Starting phenix.real_space_refine on Fri Feb 6 00:47:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lly_63208/02_2026/9lly_63208.map" } resolution = 3.18 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 13416 2.51 5 N 3501 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21219 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 969 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "I" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 103} Chain: "B" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "E" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 969 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "G" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 103} Chain: "C" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 969 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "O" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 103} Time building chain proxies: 5.63, per 1000 atoms: 0.27 Number of scatterers: 21219 At special positions: 0 Unit cell: (157.3, 157.95, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4191 8.00 N 3501 7.00 C 13416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.16 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.32 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=1.78 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=1.95 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.16 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.32 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=1.78 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " distance=1.95 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.16 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.32 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=1.78 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=1.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5082 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 18.9% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 73 through 97 Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.657A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.681A pdb=" N ILE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 216 through 240 removed outlier: 4.143A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.535A pdb=" N LYS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.672A pdb=" N GLN A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.930A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.789A pdb=" N ASP D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.205A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 removed outlier: 4.277A pdb=" N TYR H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 97 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.658A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.681A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.143A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.535A pdb=" N LYS B 272 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.672A pdb=" N GLN B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.930A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.790A pdb=" N ASP E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 92' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.205A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 114 removed outlier: 4.276A pdb=" N TYR G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 97 Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.658A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 removed outlier: 3.681A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 216 through 240 removed outlier: 4.143A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.535A pdb=" N LYS C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.672A pdb=" N GLN C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.930A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.790A pdb=" N ASP F 91 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR F 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.205A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 4.276A pdb=" N TYR J 113 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.233A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 341 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.233A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 3.591A pdb=" N ALA A 177 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.712A pdb=" N SER A 398 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 434 removed outlier: 3.866A pdb=" N LYS A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 449 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.676A pdb=" N PHE D 80 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 72 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 59 through 61 removed outlier: 5.164A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.590A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.092A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.629A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.522A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.495A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR I 98 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.665A pdb=" N ASP L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.618A pdb=" N VAL L 90 " --> pdb=" O HIS L 43 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.234A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.234A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 180 removed outlier: 3.591A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.711A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AC3, first strand: chain 'B' and resid 431 through 434 removed outlier: 3.866A pdb=" N LYS B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.676A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 72 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.164A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.590A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.092A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.630A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE K 75 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.522A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.494A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU K 33 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR K 98 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.665A pdb=" N ASP N 75 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.618A pdb=" N VAL N 90 " --> pdb=" O HIS N 43 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU N 42 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU N 51 " --> pdb=" O LEU N 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.233A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP C 341 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.233A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.590A pdb=" N ALA C 177 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.712A pdb=" N SER C 398 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AD9, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.866A pdb=" N LYS C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 449 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.676A pdb=" N PHE F 80 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER F 72 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 59 through 61 removed outlier: 5.164A pdb=" N TRP F 49 " --> pdb=" O ARG F 40 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG F 40 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 51 " --> pdb=" O TRP F 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.590A pdb=" N VAL J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.091A pdb=" N ILE J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.630A pdb=" N SER M 7 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE M 75 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.522A pdb=" N LEU M 11 " --> pdb=" O GLU M 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.494A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR M 98 