Starting phenix.real_space_refine on Sat Jul 4 11:21:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.map" model { file = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mpg_23933/07_2026/7mpg_23933.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 108 5.16 5 C 12828 2.51 5 N 3390 2.21 5 O 4040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1635 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.21 Number of scatterers: 20366 At special positions: 0 Unit cell: (196.88, 202.23, 128.4, 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 108 16.00 O 4040 8.00 N 3390 7.00 C 12828 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.05 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 B 37 " - pdb=" SG CYS B 439 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.05 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 C 37 " - pdb=" SG CYS C 439 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.05 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=2.04 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 500 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 920.2 milliseconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 48 sheets defined 21.1% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.516A pdb=" N LYS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.790A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.800A pdb=" N VAL A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' 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 369 through 372 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'B' and resid 73 through 96 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.649A pdb=" N LYS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.867A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 282' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' 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 369 through 372 Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.568A pdb=" N LYS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.884A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' 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 369 through 372 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.500A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 128 Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.788A pdb=" N LYS G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.582A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.733A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.692A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.536A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.900A pdb=" N LYS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 312 removed outlier: 6.077A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 311 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.104A 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: 10.231A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 244 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.563A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.625A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 308 through 312 removed outlier: 6.095A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR B 311 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.259A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 56 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 190 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 244 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.584A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.611A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AB5, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.146A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR C 311 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.151A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 190 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 244 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.657A pdb=" N ASN C 426 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 94 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG F 96 " --> pdb=" O MET F 100F" (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET F 100F" --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU G 105 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.174A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 144 through 149 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.305A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.387A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.231A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 33 " --> pdb=" O HIS I 49 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 115 through 118 removed outlier: 6.054A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 144 through 149 Processing sheet with id=AE3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.076A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AE8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 115 through 118 removed outlier: 5.921A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 144 through 149 950 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6565 1.35 - 1.48: 5041 1.48 - 1.61: 8994 1.61 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 20744 Sorted by residual: bond pdb=" CA MET D 82 " pdb=" CB MET D 82 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP G 1 " pdb=" CA ASP G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP I 1 " pdb=" CA ASP I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 20739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 27678 2.23 - 4.47: 438 4.47 - 6.70: 32 6.70 - 8.94: 5 8.94 - 11.17: 4 Bond angle restraints: 28157 Sorted by residual: angle pdb=" CG1 VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.80 121.97 -11.17 2.20e+00 2.07e-01 2.58e+01 angle pdb=" CA CYS B 313 " pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " ideal model delta sigma weight residual 114.40 123.45 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C LYS B 272 " pdb=" N LEU B 273 " pdb=" CA LEU B 273 " ideal model delta sigma weight residual 120.54 125.77 -5.23 1.35e+00 5.49e-01 1.50e+01 angle pdb=" CA CYS C 313 " pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.43e+01 ... (remaining 28152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 11391 17.33 - 34.66: 1022 34.66 - 51.99: 155 51.99 - 69.32: 27 69.32 - 86.65: 19 Dihedral angle restraints: 12614 sinusoidal: 4922 harmonic: 7692 Sorted by residual: dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.46 -57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS G 134 " pdb=" SG CYS G 134 " pdb=" SG CYS G 