Starting phenix.real_space_refine on Thu Mar 5 07:42:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mpg_23933/03_2026/7mpg_23933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mpg_23933/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mpg_23933/03_2026/7mpg_23933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mpg_23933/03_2026/7mpg_23933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mpg_23933/03_2026/7mpg_23933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mpg_23933/03_2026/7mpg_23933.map" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.97, per 1000 atoms: 0.24 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: 1.47 Conformation dependent library (CDL) restraints added in 621.6 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: 1.04 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: 4.61 Time building geometry restraints manager: 2.02 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 - 25.17: 12100 25.17 - 50.34: 519 50.34 - 75.52: 39 75.52 - 100.69: 18 100.69 - 125.86: 1 Dihedral angle restraints: 12677 sinusoidal: 4985 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 12674 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: 0.000 Normalize map: mean=0, sd=1: 4.180 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.590 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 13.663 125.861 7619 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 covalent geometry : bond 0.00339 (20744) covalent geometry : angle 0.71288 (28157) SS BOND : bond 0.00593 ( 36) SS BOND : angle 1.69253 ( 72) hydrogen bonds : bond 0.12183 ( 900) hydrogen bonds : angle 7.28263 ( 2403) link_NAG-ASN : bond 0.00569 ( 1) link_NAG-ASN : angle 0.74454 ( 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 : 0.745 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: 0.1442 time to fit residues: 152.0839 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 : 0.741 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4259 r_free = 0.4259 target = 0.169479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127369 restraints weight = 37587.036| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.27 r_work: 0.3614 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3413 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= 0.200 Angle : 0.732 12.033 28232 Z= 0.379 Chirality : 0.048 0.304 3286 Planarity : 0.005 0.054 3579 Dihedral : 6.509 108.936 2874 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.83 % Favored : 95.02 % Rotamer: Outliers : 2.90 % Allowed : 11.20 % Favored : 85.90 % 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: -0.53 (0.17), residues: 909 loop : -1.05 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 16 TYR 0.034 0.002 TYR F 100D PHE 0.029 0.002 PHE B 483 TRP 0.026 0.002 TRP E 35 HIS 0.007 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00429 (20744) covalent geometry : angle 0.72883 (28157) SS BOND : bond 0.00455 ( 36) SS BOND : angle 1.39966 ( 72) hydrogen bonds : bond 0.03486 ( 900) hydrogen bonds : angle 6.01926 ( 2403) link_NAG-ASN : bond 0.00585 ( 1) link_NAG-ASN : angle 2.58616 ( 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 484 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 416 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7866 (tt0) cc_final: 0.7637 (tt0) REVERT: A 156 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7803 (tttm) REVERT: A 338 ASP cc_start: 0.8573 (t0) cc_final: 0.8369 (t0) REVERT: A 448 ASP cc_start: 0.7052 (t0) cc_final: 0.6646 (t0) REVERT: B 236 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 248 SER cc_start: 0.8329 (p) cc_final: 0.7960 (m) REVERT: C 53 TYR cc_start: 0.8576 (t80) cc_final: 0.8091 (t80) REVERT: C 417 TYR cc_start: 0.8402 (m-80) cc_final: 0.8157 (m-10) REVERT: C 448 ASP cc_start: 0.7094 (t0) cc_final: 0.6872 (t0) REVERT: F 36 TRP cc_start: 0.9240 (m100) cc_final: 0.8801 (m100) REVERT: F 47 TRP cc_start: 0.9246 (t60) cc_final: 0.9010 (t60) REVERT: F 66 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7365 (ttp80) REVERT: F 83 ARG cc_start: 0.7370 (mpp80) cc_final: 0.7089 (mpp80) REVERT: F 100 TYR cc_start: 0.8943 (m-80) cc_final: 0.8391 (m-80) REVERT: G 91 TYR cc_start: 0.9059 (p90) cc_final: 0.8342 (p90) REVERT: H 58 TYR cc_start: 0.8598 (m-80) cc_final: 0.8279 (m-80) REVERT: H 81 GLN cc_start: 0.7704 (tt0) cc_final: 0.7116 (mm110) REVERT: H 150 VAL cc_start: 0.6721 (m) cc_final: 0.6369 (t) REVERT: I 35 TRP cc_start: 0.8982 (m100) cc_final: 0.8604 (m100) REVERT: I 47 LEU cc_start: 0.9103 (mt) cc_final: 0.8870 (mt) REVERT: I 48 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8484 (ptm) REVERT: I 50 ASP cc_start: 0.8496 (m-30) cc_final: 0.8146 (m-30) REVERT: I 55 GLU cc_start: 0.8870 (tp30) cc_final: 0.8509 (tp30) REVERT: E 89 GLN cc_start: 0.8905 (tt0) cc_final: 0.8697 (tt0) outliers start: 68 outliers final: 41 residues processed: 458 average time/residue: 0.1325 time to fit residues: 95.2694 Evaluate side-chains 386 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 343 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 370 MET 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 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: 0.7980 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 168 optimal weight: 0.0870 chunk 199 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN F 76 ASN G 124 GLN H 3 GLN I 34 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116606 restraints weight = 37163.829| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.10 r_work: 0.3443 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20781 Z= 0.190 Angle : 0.700 12.220 28232 Z= 0.358 Chirality : 0.047 0.361 3286 Planarity : 0.005 0.073 3579 Dihedral : 6.129 94.332 2874 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.41 % Favored : 95.44 % Rotamer: Outliers : 3.62 % Allowed : 14.44 % 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: 1.08 (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 E 61 TYR 0.021 0.002 TYR D 100C PHE 0.022 0.002 PHE B 483 TRP 0.032 0.002 TRP G 35 HIS 0.008 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00436 (20744) covalent geometry : angle 0.69631 (28157) SS BOND : bond 0.00539 ( 36) SS BOND : angle 1.41491 ( 72) hydrogen bonds : bond 0.03248 ( 900) hydrogen bonds : angle 5.67717 ( 2403) link_NAG-ASN : bond 0.00392 ( 1) link_NAG-ASN : angle 2.73014 ( 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 491 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 406 time to evaluate : 0.765 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: A 31 GLU cc_start: 0.8297 (pt0) cc_final: 0.7818 (pt0) REVERT: A 49 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8176 (ptm-80) REVERT: A 156 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8104 (tttm) REVERT: A 235 ARG cc_start: 0.8941 (ttm170) cc_final: 0.8388 (ttp80) REVERT: A 338 ASP cc_start: 0.8475 (t0) cc_final: 0.8174 (t0) REVERT: A 483 PHE cc_start: 0.7731 (t80) cc_final: 0.7176 (t80) REVERT: A 505 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7399 (t80) REVERT: B 141 LEU cc_start: 0.8514 (pt) cc_final: 0.8303 (pp) REVERT: B 248 SER cc_start: 0.9150 (p) cc_final: 0.8790 (p) REVERT: B 462 GLN cc_start: 0.8486 (tp40) cc_final: 0.8257 (tp-100) REVERT: C 370 MET cc_start: 0.9279 (ttm) cc_final: 0.9070 (ttp) REVERT: C 448 ASP cc_start: 0.7289 (t0) cc_final: 0.7008 (t0) REVERT: F 36 TRP cc_start: 0.9323 (m100) cc_final: 0.9021 (m100) REVERT: F 43 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8951 (mmtp) REVERT: F 47 TRP cc_start: 0.9211 (t60) cc_final: 0.8877 (t60) REVERT: F 58 TYR cc_start: 0.8049 (m-80) cc_final: 0.7599 (m-10) REVERT: F 176 TYR cc_start: 0.7003 (m-80) cc_final: 0.6701 (m-80) REVERT: G 50 ASP cc_start: 0.8825 (m-30) cc_final: 0.8531 (m-30) REVERT: G 87 TYR cc_start: 0.8608 (m-80) cc_final: 0.8372 (m-80) REVERT: H 58 TYR cc_start: 0.8651 (m-80) cc_final: 0.7811 (m-80) REVERT: H 72 ASP cc_start: 0.8190 (t0) cc_final: 0.7890 (t0) REVERT: H 83 ARG cc_start: 0.8253 (mpt-90) cc_final: 0.7965 (mpt-90) REVERT: H 100 TYR cc_start: 0.8680 (m-10) cc_final: 0.7625 (m-80) REVERT: H 100 TYR cc_start: 0.8448 (m-80) cc_final: 0.7822 (m-80) REVERT: H 176 TYR cc_start: 0.6176 (m-80) cc_final: 0.5676 (m-80) REVERT: I 4 MET cc_start: 0.7615 (mtp) cc_final: 0.7283 (mtp) REVERT: I 35 TRP cc_start: 0.9363 (m100) cc_final: 0.8739 (m100) REVERT: I 48 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8468 (ptm) REVERT: I 87 TYR cc_start: 0.8633 (m-80) cc_final: 0.8167 (m-80) REVERT: I 91 TYR cc_start: 0.8919 (p90) cc_final: 0.8611 (p90) REVERT: D 47 TRP cc_start: 0.8963 (t60) cc_final: 0.8329 (t60) REVERT: D 72 ASP cc_start: 0.8236 (t0) cc_final: 0.8015 (t0) REVERT: D 75 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7694 (mmtt) REVERT: D 76 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8131 (t0) REVERT: D 81 GLN cc_start: 0.7774 (tt0) cc_final: 0.7456 (tp40) REVERT: D 83 ARG cc_start: 0.8190 (mpt-90) cc_final: 0.7663 (mpt-90) REVERT: E 87 TYR cc_start: 0.8618 (m-80) cc_final: 0.8207 (m-80) outliers start: 85 outliers final: 47 residues processed: 459 average time/residue: 0.1334 time to fit residues: 96.3836 Evaluate side-chains 401 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 350 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 A residue 505 PHE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 84 ASP 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 313 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 370 MET 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 141 LEU 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 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 196 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 108 THR 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 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LEU 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: 5.9990 chunk 55 optimal weight: 1.9990 chunk 155 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN B 454 ASN C 454 ASN F 76 ASN I 53 ASN I 93 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS E 124 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.160715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116033 restraints weight = 37503.971| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.18 r_work: 0.3451 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20781 Z= 0.132 Angle : 0.644 12.778 28232 Z= 0.326 Chirality : 0.046 0.355 3286 Planarity : 0.005 0.047 3579 Dihedral : 5.823 88.817 2874 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 3.58 % Allowed : 17.12 % Favored : 79.30 % 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: -0.60 (0.17), residues: 2610 helix: 1.03 (0.26), residues: 426 sheet: -0.37 (0.17), residues: 915 loop : -0.84 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 49 TYR 0.021 0.001 TYR H 52A PHE 0.020 0.002 PHE F 67 TRP 0.028 0.002 TRP E 35 HIS 0.006 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00304 (20744) covalent geometry : angle 0.64011 (28157) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.37449 ( 72) hydrogen bonds : bond 0.02912 ( 900) hydrogen bonds : angle 5.42792 ( 2403) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 3.02479 ( 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 475 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 391 time to evaluate : 0.830 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 31 GLU cc_start: 0.8409 (pt0) cc_final: 0.7875 (pt0) REVERT: A 156 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8081 (tttm) REVERT: A 338 ASP cc_start: 0.8477 (t0) cc_final: 0.8104 (t0) REVERT: A 398 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 448 ASP cc_start: 0.7728 (t0) cc_final: 0.7328 (t0) REVERT: A 483 PHE cc_start: 0.7784 (t80) cc_final: 0.7477 (t80) REVERT: A 505 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 