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 6 through 7 removed outlier: 3.665A pdb=" N ASP O 75 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.618A pdb=" N VAL O 90 " --> pdb=" O HIS O 43 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU O 42 " --> pdb=" O LEU O 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU O 51 " --> pdb=" O LEU O 42 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2205 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: 4.43 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6771 1.34 - 1.46: 5107 1.46 - 1.58: 9635 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 21657 Sorted by residual: bond pdb=" C ARG G 76 " pdb=" N TYR G 77 " ideal model delta sigma weight residual 1.333 1.274 0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" C ARG H 76 " pdb=" N TYR H 77 " ideal model delta sigma weight residual 1.333 1.274 0.058 1.28e-02 6.10e+03 2.08e+01 bond pdb=" C ARG J 76 " pdb=" N TYR J 77 " ideal model delta sigma weight residual 1.333 1.274 0.058 1.28e-02 6.10e+03 2.07e+01 bond pdb=" N PRO E 43 " pdb=" CD PRO E 43 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N PRO D 43 " pdb=" CD PRO D 43 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 ... (remaining 21652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 28640 1.28 - 2.56: 598 2.56 - 3.84: 133 3.84 - 5.12: 41 5.12 - 6.40: 9 Bond angle restraints: 29421 Sorted by residual: angle pdb=" O ARG J 76 " pdb=" C ARG J 76 " pdb=" N TYR J 77 " ideal model delta sigma weight residual 122.65 127.37 -4.72 1.23e+00 6.61e-01 1.47e+01 angle pdb=" O ARG H 76 " pdb=" C ARG H 76 " pdb=" N TYR H 77 " ideal model delta sigma weight residual 122.65 127.37 -4.72 1.23e+00 6.61e-01 1.47e+01 angle pdb=" O ARG G 76 " pdb=" C ARG G 76 " pdb=" N TYR G 77 " ideal model delta sigma weight residual 122.65 127.35 -4.70 1.23e+00 6.61e-01 1.46e+01 angle pdb=" CA ARG H 76 " pdb=" C ARG H 76 " pdb=" N TYR H 77 " ideal model delta sigma weight residual 115.35 110.69 4.66 1.42e+00 4.96e-01 1.08e+01 angle pdb=" CA ARG J 76 " pdb=" C ARG J 76 " pdb=" N TYR J 77 " ideal model delta sigma weight residual 115.35 110.69 4.66 1.42e+00 4.96e-01 1.08e+01 ... (remaining 29416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11315 17.90 - 35.80: 1354 35.80 - 53.70: 288 53.70 - 71.59: 51 71.59 - 89.49: 27 Dihedral angle restraints: 13035 sinusoidal: 5097 harmonic: 7938 Sorted by residual: dihedral pdb=" CB CYS C 37 " pdb=" SG CYS C 37 " pdb=" SG CYS C 439 " pdb=" CB CYS C 439 " ideal model delta sinusoidal sigma weight residual 93.00 160.17 -67.17 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS B 37 " pdb=" SG CYS B 37 " pdb=" SG CYS B 439 " pdb=" CB CYS B 439 " ideal model delta sinusoidal sigma weight residual 93.00 160.17 -67.17 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS A 37 " pdb=" SG CYS A 37 " pdb=" SG CYS A 439 " pdb=" CB CYS A 439 " ideal model delta sinusoidal sigma weight residual 93.00 160.17 -67.17 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 13032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1995 0.028 - 0.055: 894 0.055 - 0.083: 211 0.083 - 0.110: 206 0.110 - 0.138: 72 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA GLN O 95 " pdb=" N GLN O 95 " pdb=" C GLN O 95 " pdb=" CB GLN O 95 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA GLN L 95 " pdb=" N GLN L 95 " pdb=" C GLN L 95 " pdb=" CB GLN L 95 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE O 21 " pdb=" N ILE O 21 " pdb=" C ILE O 21 " pdb=" CB ILE O 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 3375 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG N 99 " 0.060 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO N 100 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO N 100 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO N 100 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG O 99 " 0.060 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO O 100 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO O 100 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO O 100 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 99 " 0.060 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO L 100 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO L 100 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 100 " 0.049 5.00e-02 4.00e+02 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5556 2.80 - 3.32: 17909 3.32 - 3.85: 33914 3.85 - 4.37: 41123 4.37 - 4.90: 73128 Nonbonded interactions: 171630 Sorted by model distance: nonbonded pdb=" OH TYR I 36 " pdb=" OE1 GLN I 89 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR M 36 " pdb=" OE1 GLN M 89 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 150 " pdb=" OE1 GLN A 302 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OE1 GLN B 302 " model vdw 2.302 3.040 ... (remaining 171625 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } 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=0.53 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: 8.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.770 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.580 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.005 0.293 21693 Z= 0.277 Angle : 0.608 18.065 29493 Z= 0.320 Chirality : 0.041 0.138 3378 Planarity : 0.005 0.089 3729 Dihedral : 15.881 89.491 7845 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.08 % Allowed : 21.93 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2697 helix: -0.55 (0.26), residues: 399 sheet: -0.97 (0.17), residues: 996 loop : -1.22 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 40 TYR 0.009 0.001 TYR D 55 PHE 0.011 0.001 PHE M 91 TRP 0.008 0.001 TRP E 102 HIS 0.003 0.001 HIS O 98 Details of bonding type rmsd covalent geometry : bond 0.00255 (21657) covalent geometry : angle 0.50007 (29421) SS BOND : bond 0.11924 ( 36) SS BOND : angle 7.02074 ( 72) hydrogen bonds : bond 0.26950 ( 837) hydrogen bonds : angle 9.13621 ( 2205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 550 time to evaluate : 0.907 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: A 29 THR cc_start: 0.8372 (p) cc_final: 0.8142 (p) REVERT: A 173 SER cc_start: 0.8488 (p) cc_final: 0.8060 (t) REVERT: A 176 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7782 (ttmm) REVERT: A 201 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7476 (mtmm) REVERT: A 268 ASN cc_start: 0.8386 (t0) cc_final: 0.8122 (t0) REVERT: A 370 MET cc_start: 0.7477 (tpt) cc_final: 0.7112 (tpt) REVERT: A 390 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8153 (mttm) REVERT: A 399 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7767 (mptt) REVERT: A 401 ASP cc_start: 0.7689 (p0) cc_final: 0.7370 (p0) REVERT: A 463 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 469 VAL cc_start: 0.8480 (t) cc_final: 0.8229 (m) REVERT: A 481 LEU cc_start: 0.8277 (mt) cc_final: 0.8048 (mt) REVERT: A 494 GLN cc_start: 0.8410 (mt0) cc_final: 0.8126 (mt0) REVERT: D 19 SER cc_start: 0.8020 (m) cc_final: 0.7798 (t) REVERT: H 35 SER cc_start: 0.8194 (p) cc_final: 0.7973 (t) REVERT: H 85 SER cc_start: 0.8188 (m) cc_final: 0.7904 (p) REVERT: H 90 ASP cc_start: 0.7241 (m-30) cc_final: 0.6550 (m-30) REVERT: I 4 MET cc_start: 0.7928 (mmm) cc_final: 0.6739 (mmm) REVERT: L 30 LEU cc_start: 0.7826 (tp) cc_final: 0.7621 (tt) REVERT: B 95 LEU cc_start: 0.8326 (mt) cc_final: 0.8061 (mp) REVERT: B 152 VAL cc_start: 0.8585 (p) cc_final: 0.8313 (t) REVERT: B 189 THR cc_start: 0.8565 (p) cc_final: 0.8273 (m) REVERT: B 196 LYS cc_start: 0.8716 (tttt) cc_final: 0.8343 (tttp) REVERT: B 197 ASN cc_start: 0.7971 (m-40) cc_final: 0.7535 (m110) REVERT: B 201 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7363 (mttp) REVERT: B 206 ILE cc_start: 0.7932 (tt) cc_final: 0.7731 (mt) REVERT: B 225 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7772 (mm-40) REVERT: B 232 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 401 ASP cc_start: 0.7518 (p0) cc_final: 0.7252 (p0) REVERT: B 406 VAL cc_start: 0.8117 (t) cc_final: 0.7736 (m) REVERT: B 465 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7373 (mm-40) REVERT: B 469 VAL cc_start: 0.8331 (t) cc_final: 0.8119 (t) REVERT: E 81 SER cc_start: 0.8353 (p) cc_final: 0.8145 (p) REVERT: G 54 SER cc_start: 0.8088 (m) cc_final: 0.7536 (m) REVERT: G 85 SER cc_start: 0.8231 (m) cc_final: 0.7792 (p) REVERT: K 74 THR cc_start: 0.8117 (m) cc_final: 0.7736 (t) REVERT: C 95 LEU cc_start: 0.8367 (mt) cc_final: 0.8147 (mp) REVERT: C 152 VAL cc_start: 0.8587 (p) cc_final: 0.8259 (t) REVERT: C 196 LYS cc_start: 0.8636 (tttt) cc_final: 0.8232 (tttm) REVERT: C 197 ASN cc_start: 0.8079 (m-40) cc_final: 0.7652 (m-40) REVERT: C 198 TYR cc_start: 0.8593 (t80) cc_final: 0.8247 (t80) REVERT: C 201 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7553 (mttt) REVERT: C 216 ASN cc_start: 0.7250 (m-40) cc_final: 0.7040 (m-40) REVERT: C 227 ASN cc_start: 0.7952 (t0) cc_final: 0.7611 (t0) REVERT: C 236 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6950 (mt-10) REVERT: C 268 ASN cc_start: 0.8354 (t0) cc_final: 0.7980 (t0) REVERT: C 370 MET cc_start: 0.7385 (tpt) cc_final: 0.7123 (tpt) REVERT: C 390 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8235 (mtpp) REVERT: C 406 VAL cc_start: 0.8316 (t) cc_final: 0.7894 (m) REVERT: C 448 ASP cc_start: 0.7799 (m-30) cc_final: 0.7528 (m-30) REVERT: C 454 ASN cc_start: 0.7584 (m-40) cc_final: 0.7285 (p0) REVERT: C 468 TYR cc_start: 0.8575 (t80) cc_final: 0.8354 (t80) REVERT: C 470 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7807 (mttp) REVERT: C 479 ASP cc_start: 0.7606 (m-30) cc_final: 0.7405 (m-30) REVERT: F 73 MET cc_start: 0.7938 (ttm) cc_final: 0.7646 (ttt) REVERT: J 7 SER cc_start: 0.8291 (m) cc_final: 0.7970 (t) REVERT: J 39 GLN cc_start: 0.8209 (tt0) cc_final: 0.8001 (tt0) REVERT: M 5 THR cc_start: 0.8024 (p) cc_final: 0.7729 (t) REVERT: O 20 SER cc_start: 0.8372 (m) cc_final: 0.8090 (t) outliers start: 2 outliers final: 0 residues processed: 552 average time/residue: 0.1354 time to fit residues: 121.9313 Evaluate side-chains 481 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 383 ASN A 388 ASN A 501 GLN D 85 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 383 ASN B 454 ASN E 85 HIS E 100 HIS G 39 GLN N 43 HIS C 81 GLN C 270 GLN C 380 ASN C 383 ASN C 388 ASN C 494 GLN C 501 GLN F 85 HIS F 100 HIS M 101 GLN O 95 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100790 restraints weight = 31438.438| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.07 r_work: 0.3074 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21693 Z= 0.124 Angle : 0.537 7.153 29493 Z= 0.287 Chirality : 0.042 0.169 3378 Planarity : 0.005 0.063 3729 Dihedral : 4.024 23.111 2958 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.89 % Allowed : 23.17 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2697 helix: 0.46 (0.27), residues: 405 sheet: -0.58 (0.17), residues: 981 loop : -1.30 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 87 TYR 0.015 0.001 TYR C 299 PHE 0.015 0.001 PHE I 91 TRP 0.007 0.001 TRP E 36 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00271 (21657) covalent geometry : angle 0.53322 (29421) SS BOND : bond 0.00318 ( 36) SS BOND : angle 1.33788 ( 72) hydrogen bonds : bond 0.04305 ( 837) hydrogen bonds : angle 5.98044 ( 2205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 495 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 SER cc_start: 0.8493 (p) cc_final: 0.8131 (t) REVERT: A 176 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7682 (ttmm) REVERT: A 201 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7564 (mtmm) REVERT: A 225 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7693 (mt0) REVERT: A 289 MET cc_start: 0.8181 (tpt) cc_final: 0.7533 (tpt) REVERT: A 354 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7394 (mm-40) REVERT: A 370 MET cc_start: 0.7576 (tpt) cc_final: 0.7227 (tpt) REVERT: A 399 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7726 (mptt) REVERT: A 401 ASP cc_start: 0.7727 (p0) cc_final: 0.7179 (p0) REVERT: A 405 SER cc_start: 0.8223 (t) cc_final: 0.7773 (p) REVERT: A 457 TYR cc_start: 0.8358 (m-80) cc_final: 0.7817 (m-80) REVERT: A 463 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 478 TYR cc_start: 0.8918 (m-80) cc_final: 0.8716 (m-80) REVERT: A 494 GLN cc_start: 0.8486 (mt0) cc_final: 0.8272 (mt0) REVERT: H 85 SER cc_start: 0.8168 (m) cc_final: 0.7815 (p) REVERT: I 4 MET cc_start: 0.8016 (mmm) cc_final: 0.6997 (mmm) REVERT: L 30 LEU cc_start: 0.7858 (tp) cc_final: 0.7654 (tt) REVERT: B 55 SER cc_start: 0.8432 (p) cc_final: 0.8139 (m) REVERT: B 95 LEU cc_start: 0.8354 (mt) cc_final: 0.8146 (mp) REVERT: B 176 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7952 (tttm) REVERT: B 196 LYS cc_start: 0.8647 (tttt) cc_final: 0.8360 (tttp) REVERT: B 197 ASN cc_start: 0.8101 (m-40) cc_final: 0.7775 (m110) REVERT: B 201 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7443 (mttp) REVERT: B 225 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7687 (mt0) REVERT: B 232 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 268 ASN cc_start: 0.8109 (t0) cc_final: 0.7669 (t0) REVERT: B 406 VAL cc_start: 0.8034 (t) cc_final: 0.7601 (m) REVERT: B 428 ASN cc_start: 0.8521 (p0) cc_final: 0.8306 (p0) REVERT: B 468 TYR cc_start: 0.8449 (t80) cc_final: 0.8048 (t80) REVERT: B 469 VAL cc_start: 0.8223 (t) cc_final: 0.8010 (t) REVERT: B 489 ASP cc_start: 0.6383 (t0) cc_final: 0.6160 (t70) REVERT: B 498 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8051 (mttp) REVERT: G 85 SER cc_start: 0.8101 (m) cc_final: 0.7866 (p) REVERT: K 74 THR cc_start: 0.8086 (m) cc_final: 0.7752 (t) REVERT: C 42 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7914 (ptpp) REVERT: C 152 VAL cc_start: 0.8325 (p) cc_final: 0.8108 (t) REVERT: C 176 LYS cc_start: 0.8001 (tttp) cc_final: 0.7638 (tttp) REVERT: C 194 ASP cc_start: 0.7544 (t0) cc_final: 0.7050 (t0) REVERT: C 196 LYS cc_start: 0.8617 (tttt) cc_final: 0.8323 (ttpp) REVERT: C 197 ASN cc_start: 0.8207 (m-40) cc_final: 0.7639 (m-40) REVERT: C 201 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7697 (mttt) REVERT: C 226 LYS cc_start: 0.8242 (mttm) cc_final: 0.7922 (mtpt) REVERT: C 227 ASN cc_start: 0.7735 (t0) cc_final: 0.7315 (t0) REVERT: C 268 ASN cc_start: 0.8125 (t0) cc_final: 0.7833 (t0) REVERT: C 406 VAL cc_start: 0.8215 (t) cc_final: 0.7810 (m) REVERT: C 427 LYS cc_start: 0.8294 (ptpp) cc_final: 0.8049 (ptpp) REVERT: C 452 VAL cc_start: 0.8398 (t) cc_final: 0.8100 (p) REVERT: C 454 ASN cc_start: 0.7608 (m-40) cc_final: 0.7293 (p0) REVERT: F 77 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7447 (mtmm) REVERT: J 7 SER cc_start: 0.8266 (m) cc_final: 0.7886 (t) REVERT: J 91 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7947 (t) REVERT: M 4 MET cc_start: 0.7970 (mmm) cc_final: 0.6869 (mmm) REVERT: O 20 SER cc_start: 0.8288 (m) cc_final: 0.8013 (t) outliers start: 46 outliers final: 31 residues processed: 518 average time/residue: 0.1377 time to fit residues: 115.7585 Evaluate side-chains 513 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 481 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain O residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 380 ASN D 100 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 216 ASN B 270 GLN N 43 HIS C 380 ASN C 501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099729 restraints weight = 30830.609| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.09 r_work: 0.3071 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21693 Z= 0.127 Angle : 0.509 6.460 29493 Z= 0.273 Chirality : 0.042 0.152 3378 Planarity : 0.004 0.054 3729 Dihedral : 4.050 24.462 2958 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.17 % Allowed : 22.92 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2697 helix: 0.83 (0.27), residues: 408 sheet: -0.43 (0.17), residues: 963 loop : -1.25 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.016 0.001 TYR C 299 PHE 0.014 0.001 PHE I 91 TRP 0.008 0.001 TRP F 102 HIS 0.017 0.002 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00291 (21657) covalent geometry : angle 0.50744 (29421) SS BOND : bond 0.00272 ( 36) SS BOND : angle 1.00073 ( 