194 " pdb=" CB CYS G 194 " ideal model delta sinusoidal sigma weight residual 93.00 43.30 49.70 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CB CYS I 134 " pdb=" SG CYS I 134 " pdb=" SG CYS I 194 " pdb=" CB CYS I 194 " ideal model delta sinusoidal sigma weight residual 93.00 44.72 48.28 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 12611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 3284 0.333 - 0.667: 0 0.667 - 1.000: 0 1.000 - 1.334: 0 1.334 - 1.667: 2 Chirality restraints: 3286 Sorted by residual: chirality pdb=" CG LEU I 94 " pdb=" CB LEU I 94 " pdb=" CD1 LEU I 94 " pdb=" CD2 LEU I 94 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.95e+01 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.28e+01 chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3283 not shown) Planarity restraints: 3580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.76e+00 pdb=" CG TRP H 36 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 122 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO H 123 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 123 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 43 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 44 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 44 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 44 " -0.024 5.00e-02 4.00e+02 ... (remaining 3577 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 192 2.51 - 3.10: 16050 3.10 - 3.70: 30894 3.70 - 4.30: 43610 4.30 - 4.90: 72914 Nonbonded interactions: 163660 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 1.908 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 1.917 3.040 nonbonded pdb=" OG1 THR C 267 " pdb=" OD1 ASP C 269 " model vdw 1.935 3.040 nonbonded pdb=" OG1 THR B 267 " pdb=" OD1 ASP B 269 " model vdw 1.943 3.040 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 1.964 3.040 ... (remaining 163655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = (chain 'F' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.860 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.003 0.057 20781 Z= 0.174 Angle : 0.717 11.174 28232 Z= 0.415 Chirality : 0.058 1.667 3286 Planarity : 0.004 0.051 3579 Dihedral : 13.375 86.655 7556 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.25 (0.17), residues: 2610 helix: 0.18 (0.26), residues: 417 sheet: -0.62 (0.18), residues: 907 loop : -1.27 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 108 TYR 0.017 0.002 TYR D 100C PHE 0.016 0.001 PHE F 29 TRP 0.032 0.002 TRP H 36 HIS 0.005 0.001 HIS G 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (20744) covalent geometry : angle 0.71288 / 0.41 (28157) SS BOND : bond 0.00593 / 0.36 ( 36) SS BOND : angle 1.69253 / 1.09 ( 72) hydrogen bonds : bond 0.12183 / 8.03 ( 900) hydrogen bonds : angle 7.28263 / 5.01 ( 2403) link_NAG-ASN : bond 0.00569 / 0.30 ( 1) link_NAG-ASN : angle 0.74454 / 0.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8192 (tt) cc_final: 0.7990 (tt) REVERT: C 392 ASP cc_start: 0.7107 (t0) cc_final: 0.6876 (t0) REVERT: F 143 LYS cc_start: 0.6479 (mmtm) cc_final: 0.6026 (tptp) REVERT: E 94 LEU cc_start: 0.6626 (mt) cc_final: 0.6182 (mt) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.1362 time to fit residues: 144.7739 Evaluate side-chains 405 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.3980 chunk 258 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 81 GLN A 361 GLN B 67 ASN B 302 GLN B 460 ASN C 277 ASN C 302 GLN F 76 ASN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 76 ASN D 31 HIS D 76 ASN D 200 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.170482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128683 restraints weight = 37573.122| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.23 r_work: 0.3609 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20781 Z= 0.186 Angle : 0.729 12.018 28232 Z= 0.376 Chirality : 0.048 0.271 3286 Planarity : 0.005 0.054 3579 Dihedral : 5.169 21.568 2811 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.83 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 11.50 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2610 helix: 0.76 (0.25), residues: 411 sheet: -0.54 (0.17), residues: 909 loop : -1.04 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 16 TYR 0.036 0.002 TYR F 100D PHE 0.028 0.002 PHE B 483 TRP 0.026 0.002 TRP E 35 HIS 0.009 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (20744) covalent geometry : angle 0.72693 / 0.38 (28157) SS BOND : bond 0.00446 / 0.28 ( 36) SS BOND : angle 1.35974 / 0.89 ( 72) hydrogen bonds : bond 0.03495 / 2.36 ( 900) hydrogen bonds : angle 6.00770 / 4.14 ( 2403) link_NAG-ASN : bond 0.00771 / 0.41 ( 1) link_NAG-ASN : angle 0.72352 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 419 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7897 (tt0) cc_final: 0.7668 (tt0) REVERT: A 156 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7817 (tttm) REVERT: A 338 ASP cc_start: 0.8606 (t0) cc_final: 0.8389 (t0) REVERT: A 448 ASP cc_start: 0.7091 (t0) cc_final: 0.6674 (t0) REVERT: A 483 PHE cc_start: 0.7514 (t80) cc_final: 0.6937 (t80) REVERT: B 236 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 248 SER cc_start: 0.8423 (p) cc_final: 0.8066 (m) REVERT: C 53 TYR cc_start: 0.8595 (t80) cc_final: 0.8100 (t80) REVERT: C 417 TYR cc_start: 0.8429 (m-80) cc_final: 0.8191 (m-10) REVERT: C 448 ASP cc_start: 0.7131 (t0) cc_final: 0.6905 (t0) REVERT: F 36 TRP cc_start: 0.9259 (m100) cc_final: 0.8820 (m100) REVERT: F 47 TRP cc_start: 0.9256 (t60) cc_final: 0.9013 (t60) REVERT: F 100 TYR cc_start: 0.8978 (m-80) cc_final: 0.8389 (m-80) REVERT: G 50 ASP cc_start: 0.8750 (m-30) cc_final: 0.8480 (m-30) REVERT: H 58 TYR cc_start: 0.8589 (m-80) cc_final: 0.8258 (m-80) REVERT: H 81 GLN cc_start: 0.7692 (tt0) cc_final: 0.7094 (mm110) REVERT: H 150 VAL cc_start: 0.6662 (m) cc_final: 0.6309 (t) REVERT: I 35 TRP cc_start: 0.8984 (m100) cc_final: 0.8599 (m100) REVERT: I 47 LEU cc_start: 0.9112 (mt) cc_final: 0.8871 (mt) REVERT: I 48 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8400 (ptm) REVERT: I 50 ASP cc_start: 0.8485 (m-30) cc_final: 0.8126 (m-30) REVERT: I 55 GLU cc_start: 0.8915 (tp30) cc_final: 0.8548 (tp30) REVERT: I 81 GLU cc_start: 0.8494 (pp20) cc_final: 0.8292 (pp20) REVERT: D 81 GLN cc_start: 0.7654 (tt0) cc_final: 0.7188 (mm110) REVERT: E 89 GLN cc_start: 0.8934 (tt0) cc_final: 0.8695 (tt0) outliers start: 69 outliers final: 41 residues processed: 462 average time/residue: 0.1349 time to fit residues: 98.3372 Evaluate side-chains 380 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 337 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN B 67 ASN C 454 ASN F 