623 (ptt) REVERT: C 129 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.7866 (mt) REVERT: C 130 GLU cc_start: 0.8193 (tp30) cc_final: 0.7971 (tp30) REVERT: C 354 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8214 (mtt90) REVERT: C 385 ASP cc_start: 0.7907 (m-30) cc_final: 0.7647 (m-30) REVERT: C 402 LEU cc_start: 0.6496 (mp) cc_final: 0.6270 (tp) REVERT: C 489 LYS cc_start: 0.8349 (mttp) cc_final: 0.8129 (mttp) REVERT: A 15 GLN cc_start: 0.8272 (mt0) cc_final: 0.7749 (mt0) REVERT: A 250 MET cc_start: 0.9117 (ttp) cc_final: 0.8869 (ttt) REVERT: A 326 ILE cc_start: 0.9172 (tt) cc_final: 0.8892 (tt) REVERT: A 393 GLU cc_start: 0.7504 (pp20) cc_final: 0.7206 (pp20) REVERT: B 60 MET cc_start: 0.9117 (mmt) cc_final: 0.8835 (mmt) REVERT: B 289 ASP cc_start: 0.8898 (p0) cc_final: 0.8633 (p0) REVERT: F 17 LYS cc_start: 0.8784 (tttt) cc_final: 0.8572 (tttm) REVERT: F 77 ILE cc_start: 0.8907 (mt) cc_final: 0.8666 (mp) REVERT: F 375 GLN cc_start: 0.8675 (tp40) cc_final: 0.8439 (tp40) REVERT: F 381 GLN cc_start: 0.8309 (tt0) cc_final: 0.7691 (tp40) REVERT: D 10 MET cc_start: 0.8623 (mtp) cc_final: 0.8283 (mtm) REVERT: D 378 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8253 (tppt) REVERT: E 39 GLU cc_start: 0.8227 (pm20) cc_final: 0.7946 (pm20) REVERT: E 170 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: E 177 GLN cc_start: 0.8355 (mt0) cc_final: 0.7763 (mp10) REVERT: G 40 LYS cc_start: 0.8501 (ttpp) cc_final: 0.7928 (tmmt) REVERT: G 84 ASP cc_start: 0.8873 (t0) cc_final: 0.8526 (t0) REVERT: G 107 HIS cc_start: 0.8157 (m-70) cc_final: 0.7325 (m-70) REVERT: G 127 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7588 (ttm-80) REVERT: G 204 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7100 (tm-30) REVERT: H 4 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6033 (pp) REVERT: H 32 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7300 (tt) REVERT: H 35 LEU cc_start: 0.8699 (mm) cc_final: 0.8480 (mm) REVERT: H 112 ASP cc_start: 0.8103 (m-30) cc_final: 0.7696 (m-30) REVERT: I 16 GLN cc_start: 0.8316 (mt0) cc_final: 0.7948 (mt0) REVERT: I 74 GLN cc_start: 0.8529 (mm110) cc_final: 0.8260 (mm-40) REVERT: I 88 LEU cc_start: 0.7138 (tt) cc_final: 0.6898 (mm) REVERT: I 97 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8298 (mm) REVERT: I 175 GLN cc_start: 0.8078 (tt0) cc_final: 0.7650 (tt0) outliers start: 87 outliers final: 67 residues processed: 540 average time/residue: 0.2057 time to fit residues: 184.0943 Evaluate side-chains 527 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 454 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [14, 9, 440, 414, 6, 331, 388, 179, 128, 159, 117] chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 50.0000 chunk 440 optimal weight: 4.9990 chunk 414 optimal weight: 0.7980 chunk 6 optimal weight: 50.0000 chunk 331 optimal weight: 0.5980 chunk 388 optimal weight: 0.6980 chunk 179 optimal weight: 0.0570 chunk 128 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.185127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128008 restraints weight = 39053.333| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.21 r_work: 0.3106 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35394 Z= 0.133 Angle : 0.652 16.569 48101 Z= 0.312 Chirality : 0.046 0.382 5774 Planarity : 0.004 0.075 6223 Dihedral : 4.988 85.708 5077 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.46 % Allowed : 