72) hydrogen bonds : bond 0.03972 ( 837) hydrogen bonds : angle 5.46687 ( 2205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 472 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8145 (ptpp) REVERT: A 152 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8047 (t) REVERT: A 173 SER cc_start: 0.8501 (p) cc_final: 0.8165 (t) REVERT: A 174 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 176 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7789 (mtmm) REVERT: A 201 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7570 (mtmm) REVERT: A 225 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7745 (mt0) REVERT: A 289 MET cc_start: 0.8136 (tpt) cc_final: 0.7598 (tpt) REVERT: A 370 MET cc_start: 0.7579 (tpt) cc_final: 0.7219 (tpt) REVERT: A 399 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7784 (mptt) REVERT: A 401 ASP cc_start: 0.7707 (p0) cc_final: 0.7198 (p0) REVERT: A 478 TYR cc_start: 0.8939 (m-80) cc_final: 0.8700 (m-80) REVERT: A 494 GLN cc_start: 0.8486 (mt0) cc_final: 0.8265 (mt0) REVERT: H 85 SER cc_start: 0.8184 (m) cc_final: 0.7819 (p) REVERT: I 4 MET cc_start: 0.7986 (mmm) cc_final: 0.6937 (mmm) REVERT: L 80 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7475 (mt) REVERT: B 34 GLN cc_start: 0.8505 (tt0) cc_final: 0.8303 (tt0) REVERT: B 55 SER cc_start: 0.8386 (p) cc_final: 0.8153 (m) REVERT: B 87 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7813 (mttp) REVERT: B 176 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7975 (tttm) REVERT: B 196 LYS cc_start: 0.8613 (tttt) cc_final: 0.8326 (tttp) REVERT: B 197 ASN cc_start: 0.8142 (m-40) cc_final: 0.7672 (m110) REVERT: B 201 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7551 (mttp) REVERT: B 225 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7622 (mt0) REVERT: B 232 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 268 ASN cc_start: 0.8023 (t0) cc_final: 0.7714 (m-40) REVERT: B 406 VAL cc_start: 0.8085 (t) cc_final: 0.7659 (m) REVERT: B 427 LYS cc_start: 0.7884 (ptpp) cc_final: 0.7606 (ptpp) REVERT: B 428 ASN cc_start: 0.8570 (p0) cc_final: 0.8359 (p0) REVERT: B 461 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7479 (mmtt) REVERT: B 469 VAL cc_start: 0.8250 (t) cc_final: 0.8037 (t) REVERT: B 498 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8041 (mttp) REVERT: B 511 GLU cc_start: 0.5424 (pm20) cc_final: 0.5131 (pm20) REVERT: G 80 SER cc_start: 0.8250 (p) cc_final: 0.7811 (m) REVERT: G 85 SER cc_start: 0.8134 (m) cc_final: 0.7824 (p) REVERT: K 74 THR cc_start: 0.8126 (m) cc_final: 0.7790 (t) REVERT: N 80 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7533 (mt) REVERT: C 152 VAL cc_start: 0.8362 (p) cc_final: 0.8162 (t) REVERT: C 194 ASP cc_start: 0.7562 (t0) cc_final: 0.7171 (t0) REVERT: C 196 LYS cc_start: 0.8604 (tttt) cc_final: 0.8332 (ttpp) REVERT: C 197 ASN cc_start: 0.8273 (m-40) cc_final: 0.7779 (m-40) REVERT: C 201 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7728 (mttt) REVERT: C 225 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7542 (mt0) REVERT: C 227 ASN cc_start: 0.7729 (t0) cc_final: 0.7253 (t0) REVERT: C 254 ASN cc_start: 0.7959 (m-40) cc_final: 0.7658 (m-40) REVERT: C 268 ASN cc_start: 0.8069 (t0) cc_final: 0.7786 (t0) REVERT: C 348 SER cc_start: 0.8833 (m) cc_final: 0.8514 (p) REVERT: C 427 LYS cc_start: 0.8308 (ptpp) cc_final: 0.8077 (ptpp) REVERT: C 452 VAL cc_start: 0.8292 (t) cc_final: 0.8007 (p) REVERT: C 511 GLU cc_start: 0.5512 (pm20) cc_final: 0.5248 (pm20) REVERT: F 53 ILE cc_start: 0.8378 (tp) cc_final: 0.8054 (tt) REVERT: F 73 MET cc_start: 0.8026 (ttm) cc_final: 0.7797 (ttm) REVERT: J 7 SER cc_start: 0.8288 (m) cc_final: 0.7911 (t) REVERT: J 91 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7892 (t) REVERT: O 20 SER cc_start: 0.8283 (m) cc_final: 0.7979 (t) REVERT: O 42 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7943 (tt) outliers start: 77 outliers final: 45 residues processed: 509 average time/residue: 0.1365 time to fit residues: 112.8209 Evaluate side-chains 516 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 464 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 155 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 216 ASN A 388 ASN D 62 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 388 ASN E 62 ASN K 101 GLN N 43 HIS ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 380 ASN C 388 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098751 restraints weight = 30496.101| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.08 r_work: 0.3032 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21693 Z= 0.200 Angle : 0.565 9.909 29493 Z= 0.299 Chirality : 0.044 0.169 3378 Planarity : 0.004 0.051 3729 Dihedral : 4.383 26.095 2958 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.79 % Allowed : 22.80 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.16), residues: 2697 helix: 0.81 (0.27), residues: 408 sheet: -0.29 (0.17), residues: 966 loop : -1.27 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 282 TYR 0.019 0.002 TYR B 86 PHE 0.019 0.002 PHE I 91 TRP 0.008 0.002 TRP F 114 HIS 0.011 0.002 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00471 (21657) covalent geometry : angle 0.56321 (29421) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.04748 ( 72) hydrogen bonds : bond 0.04184 ( 837) hydrogen bonds : angle 5.32728 ( 2205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 478 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8125 (ptpp) REVERT: A 173 SER cc_start: 0.8530 (p) cc_final: 0.8210 (t) REVERT: A 176 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7787 (mtmm) REVERT: A 201 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7698 (mtmm) REVERT: A 225 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7699 (mt0) REVERT: A 268 ASN cc_start: 0.7813 (t0) cc_final: 0.7587 (t0) REVERT: A 309 ILE cc_start: 0.8480 (pt) cc_final: 0.8136 (mt) REVERT: A 354 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7466 (mm-40) REVERT: A 370 MET cc_start: 0.7509 (tpt) cc_final: 0.7200 (tpt) REVERT: A 399 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7802 (mptt) REVERT: A 401 ASP cc_start: 0.7734 (p0) cc_final: 0.7503 (p0) REVERT: A 457 TYR cc_start: 0.8388 (m-80) cc_final: 0.8164 (m-80) REVERT: A 470 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7819 (mtmm) REVERT: A 494 GLN cc_start: 0.8473 (mt0) cc_final: 0.8251 (mt0) REVERT: D 19 SER cc_start: 0.8029 (m) cc_final: 0.7728 (t) REVERT: H 85 SER cc_start: 0.8190 (m) cc_final: 0.7779 (p) REVERT: I 4 MET cc_start: 0.7987 (mmm) cc_final: 0.7019 (mmm) REVERT: L 80 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 31 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 55 SER cc_start: 0.8396 (p) cc_final: 0.8123 (m) REVERT: B 96 LEU cc_start: 0.8514 (tt) cc_final: 0.8151 (tp) REVERT: B 196 LYS cc_start: 0.8607 (tttt) cc_final: 0.8293 (tttp) REVERT: B 197 ASN cc_start: 0.8190 (m-40) cc_final: 0.7741 (m110) REVERT: B 201 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7608 (mttp) REVERT: B 225 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7602 (mt0) REVERT: B 232 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 309 ILE cc_start: 0.8529 (pt) cc_final: 0.8269 (mt) REVERT: B 428 ASN cc_start: 0.8633 (p0) cc_final: 0.8357 (p0) REVERT: B 461 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7444 (mmtt) REVERT: B 469 VAL cc_start: 0.8257 (t) cc_final: 0.8054 (t) REVERT: B 511 GLU cc_start: 0.5457 (pm20) cc_final: 0.5245 (pm20) REVERT: G 80 SER cc_start: 0.8322 (p) cc_final: 0.7879 (m) REVERT: G 85 SER cc_start: 0.8147 (m) cc_final: 0.7761 (p) REVERT: K 74 THR cc_start: 0.8143 (m) cc_final: 0.7818 (t) REVERT: N 80 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7527 (mt) REVERT: C 176 LYS cc_start: 0.8069 (tttp) cc_final: 0.7857 (tttp) REVERT: C 194 ASP cc_start: 0.7563 (t0) cc_final: 0.7181 (t0) REVERT: C 197 ASN cc_start: 0.8369 (m-40) cc_final: 0.8015 (m110) REVERT: C 201 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7775 (mttt) REVERT: C 225 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7520 (mt0) REVERT: C 227 ASN cc_start: 