76 ASN G 124 GLN H 3 GLN I 34 ASN I 147 GLN D 31 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116167 restraints weight = 37169.515| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.13 r_work: 0.3437 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20781 Z= 0.184 Angle : 0.695 12.599 28232 Z= 0.357 Chirality : 0.047 0.300 3286 Planarity : 0.005 0.055 3579 Dihedral : 5.083 22.312 2811 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.33 % Favored : 95.52 % Rotamer: Outliers : 3.49 % Allowed : 14.57 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.71 (0.17), residues: 2610 helix: 1.07 (0.26), residues: 408 sheet: -0.44 (0.17), residues: 908 loop : -0.93 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 16 TYR 0.021 0.002 TYR D 100C PHE 0.023 0.002 PHE B 483 TRP 0.033 0.002 TRP G 35 HIS 0.007 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (20744) covalent geometry : angle 0.69248 / 0.36 (28157) SS BOND : bond 0.00522 / 0.34 ( 36) SS BOND : angle 1.38809 / 0.90 ( 72) hydrogen bonds : bond 0.03239 / 2.21 ( 900) hydrogen bonds : angle 5.64928 / 3.91 ( 2403) link_NAG-ASN : bond 0.00711 / 0.37 ( 1) link_NAG-ASN : angle 0.89620 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 413 time to evaluate : 0.717 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: A 49 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8116 (ptm-80) REVERT: A 156 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8077 (tttm) REVERT: A 235 ARG cc_start: 0.8955 (ttm170) cc_final: 0.8420 (ttp80) REVERT: A 338 ASP cc_start: 0.8443 (t0) cc_final: 0.8148 (t0) REVERT: A 426 ASN cc_start: 0.8518 (t0) cc_final: 0.8264 (t0) REVERT: B 49 ARG cc_start: 0.8532 (ttp80) cc_final: 0.7606 (ttp80) REVERT: B 141 LEU cc_start: 0.8430 (pt) cc_final: 0.8177 (pp) REVERT: B 166 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7672 (ptpt) REVERT: B 248 SER cc_start: 0.9189 (p) cc_final: 0.8835 (p) REVERT: B 462 GLN cc_start: 0.8570 (tp40) cc_final: 0.8312 (tp-100) REVERT: C 321 LEU cc_start: 0.8717 (mt) cc_final: 0.8515 (mt) REVERT: C 448 ASP cc_start: 0.7182 (t0) cc_final: 0.6893 (t0) REVERT: C 501 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7768 (tm-30) REVERT: F 16 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: F 36 TRP cc_start: 0.9324 (m100) cc_final: 0.9040 (m100) REVERT: F 43 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8956 (mmtp) REVERT: F 47 TRP cc_start: 0.9200 (t60) cc_final: 0.8874 (t60) REVERT: F 58 TYR cc_start: 0.8074 (m-80) cc_final: 0.7592 (m-10) REVERT: F 176 TYR cc_start: 0.7018 (m-80) cc_final: 0.6718 (m-80) REVERT: G 50 ASP cc_start: 0.8817 (m-30) cc_final: 0.8513 (m-30) REVERT: G 87 TYR cc_start: 0.8689 (m-80) cc_final: 0.8451 (m-80) REVERT: H 43 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8365 (mmtp) REVERT: H 58 TYR cc_start: 0.8651 (m-80) cc_final: 0.7796 (m-80) REVERT: H 72 ASP cc_start: 0.8218 (t0) cc_final: 0.7909 (t0) REVERT: H 83 ARG cc_start: 0.8281 (mpt-90) cc_final: 0.8006 (mpt-90) REVERT: H 100 TYR cc_start: 0.8711 (m-10) cc_final: 0.7593 (m-80) REVERT: H 100 TYR cc_start: 0.8426 (m-80) cc_final: 0.7797 (m-80) REVERT: H 176 TYR cc_start: 0.6159 (m-80) cc_final: 0.5653 (m-80) REVERT: I 35 TRP cc_start: 0.9365 (m100) cc_final: 0.8729 (m100) REVERT: I 48 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8441 (ptm) REVERT: I 81 GLU cc_start: 0.8554 (pp20) cc_final: 0.8279 (pp20) REVERT: I 87 TYR cc_start: 0.8629 (m-80) cc_final: 0.8124 (m-80) REVERT: I 91 TYR cc_start: 0.8853 (p90) cc_final: 0.8527 (p90) REVERT: D 16 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7057 (ttp-110) REVERT: D 47 TRP cc_start: 0.8938 (t60) cc_final: 0.8285 (t60) REVERT: D 72 ASP cc_start: 0.8326 (t0) cc_final: 0.8072 (t0) REVERT: D 75 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7771 (mmtt) REVERT: D 76 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8056 (t0) REVERT: D 81 GLN cc_start: 0.7721 (tt0) cc_final: 0.7403 (tp40) REVERT: D 83 ARG cc_start: 0.8282 (mpt-90) cc_final: 0.7701 (mpt-90) REVERT: E 87 TYR cc_start: 0.8667 (m-80) cc_final: 0.8144 (m-80) outliers start: 82 outliers final: 44 residues processed: 465 average time/residue: 0.1282 time to fit residues: 94.3511 Evaluate side-chains 391 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 155 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN B 454 ASN C 454 ASN F 76 ASN I 53 ASN I 93 ASN D 31 HIS E 124 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.159830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115161 restraints weight = 37428.869| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.14 r_work: 0.3440 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20781 Z= 0.136 Angle : 0.641 11.389 28232 Z= 0.327 Chirality : 0.045 0.289 3286 Planarity : 0.005 0.047 3579 Dihedral : 4.872 22.143 2811 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 3.36 % Allowed : 17.59 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2610 helix: 1.28 (0.26), residues: 408 sheet: -0.41 (0.17), residues: 918 loop : -0.83 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.021 0.001 TYR H 52A PHE 0.021 0.002 PHE F 67 TRP 0.027 0.002 TRP E 35 HIS 0.006 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20744) covalent geometry : angle 0.63680 / 0.33 (28157) SS BOND : bond 0.00554 / 0.37 ( 36) SS BOND : angle 1.49980 / 0.98 ( 72) hydrogen bonds : bond 0.02949 / 2.01 ( 900) hydrogen bonds : angle 5.44730 / 3.78 ( 2403) link_NAG-ASN : bond 0.00617 / 0.32 ( 1) link_NAG-ASN : angle 0.94933 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 385 time to evaluate : 0.835 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: A 156 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: A 338 ASP cc_start: 0.8496 (t0) cc_final: 0.8117 (t0) REVERT: A 395 ILE cc_start: 0.8305 (pt) cc_final: 0.8080 (pt) REVERT: A 398 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8782 (p) REVERT: A 417 TYR cc_start: 0.8607 (m-80) cc_final: 0.8322 (m-80) REVERT: A 426 ASN cc_start: 0.8584 (t0) cc_final: 0.8334 (t0) REVERT: A 448 ASP cc_start: 0.7747 (t0) cc_final: 0.7423 (t0) REVERT: B 141 LEU cc_start: 0.8472 (pt) cc_final: 0.8137 (pp) REVERT: B 335 THR cc_start: 0.9376 (t) cc_final: 0.8995 (p) REVERT: B 338 ASP cc_start: 0.8939 (t0) cc_final: 0.8574 (t0) REVERT: B 417 TYR cc_start: 0.8744 (m-80) cc_final: 0.8269 (m-10) REVERT: B 428 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8437 (p0) REVERT: B 462 GLN cc_start: 0.8621 (tp40) cc_final: 0.8349 (tp-100) REVERT: C 49 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7894 (ttp80) REVERT: C 53 TYR cc_start: 0.8893 (t80) cc_final: 0.8648 (t80) REVERT: C 363 ASN cc_start: 0.8495 (t0) cc_final: 0.8264 (t0) REVERT: C 426 ASN cc_start: 0.8200 (t0) cc_final: 0.7834 (t0) REVERT: C 440 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7524 (t0) REVERT: C 448 ASP cc_start: 0.7306 (t0) cc_final: 0.6874 (t0) REVERT: C 494 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 501 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7750 (tm-30) REVERT: F 43 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8966 (mmtp) REVERT: F 47 TRP cc_start: 0.9209 (t60) cc_final: 0.8875 (t60) REVERT: F 58 TYR cc_start: 0.8216 (m-80) cc_final: 0.7796 (m-10) REVERT: F 83 ARG cc_start: 0.8092 (mpp80) cc_final: 0.7872 (mpt-90) REVERT: F 176 TYR cc_start: 0.7057 (m-80) cc_final: 0.6744 (m-80) REVERT: G 4 MET cc_start: 0.7124 (ttt) cc_final: 0.6909 (ttt) REVERT: G 27 GLN cc_start: 0.8216 (pp30) cc_final: 0.7734 (pp30) REVERT: G 35 TRP cc_start: 0.9166 (m100) cc_final: 0.8886 (m100) REVERT: H 21 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8170 (p) REVERT: H 43 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8357 (mmtp) REVERT: H 58 TYR cc_start: 0.8630 (m-80) cc_final: 0.7737 (m-80) REVERT: H 72 ASP cc_start: 0.8126 (t0) cc_final: 0.7678 (t0) REVERT: H 83 ARG cc_start: 0.8252 (mpt-90) cc_final: 0.7815 (mpt-90) REVERT: H 100 ASP cc_start: 0.8732 (t0) cc_final: 0.7452 (t0) REVERT: H 100 TYR cc_start: 0.8651 (m-10) cc_final: 0.7181 (m-80) REVERT: H 100 TYR cc_start: 0.8364 (m-80) cc_final: 0.7842 (m-80) REVERT: H 100 TYR cc_start: 0.8333 (m-80) cc_final: 0.8026 (m-80) REVERT: H 176 TYR cc_start: 0.6159 (m-80) cc_final: 0.5746 (m-80) REVERT: I 35 TRP cc_start: 0.9298 (m100) cc_final: 0.8535 (m100) REVERT: I 81 GLU cc_start: 0.8570 (pp20) cc_final: 0.8258 (pp20) REVERT: I 91 TYR cc_start: 0.8863 (p90) cc_final: 0.8529 (p90) REVERT: I 93 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7994 (t0) REVERT: D 16 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.6949 (ttp-110) REVERT: D 36 TRP cc_start: 0.9292 (m100) cc_final: 0.8932 (m100) REVERT: D 47 TRP cc_start: 0.9050 (t60) cc_final: 0.8153 (t60) REVERT: D 72 ASP cc_start: 0.8340 (t0) cc_final: 0.8002 (t0) REVERT: D 75 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7947 (mmtt) REVERT: D 76 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8029 (t0) REVERT: D 81 GLN cc_start: 0.7780 (tt0) cc_final: 0.7389 (tp40) REVERT: D 83 ARG cc_start: 0.8231 (mpt-90) cc_final: 0.7817 (mpt-90) outliers start: 79 outliers final: 45 residues processed: 435 average time/residue: 0.1419 time to fit residues: 97.1037 Evaluate side-chains 392 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 340 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 135 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 63 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 227 ASN B 302 GLN B 454 ASN D 31 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.152301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107442 restraints weight = 37053.169| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.04 r_work: 0.3303 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20781 Z= 0.251 Angle : 0.713 11.810 28232 Z= 0.367 Chirality : 0.047 0.296 3286 Planarity : 0.005 0.049 3579 Dihedral : 5.145 21.277 2811 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 4.64 % Allowed : 18.19 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.69 (0.17), residues: 2610 helix: 1.07 (0.26), residues: 417 sheet: -0.50 (0.17), residues: 918 loop : -0.86 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 65 TYR 0.022 0.002 TYR D 100C PHE 0.022 0.002 PHE F 67 TRP 0.019 0.002 TRP E 35 HIS 0.006 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (20744) covalent geometry : angle 0.70942 / 0.37 (28157) SS BOND : bond 0.00659 / 0.45 ( 36) SS BOND : angle 1.63943 / 1.07 ( 72) hydrogen bonds : bond 0.03368 / 2.29 ( 900) hydrogen bonds : angle 5.57678 / 3.87 ( 2403) link_NAG-ASN : bond 0.00582 / 0.31 ( 1) link_NAG-ASN : angle 1.15714 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 364 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: A 338 ASP cc_start: 0.8726 (t0) cc_final: 0.8233 (t0) REVERT: A 428 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8741 (p0) REVERT: A 448 ASP cc_start: 0.7832 (t0) cc_final: 0.7508 (t0) REVERT: B 78 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 334 LEU cc_start: 0.8838 (tp) cc_final: 0.8622 (tp) REVERT: B 338 ASP cc_start: 0.8900 (t0) cc_final: 0.8363 (t0) REVERT: B 417 TYR cc_start: 0.8875 (m-80) cc_final: 0.8308 (m-10) REVERT: B 462 GLN cc_start: 0.8722 (tp40) cc_final: 0.8449 (tp-100) REVERT: C 49 ARG cc_start: 0.8642 (ttp80) cc_final: 0.7837 (ttp80) REVERT: C 363 ASN cc_start: 0.8646 (t0) cc_final: 0.8151 (t0) REVERT: C 426 ASN cc_start: 0.8663 (t0) cc_final: 0.8327 (t0) REVERT: C 448 ASP cc_start: 0.7538 (t0) cc_final: 0.7066 (t0) REVERT: C 501 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 16 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7667 (ttp-110) REVERT: F 43 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8942 (mmtp) REVERT: F 47 TRP cc_start: 0.9205 (t60) cc_final: 0.8848 (t60) REVERT: F 58 TYR cc_start: 0.8397 (m-80) cc_final: 0.7795 (m-10) REVERT: F 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7838 (t0) REVERT: F 74 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8337 (t) REVERT: F 75 LYS cc_start: 0.8244 (mptt) cc_final: 0.7737 (mmtp) REVERT: F 176 TYR cc_start: 0.7323 (m-80) cc_final: 0.6980 (m-80) REVERT: G 48 MET cc_start: 0.8147 (ptm) cc_final: 0.7862 (ptm) REVERT: G 91 TYR cc_start: 0.9155 (p90) cc_final: 0.8699 (p90) REVERT: G 116 PHE cc_start: 0.0675 (OUTLIER) cc_final: -0.0536 (m-80) REVERT: H 47 TRP cc_start: 0.8877 (t60) cc_final: 0.8534 (t60) REVERT: H 72 ASP cc_start: 0.8188 (t0) cc_final: 0.7972 (t0) REVERT: H 76 ASN cc_start: 0.8551 (t0) cc_final: 0.8311 (t0) REVERT: H 83 ARG cc_start: 0.8299 (mpt-90) cc_final: 0.7875 (mpt-90) REVERT: H 100 ASP cc_start: 0.8929 (t0) cc_final: 0.8557 (t70) REVERT: H 100 TYR cc_start: 0.8762 (m-10) cc_final: 0.7352 (m-80) REVERT: H 100 TYR cc_start: 0.8485 (m-80) cc_final: 0.8146 (m-80) REVERT: H 176 TYR cc_start: 0.6189 (m-80) cc_final: 0.5804 (m-80) REVERT: I 81 GLU cc_start: 0.8518 (pp20) cc_final: 0.8153 (pp20) REVERT: I 91 TYR cc_start: 0.8973 (p90) cc_final: 0.8428 (p90) REVERT: D 36 TRP cc_start: 0.9275 (m100) cc_final: 0.8735 (m100) REVERT: D 47 TRP cc_start: 0.9142 (t60) cc_final: 0.8165 (t60) REVERT: D 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7855 (t0) REVERT: D 75 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8159 (mmtt) REVERT: D 76 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8047 (t0) REVERT: D 81 GLN cc_start: 0.7720 (tt0) cc_final: 0.7446 (tp40) REVERT: D 83 ARG cc_start: 