16.12 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.12), residues: 4646 helix: 1.79 (0.10), residues: 2486 sheet: -0.74 (0.21), residues: 540 loop : -0.81 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.024 0.001 TYR C 438 PHE 0.017 0.001 PHE a 221 TRP 0.025 0.002 TRP a 206 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (35388) covalent geometry : angle 0.65218 / 0.31 (48101) hydrogen bonds : bond 0.03880 / 2.76 ( 2195) hydrogen bonds : angle 4.21355 / 3.10 ( 6444) Misc. bond : bond 0.00236 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 464 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 15 LEU cc_start: 0.7710 (tp) cc_final: 0.7425 (pp) REVERT: b2 17 MET cc_start: 0.3645 (ppp) cc_final: 0.3387 (ppp) REVERT: b2 27 LYS cc_start: 0.6110 (mmtm) cc_final: 0.5473 (mmtp) REVERT: b2 31 GLN cc_start: 0.8368 (mm110) cc_final: 0.8042 (mp10) REVERT: a 91 MET cc_start: 0.7276 (mtp) cc_final: 0.6731 (mtm) REVERT: a 122 MET cc_start: 0.8421 (tmm) cc_final: 0.8090 (tmm) REVERT: a 223 MET cc_start: 0.9038 (tmm) cc_final: 0.8551 (tmm) REVERT: a 226 MET cc_start: 0.9231 (mmm) cc_final: 0.8110 (tpt) REVERT: c4 32 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: C 129 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.7887 (mt) REVERT: C 130 GLU cc_start: 0.8256 (tp30) cc_final: 0.8041 (tp30) REVERT: C 354 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8337 (mtt90) REVERT: C 385 ASP cc_start: 0.7983 (m-30) cc_final: 0.7737 (m-30) REVERT: C 402 LEU cc_start: 0.6523 (mp) cc_final: 0.6298 (tp) REVERT: A 15 GLN cc_start: 0.8349 (mt0) cc_final: 0.8121 (mt0) REVERT: A 250 MET cc_start: 0.9099 (ttp) cc_final: 0.8838 (ttt) REVERT: A 326 ILE cc_start: 0.9173 (tt) cc_final: 0.8911 (tt) REVERT: A 393 GLU cc_start: 0.7543 (pp20) cc_final: 0.7260 (pp20) REVERT: B 60 MET cc_start: 0.9179 (mmt) cc_final: 0.8905 (mmt) REVERT: B 95 MET cc_start: 0.9057 (mmm) cc_final: 0.8636 (tpt) REVERT: B 101 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: B 289 ASP cc_start: 0.8883 (p0) cc_final: 0.8626 (p0) REVERT: F 17 LYS cc_start: 0.8858 (tttt) cc_final: 0.8646 (tttm) REVERT: F 77 ILE cc_start: 0.8976 (mt) cc_final: 0.8748 (mp) REVERT: F 381 GLN cc_start: 0.8382 (tt0) cc_final: 0.7838 (tp40) REVERT: F 391 GLU cc_start: 0.8354 (pp20) cc_final: 0.8049 (pp20) REVERT: D 10 MET cc_start: 0.8703 (mtp) cc_final: 0.8390 (mtm) REVERT: D 378 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8301 (tppt) REVERT: E 39 GLU cc_start: 0.8197 (pm20) cc_final: 0.7929 (pm20) REVERT: E 124 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8110 (mmtt) REVERT: E 170 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: G 40 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8021 (tmmt) REVERT: G 84 ASP cc_start: 0.8893 (t0) cc_final: 0.8627 (t0) REVERT: G 107 HIS cc_start: 0.8127 (m-70) cc_final: 0.7440 (m-70) REVERT: G 127 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7642 (ttm-80) REVERT: G 204 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7131 (tm-30) REVERT: H 4 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6130 (pp) REVERT: H 32 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7432 (tt) REVERT: H 112 ASP cc_start: 0.8082 (m-30) cc_final: 0.7684 (m-30) REVERT: I 16 GLN cc_start: 0.8325 (mt0) cc_final: 0.7958 (mt0) REVERT: I 74 GLN cc_start: 0.8525 (mm110) cc_final: 0.8223 (mm-40) REVERT: I 97 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8295 (mm) REVERT: I 175 GLN cc_start: 0.8085 (tt0) cc_final: 0.7647 (tt0) outliers start: 85 outliers final: 67 residues processed: 519 average time/residue: 0.1963 time to fit residues: 170.6632 Evaluate side-chains 520 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 446 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c9 residue 5 VAL Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [304, 72, 250, 178, 0, 10, 188, 395, 295, 449, 323] chunk 304 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 178 optimal weight: 0.0370 chunk 0 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 188 optimal weight: 0.9980 chunk 395 optimal weight: 0.4980 chunk 295 optimal weight: 0.9990 chunk 449 optimal weight: 30.0000 chunk 323 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c6 23 ASN A 163 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130015 restraints weight = 39490.860| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.40 r_work: 0.3106 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35394 Z= 0.126 Angle : 0.664 26.882 48101 Z= 0.313 Chirality : 0.045 0.398 5774 Planarity : 0.004 0.074 6223 Dihedral : 4.946 87.458 5077 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.23 % Allowed : 16.44 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4646 helix: 1.85 (0.10), residues: 2488 sheet: -0.69 (0.21), residues: 540 loop : -0.76 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.024 0.001 TYR C 438 PHE 0.020 0.001 PHE a 221 TRP 0.026 0.002 TRP a 206 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (35388) covalent geometry : angle 0.66357 / 0.31 (48101) hydrogen bonds : bond 0.03803 / 2.70 ( 2195) hydrogen bonds : angle 4.17805 / 3.07 ( 6444) Misc. bond : bond 0.00227 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 475 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 15 LEU cc_start: 0.7644 (tp) cc_final: 0.7398 (pp) REVERT: b2 17 MET cc_start: 0.3434 (ppp) cc_final: 0.3147 (ppp) REVERT: b2 27 LYS cc_start: 0.6084 (mmtm) cc_final: 0.5460 (mmtp) REVERT: b2 31 GLN cc_start: 0.8312 (mm110) cc_final: 0.7972 (mp10) REVERT: a 91 MET cc_start: 0.7401 (mtp) cc_final: 0.6858 (mtm) REVERT: a 122 MET cc_start: 0.8284 (tmm) cc_final: 0.8030 (tmm) REVERT: a 223 MET cc_start: 0.9068 (tmm) cc_final: 0.8598 (tmm) REVERT: a 224 LEU cc_start: 0.9345 (tp) cc_final: 0.9117 (tt) REVERT: a 226 MET cc_start: 0.9279 (mmm) cc_final: 0.8127 (tpt) REVERT: c4 32 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: C 129 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 130 GLU cc_start: 0.8187 (tp30) cc_final: 0.7948 (tp30) REVERT: C 250 MET cc_start: 0.9050 (ttp) cc_final: 0.8829 (ttm) REVERT: C 354 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8341 (mtt90) REVERT: C 385 ASP cc_start: 0.8030 (m-30) cc_final: 0.7769 (m-30) REVERT: C 402 LEU cc_start: 0.6471 (mp) cc_final: 0.6252 (tp) REVERT: C 489 LYS cc_start: 0.8529 (mttp) cc_final: 0.8270 (mttp) REVERT: A 15 GLN cc_start: 0.8340 (mt0) cc_final: 0.8102 (mt0) REVERT: A 250 MET cc_start: 0.9076 (ttp) cc_final: 0.8814 (ttt) REVERT: A 326 ILE cc_start: 0.9186 (tt) cc_final: 0.8915 (tt) REVERT: A 373 LYS cc_start: 0.7947 (tttp) cc_final: 0.7725 (tttm) REVERT: A 393 GLU cc_start: 0.7560 (pp20) cc_final: 0.7269 (pp20) REVERT: B 60 MET cc_start: 0.9167 (mmt) cc_final: 0.8901 (mmt) REVERT: B 101 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: B 289 ASP cc_start: 0.8884 (p0) cc_final: 