0.7719 (t0) cc_final: 0.7235 (t0) REVERT: C 452 VAL cc_start: 0.8190 (t) cc_final: 0.7916 (p) REVERT: F 73 MET cc_start: 0.8059 (ttm) cc_final: 0.7744 (mtp) REVERT: J 7 SER cc_start: 0.8293 (m) cc_final: 0.7931 (t) REVERT: M 4 MET cc_start: 0.7878 (mmm) cc_final: 0.7293 (mmm) REVERT: O 20 SER cc_start: 0.8313 (m) cc_final: 0.7956 (t) REVERT: O 42 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7922 (tt) outliers start: 92 outliers final: 71 residues processed: 527 average time/residue: 0.1283 time to fit residues: 110.2514 Evaluate side-chains 541 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 466 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 187 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 216 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 216 ASN C 380 ASN C 388 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099566 restraints weight = 30285.541| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.07 r_work: 0.3073 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21693 Z= 0.149 Angle : 0.525 7.462 29493 Z= 0.280 Chirality : 0.043 0.148 3378 Planarity : 0.004 0.051 3729 Dihedral : 4.295 26.055 2958 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.46 % Allowed : 23.99 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2697 helix: 0.95 (0.27), residues: 408 sheet: -0.09 (0.17), residues: 960 loop : -1.29 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.019 0.002 TYR A 299 PHE 0.015 0.002 PHE I 49 TRP 0.007 0.001 TRP B 52 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00349 (21657) covalent geometry : angle 0.52350 (29421) SS BOND : bond 0.00270 ( 36) SS BOND : angle 0.83963 ( 72) hydrogen bonds : bond 0.03717 ( 837) hydrogen bonds : angle 5.17937 ( 2205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 458 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 SER cc_start: 0.8600 (p) cc_final: 0.8220 (t) REVERT: A 176 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7809 (mtmm) REVERT: A 201 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7913 (mtpt) REVERT: A 225 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7681 (mt0) REVERT: A 268 ASN cc_start: 0.7723 (t0) cc_final: 0.7512 (t0) REVERT: A 270 GLN cc_start: 0.8852 (mt0) cc_final: 0.8649 (mt0) REVERT: A 289 MET cc_start: 0.8146 (tpt) cc_final: 0.7652 (tpt) REVERT: A 309 ILE cc_start: 0.8446 (pt) cc_final: 0.8182 (mt) REVERT: A 370 MET cc_start: 0.7448 (tpt) cc_final: 0.7179 (tpt) REVERT: A 399 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7730 (mptt) REVERT: A 401 ASP cc_start: 0.7707 (p0) cc_final: 0.7481 (p0) REVERT: A 494 GLN cc_start: 0.8469 (mt0) cc_final: 0.8257 (mt0) REVERT: D 19 SER cc_start: 0.8007 (m) cc_final: 0.7668 (t) REVERT: H 85 SER cc_start: 0.8194 (m) cc_final: 0.7767 (p) REVERT: I 4 MET cc_start: 0.7963 (mmm) cc_final: 0.7014 (mmm) REVERT: L 80 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 31 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 96 LEU cc_start: 0.8506 (tt) cc_final: 0.8168 (tp) REVERT: B 196 LYS cc_start: 0.8598 (tttt) cc_final: 0.8289 (tttp) REVERT: B 197 ASN cc_start: 0.8200 (m-40) cc_final: 0.7634 (m110) REVERT: B 201 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7745 (mtpp) REVERT: B 225 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7589 (mt0) REVERT: B 232 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 309 ILE cc_start: 0.8505 (pt) cc_final: 0.8277 (mt) REVERT: B 392 ASP cc_start: 0.7609 (p0) cc_final: 0.7317 (p0) REVERT: B 427 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7619 (ptpp) REVERT: B 461 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7495 (mmtt) REVERT: B 469 VAL cc_start: 0.8200 (t) cc_final: 0.7976 (t) REVERT: G 80 SER cc_start: 0.8305 (p) cc_final: 0.7858 (m) REVERT: G 85 SER cc_start: 0.8145 (m) cc_final: 0.7752 (p) REVERT: K 74 THR cc_start: 0.8122 (m) cc_final: 0.7809 (t) REVERT: N 80 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7506 (mt) REVERT: C 194 ASP cc_start: 0.7543 (t0) cc_final: 0.7131 (t0) REVERT: C 197 ASN cc_start: 0.8387 (m-40) cc_final: 0.7960 (m110) REVERT: C 201 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7838 (mtpt) REVERT: C 203 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 225 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7511 (mt0) REVERT: C 227 ASN cc_start: 0.7668 (t0) cc_final: 0.7203 (t0) REVERT: C 348 SER cc_start: 0.8776 (m) cc_final: 0.8438 (p) REVERT: C 452 VAL cc_start: 0.8176 (t) cc_final: 0.7898 (p) REVERT: F 73 MET cc_start: 0.7940 (ttm) cc_final: 0.7696 (mtp) REVERT: F 77 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7353 (mtmm) REVERT: J 7 SER cc_start: 0.8272 (m) cc_final: 0.7908 (t) REVERT: M 4 MET cc_start: 0.7826 (mmm) cc_final: 0.7322 (mmm) REVERT: M 14 THR cc_start: 0.8714 (p) cc_final: 0.8482 (m) REVERT: O 20 SER cc_start: 0.8309 (m) cc_final: 0.7934 (t) REVERT: O 42 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7837 (tp) outliers start: 84 outliers final: 68 residues processed: 508 average time/residue: 0.1235 time to fit residues: 101.5764 Evaluate side-chains 526 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 453 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 66 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 150 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 216 ASN A 380 ASN A 388 ASN H 39 GLN I 101 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 388 ASN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 216 ASN C 380 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099907 restraints weight = 30380.933| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.07 r_work: 0.3086 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21693 Z= 0.136 Angle : 0.507 6.990 29493 Z= 0.270 Chirality : 0.042 0.148 3378 Planarity : 0.004 0.047 3729 Dihedral : 4.225 25.817 2958 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.42 % Allowed : 24.36 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2697 helix: 1.05 (0.27), residues: 408 sheet: -0.04 (0.17), residues: 972 loop : -1.26 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.018 0.002 TYR A 299 PHE 0.015 0.002 PHE I 49 TRP 0.007 0.001 TRP A 52 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00318 (21657) covalent geometry : angle 0.50584 (29421) SS BOND : bond 0.00236 ( 36) SS BOND : angle 0.76194 ( 72) hydrogen bonds : bond 0.03514 ( 837) hydrogen bonds : angle 5.04915 ( 2205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 445 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7839 (mtmt) REVERT: A 173 SER cc_start: 0.8588 (p) cc_final: 0.8213 (t) REVERT: A 176 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7796 (mtmm) REVERT: A 197 ASN cc_start: 0.8282 (m-40) cc_final: 0.7938 (m110) REVERT: A 201 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7693 (mtmm) REVERT: A 225 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7703 (mt0) REVERT: A 268 ASN cc_start: 0.7666 (t0) cc_final: 0.7441 (t0) REVERT: A 289 MET cc_start: 0.8114 (tpt) cc_final: 0.7654 (tpt) REVERT: A 309 ILE cc_start: 0.8402 (pt) cc_final: 0.8184 (mt) REVERT: A 370 MET cc_start: 0.7388 (tpt) cc_final: 0.7140 (tpt) REVERT: A 399 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7738 (mptt) REVERT: A 401 ASP cc_start: 0.7704 (p0) cc_final: 0.7487 (p0) REVERT: A 470 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7790 (mtmm) REVERT: A 494 GLN cc_start: 0.8478 (mt0) cc_final: 0.8261 (mt0) REVERT: D 19 SER cc_start: 0.7996 (m) cc_final: 0.7441 (p) REVERT: H 85 SER cc_start: 0.8213 (m) cc_final: 0.7784 (p) REVERT: L 20 SER cc_start: 0.8335 (m) cc_final: 0.8001 (t) REVERT: L 80 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7421 (mt) REVERT: B 31 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 95 LEU cc_start: 0.8408 (mt) cc_final: 0.8111 (mp) REVERT: B 96 LEU cc_start: 0.8528 (tt) cc_final: 0.8199 (tp) REVERT: B 161 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 196 LYS cc_start: 0.8590 (tttt) cc_final: 0.8278 (tttp) REVERT: B 197 ASN cc_start: 0.8199 (m-40) cc_final: 0.7803 (m110) REVERT: B 201 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7627 (mttp) REVERT: B 225 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7597 (mt0) REVERT: B 232 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 357 THR cc_start: 0.8262 (p) cc_final: 0.8026 (m) REVERT: B 392 ASP cc_start: 0.7581 (p0) cc_final: 0.7263 (p0) REVERT: B 427 LYS cc_start: 0.7885 (ptpp) cc_final: 0.7594 (ptpp) REVERT: B 461 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7490 (mmtt) REVERT: B 479 ASP cc_start: 0.7866 (t70) cc_final: 0.7626 (t70) REVERT: G 80 SER cc_start: 0.8314 (p) cc_final: 0.7865 (m) REVERT: G 85 SER cc_start: 0.8129 (m) cc_final: 0.7715 (p) REVERT: K 74 THR cc_start: 0.8120 (m) cc_final: 0.7804 (t) REVERT: N 80 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7503 (mt) REVERT: C 54 THR cc_start: 0.8522 (p) cc_final: 0.8304 (m) REVERT: C 173 SER cc_start: 0.8575 (p) cc_final: 0.8087 (t) REVERT: C 194 ASP cc_start: 0.7534 (t0) cc_final: 0.7155 (t0) REVERT: C 197 ASN cc_start: 0.8425 (m-40) cc_final: 0.8021 (m110) REVERT: C 201 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7747 (mttt) REVERT: C 203 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 225 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7492 (mt0) REVERT: C 227 ASN cc_start: 0.7621 (t0) cc_final: 0.7182 (t0) REVERT: C 309 ILE cc_start: 0.8416 (pt) cc_final: 0.7939 (mm) REVERT: C 348 SER cc_start: 0.8739 (m) cc_final: 0.8418 (p) REVERT: C 452 VAL cc_start: 0.8127 (t) cc_final: 0.7859 (p) REVERT: C 498 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7859 (mttt) REVERT: F 73 MET cc_start: 0.7944 (ttm) cc_final: 0.7714 (mtp) REVERT: F 77 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7327 (mtmm) REVERT: J 7 SER cc_start: 0.8257 (m) cc_final: 0.7894 (t) REVERT: M 4 MET cc_start: 0.7795 (mmm) cc_final: 0.7382 (mmm) REVERT: M 14 THR cc_start: 0.8724 (p) cc_final: 0.8493 (m) REVERT: M 61 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7916 (mtm-85) REVERT: O 20 SER cc_start: 0.8311 (m) cc_final: 0.7946 (t) REVERT: O 42 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7823 (tp) outliers start: 83 outliers final: 66 residues processed: 499 average time/residue: 0.1255 time to fit residues: 100.9639 Evaluate side-chains 517 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 445 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 227 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 388 ASN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 94 GLN B 268 ASN C 98 GLN C 216 ASN C 380 ASN C 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100659 restraints weight = 30832.971| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.01 r_work: 0.3098 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21693 Z= 0.136 Angle : 0.505 6.743 29493 Z= 0.270 Chirality : 0.042 0.146 3378 Planarity : 0.004 0.044 3729 Dihedral : 4.201 25.842 2958 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.91 % Allowed : 23.91 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2697 helix: 1.08 (0.27), residues: 408 sheet: 0.04 (0.17), residues: 972 loop : -1.24 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 282 TYR 0.018 0.002 TYR C 299 PHE 0.015 0.001 PHE I 49 TRP 0.007 0.001 TRP A 52 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00319 (21657) covalent geometry : angle 0.50480 (29421) SS BOND : bond 0.00229 ( 36) SS BOND : angle 0.72808 ( 72) hydrogen bonds : bond 0.03463 ( 837) hydrogen bonds : angle 4.99895 ( 2205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 429 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7879 (mtmt) REVERT: A 173 SER cc_start: 0.8598 (p) cc_final: 0.8221 (t) REVERT: A 176 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7742 (mtmm) REVERT: A 197 ASN cc_start: 0.8251 (m-40) cc_final: 0.7942 (m110) REVERT: A 201 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7880 (mtpt) REVERT: A 225 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7688 (mt0) REVERT: A 289 MET cc_start: 0.8114 (tpt) cc_final: 0.7650 (tpt) REVERT: A 370 MET cc_start: 0.7379 (tpt) cc_final: 0.7172 (tpt) REVERT: A 399 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7788 (mptt) REVERT: A 401 ASP cc_start: 0.7710 (p0) cc_final: 0.7493 (p0) REVERT: A 470 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7800 (mtmm) REVERT: A 494 GLN cc_start: 0.8501 (mt0) cc_final: 0.8285 (mt0) REVERT: H 85 SER cc_start: 0.8254 (m) cc_final: 0.7827 (p) REVERT: I 4 MET cc_start: 0.7900 (mmm) cc_final: 0.6973 (mmm) REVERT: I 61 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: L 20 SER cc_start: 0.8335 (m) cc_final: 0.7998 (t) REVERT: L 80 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7431 (mt) REVERT: B 31 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 95 LEU cc_start: 0.8428 (mt) cc_final: 0.8118 (mp) REVERT: B 96 LEU cc_start: 0.8530 (tt) cc_final: 0.8188 (tp) REVERT: B 161 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 196 LYS cc_start: 0.8595 (tttt) cc_final: 0.8288 (tttp) REVERT: B 197 ASN cc_start: 0.8184 (m-40) cc_final: 0.7805 (m110) REVERT: B 201 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7622 (mttp) REVERT: B 225 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7603 (mt0) REVERT: B 232 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 357 THR cc_start: 0.8255 (p) cc_final: 0.8043 (m) REVERT: B 392 ASP cc_start: 0.7556 (p0) cc_final: 0.7233 (p0) REVERT: B 427 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7608 (ptpp) REVERT: B 461 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7488 (mmtt) REVERT: B 479 ASP cc_start: 0.7845 (t70) cc_final: 0.7614 (t70) REVERT: G 37 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7762 (mm) REVERT: G 80 SER cc_start: 0.8298 (p) cc_final: 0.7857 (m) REVERT: G 85 SER cc_start: 0.8116 (m) cc_final: 0.7688 (p) REVERT: K 74 THR cc_start: 0.8129 (m) cc_final: 0.7827 (t) REVERT: N 80 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (mt) REVERT: C 54 THR cc_start: 0.8516 (p) cc_final: 0.8305 (m) REVERT: C 173 SER cc_start: 0.8610 (p) cc_final: 0.8120 (t) REVERT: C 194 ASP cc_start: 0.7528 (t0) cc_final: 0.7144 (t0) REVERT: C 197 ASN cc_start: 0.8414 (m-40) cc_final: 0.7992 (m110) REVERT: C 201 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7743 (mttt) REVERT: C 203 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 225 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7530 (mt0) REVERT: C 227 ASN cc_start: 0.7619 (t0) cc_final: 0.7209 (t0) REVERT: C 309 ILE cc_start: 0.8390 (pt) cc_final: 0.7983 (mm) REVERT: C 348 SER cc_start: 0.8723 (m) cc_final: 0.8435 (p) REVERT: C 452 VAL cc_start: 0.8111 (t) cc_final: 0.7855 (p) REVERT: C 498 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7890 (mttt) REVERT: F 73 MET cc_start: 0.7938 (ttm) cc_final: 0.7715 (mtp) REVERT: F 77 LYS cc_start: 0.7611 (mtmm) cc_final: 0.7324 (mtmm) REVERT: J 7 SER cc_start: 0.8230 (m) cc_final: 0.7869 (t) REVERT: J 37 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8000 (mm) REVERT: M 4 MET cc_start: 0.7785 (mmm) cc_final: 0.7367 (mmm) REVERT: M 14 THR cc_start: 0.8731 (p) cc_final: 0.8500 (m) REVERT: M 61 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7931 (mtm-85) REVERT: O 20 SER cc_start: 0.8310 (m) cc_final: 0.7944 (t) REVERT: O 42 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7808 (tp) outliers start: 95 outliers final: 73 residues processed: 491 average time/residue: 0.1262 time to fit residues: 99.5973 Evaluate side-chains 521 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 439 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 249 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 268 ASN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 388 ASN C 98 GLN C 380 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100664 restraints weight = 30829.550| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3095 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21693 Z= 0.149 Angle : 0.513 6.987 29493 Z= 0.274 Chirality : 0.042 0.145 3378 Planarity : 0.004 0.043 3729 Dihedral : 4.233 26.172 2958 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.83 % Allowed : 24.36 