0.8212 (mpt-90) cc_final: 0.7809 (mpt-90) REVERT: D 100 TYR cc_start: 0.8705 (m-80) cc_final: 0.8267 (m-80) outliers start: 109 outliers final: 82 residues processed: 443 average time/residue: 0.1382 time to fit residues: 96.2053 Evaluate side-chains 427 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 339 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 135 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 462 GLN B 227 ASN B 454 ASN C 227 ASN C 302 GLN C 444 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100433 restraints weight = 37289.815| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.04 r_work: 0.3206 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 20781 Z= 0.352 Angle : 0.791 11.040 28232 Z= 0.409 Chirality : 0.049 0.300 3286 Planarity : 0.006 0.064 3579 Dihedral : 5.571 22.211 2811 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.25 % Rotamer: Outliers : 5.75 % Allowed : 18.87 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.12 (0.16), residues: 2610 helix: 0.48 (0.25), residues: 438 sheet: -0.73 (0.17), residues: 882 loop : -1.11 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 235 TYR 0.025 0.002 TYR D 100C PHE 0.023 0.002 PHE F 67 TRP 0.019 0.002 TRP F 36 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.35 (20744) covalent geometry : angle 0.78683 / 0.41 (28157) SS BOND : bond 0.00751 / 0.52 ( 36) SS BOND : angle 1.71496 / 1.13 ( 72) hydrogen bonds : bond 0.03716 / 2.53 ( 900) hydrogen bonds : angle 5.90555 / 4.10 ( 2403) link_NAG-ASN : bond 0.00582 / 0.31 ( 1) link_NAG-ASN : angle 1.23125 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 348 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8336 (tttm) REVERT: A 338 ASP cc_start: 0.8951 (t0) cc_final: 0.8443 (t0) REVERT: A 448 ASP cc_start: 0.7867 (t0) cc_final: 0.7572 (t0) REVERT: A 462 GLN cc_start: 0.8813 (tp40) cc_final: 0.8573 (tp-100) REVERT: A 482 VAL cc_start: 0.9104 (m) cc_final: 0.8802 (p) REVERT: B 251 MET cc_start: 0.9117 (ttm) cc_final: 0.8778 (ttm) REVERT: B 338 ASP cc_start: 0.8848 (t0) cc_final: 0.8193 (t0) REVERT: C 49 ARG cc_start: 0.8676 (ttp80) cc_final: 0.7800 (ttp80) REVERT: C 289 MET cc_start: 0.8194 (ttp) cc_final: 0.7751 (tmm) REVERT: C 440 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7945 (t0) REVERT: F 16 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7476 (ttp-110) REVERT: F 34 MET cc_start: 0.8854 (mmt) cc_final: 0.8580 (mmm) REVERT: F 36 TRP cc_start: 0.9360 (m100) cc_final: 0.9151 (m100) REVERT: F 43 LYS cc_start: 0.9120 (mmtm) cc_final: 0.8874 (mmtp) REVERT: F 47 TRP cc_start: 0.9195 (t60) cc_final: 0.8829 (t60) REVERT: F 58 TYR cc_start: 0.8526 (m-80) cc_final: 0.8064 (m-80) REVERT: F 72 ASP cc_start: 0.8201 (t0) cc_final: 0.7783 (t0) REVERT: F 75 LYS cc_start: 0.8593 (mptt) cc_final: 0.8112 (mmtp) REVERT: F 176 TYR cc_start: 0.7420 (m-80) cc_final: 0.7048 (m-80) REVERT: G 91 TYR cc_start: 0.9233 (p90) cc_final: 0.8889 (p90) REVERT: G 116 PHE cc_start: 0.0992 (OUTLIER) cc_final: -0.0878 (m-80) REVERT: H 32 TYR cc_start: 0.8823 (m-10) cc_final: 0.8569 (m-10) REVERT: H 47 TRP cc_start: 0.9052 (t60) cc_final: 0.8259 (t60) REVERT: H 72 ASP cc_start: 0.8232 (t0) cc_final: 0.7844 (t0) REVERT: H 76 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (t0) REVERT: H 100 ASP cc_start: 0.8961 (t0) cc_final: 0.8126 (t70) REVERT: H 100 TYR cc_start: 0.8826 (m-10) cc_final: 0.7268 (m-80) REVERT: H 100 TYR cc_start: 0.8555 (m-80) cc_final: 0.8249 (m-80) REVERT: H 100 TYR cc_start: 0.8751 (m-80) cc_final: 0.7706 (m-80) REVERT: H 176 TYR cc_start: 0.6180 (m-80) cc_final: 0.5696 (m-80) REVERT: I 55 GLU cc_start: 0.8598 (tp30) cc_final: 0.8209 (tp30) REVERT: I 81 GLU cc_start: 0.8553 (pp20) cc_final: 0.8136 (pp20) REVERT: I 91 TYR cc_start: 0.9154 (p90) cc_final: 0.8808 (p90) REVERT: D 16 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7567 (ttp-110) REVERT: D 47 TRP cc_start: 0.9169 (t60) cc_final: 0.8359 (t60) REVERT: D 72 ASP cc_start: 0.8173 (t0) cc_final: 0.7773 (t0) REVERT: D 75 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8446 (mmtt) REVERT: D 76 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7982 (t0) REVERT: D 83 ARG cc_start: 0.8457 (mpt-90) cc_final: 0.8046 (mpt-90) REVERT: D 100 TYR cc_start: 0.8794 (m-80) cc_final: 0.8399 (m-80) REVERT: E 106 ILE cc_start: 0.7585 (mm) cc_final: 0.7134 (mm) outliers start: 135 outliers final: 102 residues processed: 444 average time/residue: 0.1317 time to fit residues: 92.9046 Evaluate side-chains 426 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 319 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 ASN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 83 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN B 227 ASN C 444 ASN C 460 ASN F 76 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109221 restraints weight = 36940.255| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.08 r_work: 0.3348 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20781 Z= 0.132 Angle : 0.672 14.493 28232 Z= 0.340 Chirality : 0.046 0.315 3286 Planarity : 0.005 0.053 3579 Dihedral : 5.067 21.287 2811 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.06 % Favored : 95.79 % Rotamer: Outliers : 3.36 % Allowed : 22.27 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.77 (0.17), residues: 2610 helix: 1.19 (0.26), residues: 417 sheet: -0.65 (0.17), residues: 887 loop : -0.90 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 65 TYR 0.023 0.001 TYR G 87 PHE 0.019 0.002 PHE D 67 TRP 0.014 0.001 TRP F 36 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (20744) covalent geometry : angle 0.67047 / 0.34 (28157) SS BOND : bond 0.00523 / 0.35 ( 36) SS BOND : angle 1.20501 / 0.79 ( 72) hydrogen bonds : bond 0.03028 / 2.04 ( 900) hydrogen bonds : angle 5.52835 / 3.83 ( 2403) link_NAG-ASN : bond 0.00449 / 0.24 ( 1) link_NAG-ASN : angle 1.10964 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 401 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8178 (tttm) REVERT: A 338 ASP cc_start: 0.8793 (t0) cc_final: 0.8402 (t0) REVERT: A 448 ASP cc_start: 0.7873 (t0) cc_final: 0.7583 (t0) REVERT: A 462 GLN cc_start: 0.8712 (tp40) cc_final: 0.8503 (tp-100) REVERT: A 505 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 53 TYR cc_start: 0.8879 (t80) cc_final: 0.8639 (t80) REVERT: B 334 LEU cc_start: 0.8870 (tt) cc_final: 0.8332 (tp) REVERT: B 338 ASP cc_start: 0.8757 (t0) cc_final: 0.8295 (t0) REVERT: B 417 TYR cc_start: 0.8817 (m-80) cc_final: 0.8508 (m-10) REVERT: B 505 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 49 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7801 (ttp80) REVERT: C 75 LYS cc_start: 0.9300 (mttt) cc_final: 0.8895 (mttp) REVERT: C 363 ASN cc_start: 0.8426 (t0) cc_final: 0.8020 (t0) REVERT: C 440 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 462 GLN cc_start: 0.8832 (tp40) cc_final: 0.8540 (tp-100) REVERT: F 34 MET cc_start: 0.8587 (mmt) cc_final: 0.8356 (mmm) REVERT: F 43 LYS cc_start: 0.9046 (mmtm) cc_final: 0.8822 (mmtp) REVERT: F 47 TRP cc_start: 0.9141 (t60) cc_final: 0.8718 (t60) REVERT: F 58 TYR cc_start: 0.8508 (m-80) cc_final: 0.7817 (m-10) REVERT: F 72 ASP cc_start: 0.8227 (t0) cc_final: 0.7866 (t0) REVERT: F 86 ASP cc_start: 0.8848 (t70) cc_final: 0.8114 (t70) REVERT: F 100 ASP cc_start: 0.9050 (t0) cc_final: 0.8730 (t0) REVERT: F 144 ASP cc_start: 0.6763 (m-30) cc_final: 0.6450 (m-30) REVERT: F 176 TYR cc_start: 0.7448 (m-80) cc_final: 0.7096 (m-80) REVERT: G 35 TRP cc_start: 0.9276 (m100) cc_final: 0.9027 (m100) REVERT: G 50 ASP cc_start: 0.8948 (m-30) cc_final: 0.8693 (m-30) REVERT: G 91 TYR cc_start: 0.9083 (p90) cc_final: 0.8537 (p90) REVERT: H 43 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8431 (mmtp) REVERT: H 47 TRP cc_start: 0.8875 (t60) cc_final: 0.8237 (t60) REVERT: H 58 TYR cc_start: 0.8610 (m-80) cc_final: 0.7013 (m-80) REVERT: H 72 ASP cc_start: 0.8231 (t0) cc_final: 0.7922 (t0) REVERT: H 76 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8230 (t0) REVERT: H 100 ASP cc_start: 0.9028 (t0) cc_final: 0.8602 (t70) REVERT: H 100 TYR cc_start: 0.8695 (m-10) cc_final: 0.7059 (m-80) REVERT: H 100 TYR cc_start: 0.8357 (m-80) cc_final: 0.7611 (m-80) REVERT: H 176 TYR cc_start: 0.6169 (m-80) cc_final: 0.5691 (m-80) REVERT: I 55 GLU cc_start: 0.8350 (tp30) cc_final: 0.8047 (tp30) REVERT: I 81 GLU cc_start: 0.8498 (pp20) cc_final: 0.8135 (pp20) REVERT: I 91 TYR cc_start: 0.8817 (p90) cc_final: 0.8557 (p90) REVERT: D 16 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7400 (ttp-110) REVERT: D 36 TRP cc_start: 0.9251 (m100) cc_final: 0.8745 (m100) REVERT: D 47 TRP cc_start: 0.9120 (t60) cc_final: 0.8125 (t60) REVERT: D 58 TYR cc_start: 0.8684 (m-80) cc_final: 0.6893 (m-80) REVERT: D 72 ASP cc_start: 0.8057 (t0) cc_final: 0.7691 (t0) REVERT: D 75 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8329 (mptt) REVERT: D 76 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 83 ARG cc_start: 0.8361 (mpt-90) cc_final: 0.7899 (mpt-90) REVERT: D 100 ASP cc_start: 0.8798 (t0) cc_final: 0.8459 (t70) REVERT: D 100 TYR cc_start: 0.8660 (m-80) cc_final: 0.7718 (m-80) REVERT: D 117 LYS cc_start: 0.5248 (tptt) cc_final: 0.5019 (tptm) REVERT: E 27 GLN cc_start: 0.8526 (pp30) cc_final: 0.8312 (pp30) REVERT: E 106 ILE cc_start: 0.7519 (mm) cc_final: 0.7077 (mm) outliers start: 79 outliers final: 54 residues processed: 448 average time/residue: 0.1380 time to fit residues: 97.7326 Evaluate side-chains 415 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 179 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108115 restraints weight = 36985.887| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.07 r_work: 0.3345 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20781 Z= 0.156 Angle : 0.687 11.976 28232 Z= 0.346 Chirality : 0.046 0.299 3286 Planarity : 0.005 0.050 3579 Dihedral : 5.011 21.635 2811 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 3.24 % Allowed : 23.21 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.71 (0.17), residues: 2610 helix: 1.25 (0.26), residues: 417 sheet: -0.60 (0.17), residues: 915 loop : -0.88 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.037 0.002 TYR F 52A PHE 0.028 0.002 PHE F 67 TRP 0.026 0.002 TRP F 36 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (20744) covalent geometry : angle 0.68280 / 0.34 (28157) SS BOND : bond 0.00554 / 0.37 ( 36) SS BOND : angle 1.57328 / 0.92 ( 72) hydrogen bonds : bond 0.03016 / 2.04 ( 900) hydrogen bonds : angle 5.45184 / 3.78 ( 2403) link_NAG-ASN : bond 0.00480 / 0.25 ( 1) link_NAG-ASN : angle 1.26355 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 376 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7766 (tmm) cc_final: 0.7553 (tmm) REVERT: A 156 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8203 (tttm) REVERT: A 338 ASP cc_start: 0.8746 (t0) cc_final: 0.8357 (t0) REVERT: A 448 ASP cc_start: 0.7820 (t0) cc_final: 0.7500 (t0) REVERT: A 505 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 53 TYR cc_start: 0.8921 (t80) cc_final: 0.8674 (t80) REVERT: B 75 LYS cc_start: 0.9217 (mttt) cc_final: 0.8901 (mttp) REVERT: B 334 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8258 (tp) REVERT: B 338 ASP cc_start: 0.8677 (t0) cc_final: 0.8237 (t0) REVERT: B 363 ASN cc_start: 0.8498 (t0) cc_final: 0.8213 (t0) REVERT: B 417 TYR cc_start: 0.8811 (m-80) cc_final: 0.8435 (m-10) REVERT: B 419 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8261 (mttt) REVERT: C 49 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7795 (ttp80) REVERT: C 75 LYS cc_start: 0.9254 (mttt) cc_final: 0.8984 (mttp) REVERT: C 363 ASN cc_start: 0.8470 (t0) cc_final: 0.8043 (t0) REVERT: C 417 TYR cc_start: 0.8459 (m-10) cc_final: 0.8038 (m-10) REVERT: C 440 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7966 (t0) REVERT: C 462 GLN cc_start: 0.8796 (tp40) cc_final: 0.8574 (tp-100) REVERT: F 34 MET cc_start: 0.8665 (mmt) cc_final: 0.8403 (mmm) REVERT: F 36 TRP cc_start: 0.9265 (m100) cc_final: 0.9037 (m100) REVERT: F 43 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8853 (mmtp) REVERT: F 47 TRP cc_start: 0.9088 (t60) cc_final: 0.8798 (t60) REVERT: F 58 TYR cc_start: 0.8649 (m-80) cc_final: 0.8072 (m-80) REVERT: F 72 ASP cc_start: 0.8233 (t0) cc_final: 0.7871 (t0) REVERT: F 76 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8167 (t0) REVERT: F 86 ASP cc_start: 0.8878 (t70) cc_final: 0.8092 (t70) REVERT: F 100 ASP cc_start: 0.9022 (t0) cc_final: 0.8671 (t0) REVERT: F 144 ASP cc_start: 0.6791 (m-30) cc_final: 0.6457 (m-30) REVERT: G 35 TRP cc_start: 0.9316 (m100) cc_final: 0.8933 (m100) REVERT: G 50 ASP cc_start: 0.8949 (m-30) cc_final: 0.8679 (m-30) REVERT: G 91 TYR cc_start: 0.9197 (p90) cc_final: 0.8829 (p90) REVERT: H 43 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8310 (mmtp) REVERT: H 47 TRP cc_start: 0.8891 (t60) cc_final: 0.8176 (t60) REVERT: H 58 TYR cc_start: 0.8635 (m-80) cc_final: 0.7035 (m-80) REVERT: H 72 ASP cc_start: 0.8354 (t0) cc_final: 0.8017 (t0) REVERT: H 76 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8150 (t0) REVERT: H 100 ASP cc_start: 0.9005 (t0) cc_final: 0.8746 (t0) REVERT: H 100 TYR cc_start: 0.8714 (m-10) cc_final: 0.7297 (m-80) REVERT: H 100 TYR cc_start: 0.8408 (m-80) cc_final: 0.7713 (m-80) REVERT: H 176 TYR cc_start: 0.6230 (m-80) cc_final: 0.5819 (m-80) REVERT: I 55 GLU cc_start: 0.8281 (tp30) cc_final: 0.8005 (tp30) REVERT: I 81 GLU cc_start: 0.8523 (pp20) cc_final: 0.8114 (pp20) REVERT: I 91 TYR cc_start: 0.8923 (p90) cc_final: 0.8711 (p90) REVERT: D 16 ARG cc_start: 0.7688 (ttp-110) cc_final: 0.7397 (ttp-110) REVERT: D 47 TRP cc_start: 0.9179 (t60) cc_final: 0.8105 (t60) REVERT: D 56 ASN cc_start: 0.8761 (m-40) cc_final: 0.8502 (m-40) REVERT: D 58 TYR cc_start: 0.8721 (m-80) cc_final: 0.7073 (m-80) REVERT: D 72 ASP cc_start: 0.8079 (t0) cc_final: 0.7633 (t0) REVERT: D 75 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8426 (mmtp) REVERT: D 76 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (t0) REVERT: D 83 ARG cc_start: 0.8380 (mpt-90) cc_final: 0.7898 (mpt-90) REVERT: D 100 TYR cc_start: 0.8732 (m-80) cc_final: 0.7853 (m-80) REVERT: D 117 LYS cc_start: 0.5259 (tptt) cc_final: 0.5035 (tptm) REVERT: E 27 GLN cc_start: 0.8599 (pp30) cc_final: 0.8399 (pp30) REVERT: E 106 ILE cc_start: 0.7564 (mm) cc_final: 0.7136 (mm) outliers start: 76 outliers final: 58 residues processed: 419 average time/residue: 0.1478 time to fit residues: 97.4859 Evaluate side-chains 421 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 40 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 203 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 237 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN D 3 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.165536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117210 restraints weight = 39193.739| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.32 r_work: 0.3385 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20781 Z= 0.189 Angle : 0.709 15.184 28232 Z= 0.357 Chirality : 0.046 0.320 3286 Planarity : 0.005 0.053 3579 Dihedral : 5.067 22.131 2811 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 3.32 % Allowed : 23.47 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.71 (0.17), residues: 2610 helix: 1.25 (0.26), residues: 417 sheet: -0.60 (0.17), residues: 915 loop : -0.88 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 235 TYR 0.038 0.002 TYR F 52A PHE 0.028 0.002 PHE F 67 TRP 0.022 0.002 TRP F 36 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (20744) covalent geometry : angle 0.70610 / 0.36 (28157) SS BOND : bond 0.00597 / 0.38 ( 36) SS BOND : angle 1.52767 / 0.90 ( 72) hydrogen bonds : bond 0.03130 / 2.14 ( 900) hydrogen bonds : angle 5.46201 / 3.79 ( 2403) link_NAG-ASN : bond 0.00502 / 0.26 ( 1) link_NAG-ASN : angle 1.19970 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 367 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8197 (tttm) REVERT: A 338 ASP cc_start: 0.8819 (t0) cc_final: 0.8378 (t0) REVERT: A 448 ASP cc_start: 0.8026 (t0) cc_final: 0.7761 (t0) REVERT: A 505 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (t80) REVERT: B 53 TYR cc_start: 0.8975 (t80) cc_final: 0.8636 (t80) REVERT: B 75 LYS cc_start: 0.9172 (mttt) cc_final: 0.8879 (mttp) REVERT: B 256 GLU cc_start: 0.8772 (tp30) cc_final: 0.8323 (tp30) REVERT: B 334 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 338 ASP cc_start: 0.8776 (t0) cc_final: 0.8277 (t0) REVERT: B 363 ASN cc_start: 0.8424 (t0) cc_final: 0.8109 (t0) REVERT: B 419 LYS cc_start: 0.8706 (ptmt) cc_final: 0.8282 (mttt) REVERT: C 49 ARG cc_start: 0.8545 (ttp80) cc_final: 0.7806 (ttp80) REVERT: C 75 LYS cc_start: 0.9173 (mttt) cc_final: 0.8917 (mttp) REVERT: C 235 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8596 (tpp80) REVERT: C 291 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8783 (tp) REVERT: C 363 ASN cc_start: 0.8444 (t0) cc_final: 0.7976 (t0) REVERT: C 417 TYR cc_start: 0.8565 (m-10) cc_final: 0.7960 (m-10) REVERT: C 440 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7930 (t0) REVERT: C 462 GLN cc_start: 0.8860 (tp40) cc_final: 0.8554 (tp-100) REVERT: F 16 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7402 (ttp-110) REVERT: F 34 MET cc_start: 0.8751 (mmt) cc_final: 0.8369 (mmm) REVERT: F 36 TRP cc_start: 0.9313 (m100) cc_final: 0.8990 (m100) REVERT: F 43 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8828 (mmtp) REVERT: F 47 TRP cc_start: 0.9108 (t60) cc_final: 0.8745 (t60) REVERT: F 52 TYR cc_start: 0.8943 (p90) cc_final: 0.8699 (p90) REVERT: F 58 TYR cc_start: 0.8618 (m-80) cc_final: 0.7848 (m-80) REVERT: F 72 ASP cc_start: 0.8035 (t0) cc_final: 0.7602 (t0) REVERT: F 74 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8529 (t) REVERT: F 76 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8130 (t0) REVERT: F 86 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8126 (t70) REVERT: F 100 ASP cc_start: 0.9131 (t0) cc_final: 0.8518 (t0) REVERT: F 100 TYR cc_start: 0.8697 (m-80) cc_final: 0.7922 (m-80) REVERT: F 100 TYR cc_start: 0.8758 (m-80) cc_final: 0.8474 (m-80) REVERT: F 144 ASP cc_start: 0.6709 (m-30) cc_final: 0.6389 (m-30) REVERT: G 35 TRP cc_start: 0.9335 (m100) cc_final: 0.8858 (m100) REVERT: G 50 ASP cc_start: 0.8856 (m-30) cc_final: 0.8608 (m-30) REVERT: G 91 TYR cc_start: 0.9283 (p90) cc_final: 0.8961 (p90) REVERT: H 43 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8310 (mmtp) REVERT: H 47 TRP cc_start: 0.8887 (t60) cc_final: 0.8110 (t60) REVERT: H 58 TYR cc_start: 0.8570 (m-80) cc_final: 0.6852 (m-80) REVERT: H 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7806 (t0) REVERT: H 76 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8053 (t0) REVERT: H 82 MET cc_start: 0.6333 (mtm) cc_final: 0.5861 (mtm) REVERT: H 100 ASP cc_start: 0.9129 (t0) cc_final: 0.8912 (t0) REVERT: H 100 TYR cc_start: 0.8709 (m-10) cc_final: 0.7516 (m-80) REVERT: H 100 TYR cc_start: 0.8453 (m-80) cc_final: 0.7665 (m-80) REVERT: H 176 TYR cc_start: 0.6107 (m-80) cc_final: 0.5748 (m-80) REVERT: I 4 MET cc_start: 0.7380 (mtp) cc_final: 0.6923 (ttm) REVERT: I 55 GLU cc_start: 0.8472 (tp30) cc_final: 0.8121 (tp30) REVERT: I 81 GLU cc_start: 0.8469 (pp20) cc_final: 0.8064 (pp20) REVERT: I 91 TYR cc_start: 0.9033 (p90) cc_final: 0.8582 (p90) REVERT: D 16 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7431 (ttp-110) REVERT: D 36 TRP cc_start: 0.9165 (m100) cc_final: 0.8603 (m100) REVERT: D 47 TRP cc_start: 0.9166 (t60) cc_final: 0.8098 (t60) REVERT: D 58 TYR cc_start: 0.8618 (m-80) cc_final: 0.6878 (m-80) REVERT: D 67 PHE cc_start: 0.7886 (m-80) cc_final: 0.7488 (m-80) REVERT: D 72 ASP cc_start: 0.7903 (t0) cc_final: 0.7427 (t0) REVERT: D 75 LYS cc_start: 0.8770 (mmtp) cc_final: 0.8452 (mmtp) REVERT: D 76 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7832 (t0) REVERT: D 83 ARG cc_start: 0.8456 (mpt-90) cc_final: 0.7954 (mpt-90) REVERT: D 100 ASP cc_start: 0.8747 (t70) cc_final: 0.8457 (t70) REVERT: D 100 TYR cc_start: 0.8778 (m-80) cc_final: 0.7862 (m-80) REVERT: D 117 LYS cc_start: 0.5196 (tptt) cc_final: 0.4995 (tptm) REVERT: E 27 GLN cc_start: 0.8596 (pp30) cc_final: 0.8379 (pp30) REVERT: E 85 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (p) REVERT: E 106 ILE cc_start: 0.7465 (mm) cc_final: 0.7036 (mm) outliers start: 78 outliers final: 59 residues processed: 408 average time/residue: 0.1454 time to fit residues: 92.4022 Evaluate side-chains 424 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.161461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.113058 restraints weight = 39634.860| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.28 r_work: 0.3341 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20781 Z= 0.234 Angle : 0.734 14.569 28232 Z= 0.373 Chirality : 0.047 0.312 3286 Planarity : 0.005 0.064 3579 Dihedral : 5.224 22.468 2811 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 3.45 % Allowed : 23.51 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.80 (0.17), residues: 2610 helix: 1.15 (0.26), residues: 417 sheet: -0.68 (0.17), residues: 918 loop : -0.90 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 235 TYR 0.037 0.002 TYR F 52A PHE 0.033 0.002 PHE D 67 TRP 0.028 0.002 TRP H 36 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (20744) covalent geometry : angle 0.73019 / 0.37 (28157) SS BOND : bond 0.00635 / 0.41 ( 36) SS BOND : angle 1.56819 / 0.95 ( 72) hydrogen bonds : bond 0.03318 / 2.28 ( 900) hydrogen bonds : angle 5.57297 / 3.86 ( 2403) link_NAG-ASN : bond 0.00503 / 0.26 ( 1) link_NAG-ASN : angle 1.23173 / 0.65 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 350 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8302 (tttm) REVERT: A 338 ASP cc_start: 0.8901 (t0) cc_final: 0.8401 (t0) REVERT: A 448 ASP cc_start: 0.7990 (t0) cc_final: 0.7705 (t0) REVERT: A 482 VAL cc_start: 0.9211 (m) cc_final: 0.8924 (p) REVERT: A 505 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 75 LYS cc_start: 0.9167 (mttt) cc_final: 0.8845 (mttp) REVERT: B 256 GLU cc_start: 0.8767 (tp30) cc_final: 0.8317 (tp30) REVERT: B 338 ASP cc_start: 0.8788 (t0) cc_final: 0.8260 (t0) REVERT: B 419 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8351 (mttt) REVERT: B 482 VAL cc_start: 0.9182 (m) cc_final: 0.8885 (p) REVERT: C 49 ARG cc_start: 0.8620 (ttp80) cc_final: 0.7801 (ttp80) REVERT: C 75 LYS cc_start: 0.9213 (mttt) cc_final: 0.8950 (mttp) REVERT: C 235 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8720 (tpp80) REVERT: C 417 TYR cc_start: 0.8673 (m-10) cc_final: 0.8010 (m-10) REVERT: C 462 GLN cc_start: 0.8846 (tp40) cc_final: 0.8519 (tp-100) REVERT: F 16 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7545 (ttp-110) REVERT: F 34 MET cc_start: 0.8749 (mmt) cc_final: 0.8389 (mmm) REVERT: F 36 TRP cc_start: 0.9324 (m100) cc_final: 0.9053 (m100) REVERT: F 43 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8816 (mmtp) REVERT: F 47 TRP cc_start: 0.9131 (t60) cc_final: 0.8764 (t60) REVERT: F 58 TYR cc_start: 0.8671 (m-80) cc_final: 0.8054 (m-80) REVERT: F 72 ASP cc_start: 0.8065 (t0) cc_final: 0.7623 (t0) REVERT: F 74 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8597 (t) REVERT: F 76 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8146 (t0) REVERT: F 86 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8151 (t70) REVERT: F 100 TYR cc_start: 0.8685 (m-80) cc_final: 0.8404 (m-80) REVERT: F 144 ASP cc_start: 0.6322 (m-30) cc_final: 0.5962 (m-30) REVERT: G 35 TRP cc_start: 0.9387 (m100) cc_final: 0.8848 (m100) REVERT: G 50 ASP cc_start: 0.8913 (m-30) cc_final: 0.8672 (m-30) REVERT: G 91 TYR cc_start: 0.9317 (p90) cc_final: 0.9068 (p90) REVERT: H 47 TRP cc_start: 0.8944 (t60) cc_final: 0.8084 (t60) REVERT: H 59 TYR cc_start: 0.8856 (m-80) cc_final: 0.8650 (m-80) REVERT: H 72 ASP cc_start: 0.8165 (t0) cc_final: 0.7743 (t0) REVERT: H 76 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7922 (t0) REVERT: H 82 MET cc_start: 0.6653 (mtm) cc_final: 0.6117 (mtm) REVERT: H 100 TYR cc_start: 0.8713 (m-10) cc_final: 0.7489 (m-80) REVERT: H 100 TYR cc_start: 0.8551 (m-80) cc_final: 0.8264 (m-80) REVERT: H 176 TYR cc_start: 0.6158 (m-80) cc_final: 0.5653 (m-80) REVERT: I 4 MET cc_start: 0.7434 (mtp) cc_final: 0.7000 (ttm) REVERT: I 55 GLU cc_start: 0.8509 (tp30) cc_final: 0.8125 (tp30) REVERT: I 81 GLU cc_start: 0.8477 (pp20) cc_final: 0.8061 (pp20) REVERT: I 91 TYR cc_start: 0.9144 (p90) cc_final: 0.8762 (p90) REVERT: D 16 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7421 (ttp-110) REVERT: D 36 TRP cc_start: 0.9155 (m100) cc_final: 0.8642 (m100) REVERT: D 47 TRP cc_start: 0.9165 (t60) cc_final: 0.8172 (t60) REVERT: D 58 TYR cc_start: 0.8614 (m-80) cc_final: 0.6905 (m-80) REVERT: D 72 ASP cc_start: 0.7930 (t0) cc_final: 0.7454 (t0) REVERT: D 75 LYS cc_start: 0.8905 (mmtp) cc_final: 0.8575 (mmtp) REVERT: D 76 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7846 (t0) REVERT: D 83 ARG cc_start: 0.8459 (mpt-90) cc_final: 0.7955 (mpt-90) REVERT: D 100 ASP cc_start: 0.8865 (t70) cc_final: 0.8641 (t70) REVERT: D 100 TYR cc_start: 0.8808 (m-80) cc_final: 0.7894 (m-80) REVERT: D 100 MET cc_start: 0.8829 (mpp) cc_final: 0.8417 (mpp) REVERT: E 27 GLN cc_start: 0.8572 (pp30) cc_final: 0.8082 (pp30) REVERT: E 106 ILE cc_start: 0.7376 (mm) cc_final: 0.6938 (mm) outliers start: 81 outliers final: 67 residues processed: 399 average time/residue: 0.1412 time to fit residues: 88.7168 Evaluate side-chains 416 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 342 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 202 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111977 restraints weight = 39740.495| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.30 r_work: 0.3354 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20781 Z= 0.206 Angle : 0.723 15.358 28232 Z= 0.365 Chirality : 0.047 0.312 3286 Planarity : 0.005 0.053 3579 Dihedral : 5.195 22.477 2811 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 3.66 % Allowed : 23.55 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.17), residues: 2610 helix: 1.17 (0.26), residues: 417 sheet: -0.66 (0.17), residues: 918 loop : -0.90 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 235 TYR 0.040 0.002 TYR F 52A PHE 0.031 0.002 PHE F 67 TRP 0.043 0.002 TRP H 36 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (20744) covalent geometry : angle 0.72004 / 0.36 (28157) SS BOND : bond 0.00585 / 0.38 ( 36) SS BOND : angle 1.41598 / 0.87 ( 72) hydrogen bonds : bond 0.03226 / 2.21 ( 900) hydrogen bonds : angle 5.56080 / 3.85 ( 2403) link_NAG-ASN : bond 0.00510 / 0.27 ( 1) link_NAG-ASN : angle 1.20688 / 0.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5708.37 seconds wall clock time: 98 minutes 52.41 seconds (5932.41 seconds total)