0.8632 (p0) REVERT: B 401 ASP cc_start: 0.8304 (t70) cc_final: 0.8001 (t70) REVERT: F 17 LYS cc_start: 0.8862 (tttt) cc_final: 0.8659 (tttm) REVERT: F 77 ILE cc_start: 0.8976 (mt) cc_final: 0.8754 (mp) REVERT: F 381 GLN cc_start: 0.8362 (tt0) cc_final: 0.7817 (tp40) REVERT: F 389 MET cc_start: 0.8792 (tpt) cc_final: 0.8540 (tpp) REVERT: D 10 MET cc_start: 0.8716 (mtp) cc_final: 0.8404 (mtm) REVERT: D 378 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8310 (tppt) REVERT: E 39 GLU cc_start: 0.8211 (pm20) cc_final: 0.7946 (pm20) REVERT: E 124 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8103 (mmtt) REVERT: E 170 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: G 40 LYS cc_start: 0.8583 (ttpp) cc_final: 0.7944 (tmmt) REVERT: G 84 ASP cc_start: 0.8898 (t0) cc_final: 0.8688 (t0) REVERT: G 107 HIS cc_start: 0.8223 (m-70) cc_final: 0.7498 (m-70) REVERT: G 127 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7651 (ttm-80) REVERT: G 204 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7053 (tm-30) REVERT: H 4 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6211 (pp) REVERT: H 32 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7490 (tt) REVERT: H 69 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7971 (tm-30) REVERT: H 112 ASP cc_start: 0.8144 (m-30) cc_final: 0.7806 (m-30) REVERT: I 16 GLN cc_start: 0.8381 (mt0) cc_final: 0.8000 (mt0) REVERT: I 74 GLN cc_start: 0.8543 (mm110) cc_final: 0.8238 (mm-40) REVERT: I 88 LEU cc_start: 0.7390 (tt) cc_final: 0.7053 (mm) REVERT: I 97 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8293 (mm) REVERT: I 175 GLN cc_start: 0.8076 (tt0) cc_final: 0.7617 (tt0) outliers start: 77 outliers final: 63 residues processed: 525 average time/residue: 0.2007 time to fit residues: 176.0390 Evaluate side-chains 525 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 455 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 32 GLU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c2 residue 40 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: [339, 441, 294, 444, 307, 191, 141, 113, 254, 53, 354] chunk 339 optimal weight: 1.9990 chunk 441 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 444 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 354 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.187281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127724 restraints weight = 39607.393| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.11 r_work: 0.3094 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 35394 Z= 0.167 Angle : 0.748 59.196 48101 Z= 0.379 Chirality : 0.048 1.026 5774 Planarity : 0.004 0.074 6223 Dihedral : 4.952 87.398 5077 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.20 % Allowed : 16.79 % Favored : 81.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 4646 helix: 1.84 (0.10), residues: 2488 sheet: -0.68 (0.21), residues: 540 loop : -0.75 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.000 ARGb1 40 TYR 0.021 0.001 TYR C 438 PHE 0.018 0.001 PHE a 221 TRP 0.025 0.002 TRP a 206 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (35388) covalent geometry : angle 0.74789 / 0.38 (48101) hydrogen bonds : bond 0.03815 / 2.71 ( 2195) hydrogen bonds : angle 4.17770 / 3.07 ( 6444) Misc. bond : bond 0.00239 / 0.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11109.86 seconds wall clock time: 189 minutes 30.06 seconds (11370.06 seconds total)