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2697 helix: 1.10 (0.27), residues: 408 sheet: 0.10 (0.17), residues: 972 loop : -1.25 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 282 TYR 0.019 0.002 TYR A 299 PHE 0.015 0.002 PHE I 49 TRP 0.008 0.001 TRP A 52 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00351 (21657) covalent geometry : angle 0.51263 (29421) SS BOND : bond 0.00248 ( 36) SS BOND : angle 0.75256 ( 72) hydrogen bonds : bond 0.03529 ( 837) hydrogen bonds : angle 4.99471 ( 2205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 436 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 166 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7872 (mtmt) REVERT: A 173 SER cc_start: 0.8597 (p) cc_final: 0.8230 (t) REVERT: A 176 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7745 (mtmm) REVERT: A 197 ASN cc_start: 0.8237 (m-40) cc_final: 0.7970 (m110) REVERT: A 201 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7868 (mtpt) REVERT: A 225 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7685 (mt0) REVERT: A 251 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7792 (mtp) REVERT: A 289 MET cc_start: 0.8109 (tpt) cc_final: 0.7628 (tpt) REVERT: A 399 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7786 (mptt) REVERT: A 401 ASP cc_start: 0.7709 (p0) cc_final: 0.7490 (p0) REVERT: A 470 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7790 (mtmm) REVERT: D 19 SER cc_start: 0.8011 (m) cc_final: 0.7522 (p) REVERT: H 85 SER cc_start: 0.8256 (m) cc_final: 0.7817 (p) REVERT: I 4 MET cc_start: 0.7888 (mmm) cc_final: 0.6947 (mmm) REVERT: I 61 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7968 (mtm-85) REVERT: L 80 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7419 (mt) REVERT: B 31 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 42 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7905 (pttt) REVERT: B 95 LEU cc_start: 0.8403 (mt) cc_final: 0.8115 (mp) REVERT: B 96 LEU cc_start: 0.8530 (tt) cc_final: 0.8194 (tp) REVERT: B 161 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 196 LYS cc_start: 0.8585 (tttt) cc_final: 0.8277 (tttp) REVERT: B 197 ASN cc_start: 0.8192 (m-40) cc_final: 0.7845 (m110) REVERT: B 201 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7624 (mttp) REVERT: B 225 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7611 (mt0) REVERT: B 232 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 293 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8265 (tttt) REVERT: B 392 ASP cc_start: 0.7538 (p0) cc_final: 0.7211 (p0) REVERT: B 427 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7605 (ptpp) REVERT: B 461 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7469 (mmtt) REVERT: B 479 ASP cc_start: 0.7856 (t70) cc_final: 0.7627 (t70) REVERT: G 37 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7774 (mm) REVERT: G 80 SER cc_start: 0.8327 (p) cc_final: 0.7879 (m) REVERT: G 85 SER cc_start: 0.8118 (m) cc_final: 0.7679 (p) REVERT: K 74 THR cc_start: 0.8124 (m) cc_final: 0.7821 (t) REVERT: N 80 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7483 (mt) REVERT: C 54 THR cc_start: 0.8510 (p) cc_final: 0.8298 (m) REVERT: C 173 SER cc_start: 0.8592 (p) cc_final: 0.8109 (t) REVERT: C 194 ASP cc_start: 0.7527 (t0) cc_final: 0.7246 (t0) REVERT: C 197 ASN cc_start: 0.8424 (m-40) cc_final: 0.8178 (m110) REVERT: C 201 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7750 (mttt) REVERT: C 203 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 225 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7498 (mt0) REVERT: C 227 ASN cc_start: 0.7622 (t0) cc_final: 0.7210 (t0) REVERT: C 309 ILE cc_start: 0.8370 (pt) cc_final: 0.8017 (mm) REVERT: C 348 SER cc_start: 0.8714 (m) cc_final: 0.8422 (p) REVERT: C 370 MET cc_start: 0.7253 (tpt) cc_final: 0.6709 (tpt) REVERT: C 452 VAL cc_start: 0.8100 (t) cc_final: 0.7849 (p) REVERT: C 498 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7888 (mttt) REVERT: F 73 MET cc_start: 0.7924 (ttm) cc_final: 0.7715 (mtp) REVERT: F 77 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7322 (mtmm) REVERT: J 7 SER cc_start: 0.8230 (m) cc_final: 0.7875 (t) REVERT: J 37 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7997 (mm) REVERT: M 4 MET cc_start: 0.7783 (mmm) cc_final: 0.7406 (mmm) REVERT: M 14 THR cc_start: 0.8725 (p) cc_final: 0.8504 (m) REVERT: M 61 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7936 (mtm-85) REVERT: O 20 SER cc_start: 0.8311 (m) cc_final: 0.7942 (t) REVERT: O 42 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (tp) outliers start: 93 outliers final: 74 residues processed: 490 average time/residue: 0.1251 time to fit residues: 98.8996 Evaluate side-chains 528 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 443 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 113 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 251 optimal weight: 0.4980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 216 ASN A 388 ASN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 98 GLN C 216 ASN C 240 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099748 restraints weight = 30122.584| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.05 r_work: 0.3086 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21693 Z= 0.192 Angle : 0.544 7.412 29493 Z= 0.290 Chirality : 0.043 0.147 3378 Planarity : 0.004 0.048 3729 Dihedral : 4.391 27.953 2958 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.87 % Allowed : 24.44 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2697 helix: 1.05 (0.26), residues: 408 sheet: 0.11 (0.17), residues: 972 loop : -1.31 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 282 TYR 0.032 0.002 TYR C 299 PHE 0.018 0.002 PHE M 91 TRP 0.008 0.002 TRP G 47 HIS 0.010 0.002 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00453 (21657) covalent geometry : angle 0.54318 (29421) SS BOND : bond 0.00270 ( 36) SS BOND : angle 0.83952 ( 72) hydrogen bonds : bond 0.03833 ( 837) hydrogen bonds : angle 5.07134 ( 2205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 435 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 173 SER cc_start: 0.8597 (p) cc_final: 0.8236 (t) REVERT: A 176 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7791 (mtmm) REVERT: A 201 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7909 (mtpt) REVERT: A 225 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7692 (mt0) REVERT: A 251 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7865 (mtp) REVERT: A 289 MET cc_start: 0.8112 (tpt) cc_final: 0.7602 (tpt) REVERT: A 399 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7774 (mptt) REVERT: A 401 ASP cc_start: 0.7709 (p0) cc_final: 0.7485 (p0) REVERT: A 470 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7814 (mtmm) REVERT: D 19 SER cc_start: 0.8012 (m) cc_final: 0.7546 (p) REVERT: H 85 SER cc_start: 0.8289 (m) cc_final: 0.7798 (p) REVERT: I 4 MET cc_start: 0.7902 (mmm) cc_final: 0.6954 (mmm) REVERT: I 61 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: L 80 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7431 (mt) REVERT: B 31 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 96 LEU cc_start: 0.8520 (tt) cc_final: 0.8199 (tp) REVERT: B 161 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 189 THR cc_start: 0.8414 (p) cc_final: 0.8189 (m) REVERT: B 196 LYS cc_start: 0.8554 (tttt) cc_final: 0.8243 (tttp) REVERT: B 197 ASN cc_start: 0.8228 (m-40) cc_final: 0.7888 (m110) REVERT: B 201 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7696 (mttp) REVERT: B 225 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7585 (mt0) REVERT: B 232 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 392 ASP cc_start: 0.7471 (p0) cc_final: 0.7147 (p0) REVERT: B 427 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7623 (ptpp) REVERT: B 461 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7430 (mmtt) REVERT: B 479 ASP cc_start: 0.7886 (t70) cc_final: 0.7643 (t70) REVERT: B 498 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7871 (mttp) REVERT: G 37 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7805 (mm) REVERT: G 80 SER cc_start: 0.8376 (p) cc_final: 0.7924 (m) REVERT: G 85 SER cc_start: 0.8147 (m) cc_final: 0.7690 (p) REVERT: K 74 THR cc_start: 0.8108 (m) cc_final: 0.7801 (t) REVERT: N 80 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 173 SER cc_start: 0.8601 (p) cc_final: 0.8119 (t) REVERT: C 190 PHE cc_start: 0.8033 (t80) cc_final: 0.7796 (t80) REVERT: C 194 ASP cc_start: 0.7534 (t0) cc_final: 0.7255 (t0) REVERT: C 197 ASN cc_start: 0.8476 (m-40) cc_final: 0.8237 (m110) REVERT: C 201 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7761 (mttt) REVERT: C 203 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 225 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7494 (mt0) REVERT: C 227 ASN cc_start: 0.7653 (t0) cc_final: 0.7202 (t0) REVERT: C 309 ILE cc_start: 0.8319 (pt) cc_final: 0.8039 (mm) REVERT: C 348 SER cc_start: 0.8727 (m) cc_final: 0.8415 (p) REVERT: C 370 MET cc_start: 0.7260 (tpt) cc_final: 0.6702 (tpt) REVERT: C 498 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7860 (mttt) REVERT: F 77 LYS cc_start: 0.7611 (mtmm) cc_final: 0.7330 (mtmm) REVERT: J 7 SER cc_start: 0.8239 (m) cc_final: 0.7894 (t) REVERT: J 37 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8023 (mm) REVERT: M 4 MET cc_start: 0.7830 (mmm) cc_final: 0.7448 (mmm) REVERT: M 14 THR cc_start: 0.8699 (p) cc_final: 0.8496 (m) REVERT: M 61 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: O 20 SER cc_start: 0.8313 (m) cc_final: 0.7908 (t) REVERT: O 42 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7791 (tp) outliers start: 94 outliers final: 74 residues processed: 492 average time/residue: 0.1190 time to fit residues: 95.0821 Evaluate side-chains 523 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 439 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 130 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 197 ASN A 388 ASN B 388 ASN C 98 GLN C 388 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100340 restraints weight = 30350.738| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3093 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21693 Z= 0.149 Angle : 0.529 7.773 29493 Z= 0.282 Chirality : 0.043 0.209 3378 Planarity : 0.004 0.049 3729 Dihedral : 4.330 28.316 2958 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.66 % Allowed : 24.86 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2697 helix: 1.12 (0.26), residues: 411 sheet: 0.13 (0.17), residues: 975 loop : -1.30 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 282 TYR 0.029 0.002 TYR C 299 PHE 0.015 0.002 PHE I 91 TRP 0.007 0.001 TRP G 47 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00351 (21657) covalent geometry : angle 0.52795 (29421) SS BOND : bond 0.00238 ( 36) SS BOND : angle 0.76698 ( 72) hydrogen bonds : bond 0.03592 ( 837) hydrogen bonds : angle 5.01611 ( 2205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 439 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 173 SER cc_start: 0.8600 (p) cc_final: 0.8238 (t) REVERT: A 176 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7800 (mtmm) REVERT: A 201 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7948 (mtpt) REVERT: A 225 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7699 (mt0) REVERT: A 251 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: A 289 MET cc_start: 0.8100 (tpt) cc_final: 0.7627 (tpt) REVERT: A 399 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7763 (mptt) REVERT: A 401 ASP cc_start: 0.7703 (p0) cc_final: 0.7475 (p0) REVERT: A 470 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7813 (mtmm) REVERT: H 85 SER cc_start: 0.8296 (m) cc_final: 0.7800 (p) REVERT: I 4 MET cc_start: 0.7907 (mmm) cc_final: 0.6967 (mmm) REVERT: I 61 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: L 80 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7433 (mt) REVERT: B 31 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 42 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7880 (pttt) REVERT: B 95 LEU cc_start: 0.8380 (mt) cc_final: 0.8071 (mp) REVERT: B 96 LEU cc_start: 0.8509 (tt) cc_final: 0.8198 (tp) REVERT: B 161 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 189 THR cc_start: 0.8411 (p) cc_final: 0.8186 (m) REVERT: B 196 LYS cc_start: 0.8547 (tttt) cc_final: 0.8244 (tttp) REVERT: B 197 ASN cc_start: 0.8209 (m-40) cc_final: 0.7854 (m110) REVERT: B 201 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7650 (mttp) REVERT: B 225 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7606 (mt0) REVERT: B 232 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 392 ASP cc_start: 0.7470 (p0) cc_final: 0.7159 (p0) REVERT: B 427 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7600 (ptpp) REVERT: B 461 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7433 (mmtt) REVERT: B 479 ASP cc_start: 0.7888 (t70) cc_final: 0.7656 (t70) REVERT: G 37 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7784 (mm) REVERT: G 45 LEU cc_start: 0.8084 (mt) cc_final: 0.7717 (mt) REVERT: G 80 SER cc_start: 0.8367 (p) cc_final: 0.7910 (m) REVERT: G 85 SER cc_start: 0.8138 (m) cc_final: 0.7675 (p) REVERT: K 74 THR cc_start: 0.8100 (m) cc_final: 0.7801 (t) REVERT: N 80 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7463 (mt) REVERT: C 173 SER cc_start: 0.8620 (p) cc_final: 0.8146 (t) REVERT: C 190 PHE cc_start: 0.8048 (t80) cc_final: 0.7802 (t80) REVERT: C 194 ASP cc_start: 0.7545 (t0) cc_final: 0.7292 (t0) REVERT: C 197 ASN cc_start: 0.8485 (m-40) cc_final: 0.8276 (m110) REVERT: C 201 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7689 (mttt) REVERT: C 203 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8061 (mp) REVERT: C 225 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7491 (mt0) REVERT: C 227 ASN cc_start: 0.7615 (t0) cc_final: 0.7182 (t0) REVERT: C 309 ILE cc_start: 0.8290 (pt) cc_final: 0.8037 (mm) REVERT: C 348 SER cc_start: 0.8728 (m) cc_final: 0.8429 (p) REVERT: C 370 MET cc_start: 0.7261 (tpt) cc_final: 0.6708 (tpt) REVERT: C 498 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7837 (mttt) REVERT: F 77 LYS cc_start: 0.7587 (mtmm) cc_final: 0.7303 (mtmm) REVERT: J 7 SER cc_start: 0.8238 (m) cc_final: 0.7887 (t) REVERT: J 37 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8003 (mm) REVERT: M 4 MET cc_start: 0.7822 (mmm) cc_final: 0.7443 (mmm) REVERT: M 14 THR cc_start: 0.8708 (p) cc_final: 0.8503 (m) REVERT: M 61 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7948 (mtm-85) REVERT: O 20 SER cc_start: 0.8309 (m) cc_final: 0.7915 (t) REVERT: O 42 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7789 (tp) outliers start: 89 outliers final: 71 residues processed: 496 average time/residue: 0.1201 time to fit residues: 96.7853 Evaluate side-chains 524 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 442 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 118 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 261 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 40 optimal weight: 0.0060 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 197 ASN A 388 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100434 restraints weight = 30344.611| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.07 r_work: 0.3097 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 21693 Z= 0.177 Angle : 0.800 59.200 29493 Z= 0.494 Chirality : 0.043 0.444 3378 Planarity : 0.006 0.159 3729 Dihedral : 4.433 38.708 2958 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.33 % Allowed : 25.27 % Favored : 71.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.16), residues: 2697 helix: 1.15 (0.26), residues: 411 sheet: 0.13 (0.17), residues: 975 loop : -1.32 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 282 TYR 0.026 0.002 TYR C 299 PHE 0.015 0.002 PHE M 91 TRP 0.007 0.001 TRP G 47 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00373 (21657) covalent geometry : angle 0.79962 (29421) SS BOND : bond 0.00236 ( 36) SS BOND : angle 0.75014 ( 72) hydrogen bonds : bond 0.03558 ( 837) hydrogen bonds : angle 5.01271 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5966.90 seconds wall clock time: 102 minutes 53.60 seconds (6173.60 seconds total)