510 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7613 (p0) REVERT: B 166 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7683 (ptmt) REVERT: B 335 THR cc_start: 0.9386 (t) cc_final: 0.8957 (p) REVERT: B 338 ASP cc_start: 0.8912 (t0) cc_final: 0.8530 (t0) REVERT: B 417 TYR cc_start: 0.8703 (m-80) cc_final: 0.8252 (m-10) REVERT: B 462 GLN cc_start: 0.8605 (tp40) cc_final: 0.8331 (tp-100) REVERT: C 49 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8032 (ttp80) REVERT: C 53 TYR cc_start: 0.8867 (t80) cc_final: 0.8635 (t80) REVERT: C 363 ASN cc_start: 0.8486 (t0) cc_final: 0.8251 (t0) REVERT: C 426 ASN cc_start: 0.8127 (t0) cc_final: 0.7734 (t0) REVERT: C 440 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7522 (t0) REVERT: C 448 ASP cc_start: 0.7311 (t0) cc_final: 0.6909 (t0) REVERT: C 494 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8291 (tm-30) REVERT: F 36 TRP cc_start: 0.9305 (m100) cc_final: 0.9034 (m100) REVERT: F 43 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8984 (mmtp) REVERT: F 47 TRP cc_start: 0.9203 (t60) cc_final: 0.8867 (t60) REVERT: F 58 TYR cc_start: 0.8153 (m-80) cc_final: 0.7727 (m-10) REVERT: F 176 TYR cc_start: 0.7005 (m-80) cc_final: 0.6684 (m-80) REVERT: G 27 GLN cc_start: 0.8191 (pp30) cc_final: 0.7721 (pp30) REVERT: G 35 TRP cc_start: 0.9224 (m100) cc_final: 0.8949 (m100) REVERT: G 91 TYR cc_start: 0.9040 (p90) cc_final: 0.8459 (p90) REVERT: H 3 GLN cc_start: 0.8685 (tt0) cc_final: 0.8357 (mp10) REVERT: H 43 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8340 (mmtp) REVERT: H 58 TYR cc_start: 0.8636 (m-80) cc_final: 0.7770 (m-80) REVERT: H 72 ASP cc_start: 0.8110 (t0) cc_final: 0.7670 (t0) REVERT: H 83 ARG cc_start: 0.8248 (mpt-90) cc_final: 0.7787 (mpt-90) REVERT: H 97 ILE cc_start: 0.9474 (mm) cc_final: 0.9172 (mm) REVERT: H 100 ASP cc_start: 0.8731 (t0) cc_final: 0.7644 (t70) REVERT: H 100 TYR cc_start: 0.8595 (m-10) cc_final: 0.7296 (m-80) REVERT: H 100 TYR cc_start: 0.8332 (m-80) cc_final: 0.7914 (m-80) REVERT: H 100 TYR cc_start: 0.8285 (m-80) cc_final: 0.7989 (m-80) REVERT: H 176 TYR cc_start: 0.6176 (m-80) cc_final: 0.5754 (m-80) REVERT: I 35 TRP cc_start: 0.9303 (m100) cc_final: 0.8700 (m100) REVERT: I 91 TYR cc_start: 0.8808 (p90) cc_final: 0.8543 (p90) REVERT: I 93 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8073 (t0) REVERT: I 190 LYS cc_start: 0.5518 (tppt) cc_final: 0.5140 (tppt) REVERT: D 16 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.6946 (ttp-110) REVERT: D 36 TRP cc_start: 0.9287 (m100) cc_final: 0.8917 (m100) REVERT: D 47 TRP cc_start: 0.9049 (t60) cc_final: 0.8441 (t60) REVERT: D 72 ASP cc_start: 0.8351 (t0) cc_final: 0.8033 (t0) REVERT: D 75 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7938 (mmtt) REVERT: D 76 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8040 (t0) REVERT: D 81 GLN cc_start: 0.7740 (tt0) cc_final: 0.7334 (tp40) REVERT: D 83 ARG cc_start: 0.8242 (mpt-90) cc_final: 0.7670 (mpt-90) REVERT: E 87 TYR cc_start: 0.8712 (m-80) cc_final: 0.8247 (m-80) outliers start: 84 outliers final: 49 residues processed: 446 average time/residue: 0.1368 time to fit residues: 96.0177 Evaluate side-chains 406 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 377 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 79 ILE 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 253 THR 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 447 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 171 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 311 THR Chi-restraints excluded: chain C residue 334 LEU 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 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 H residue 21 SER Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 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 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 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 63 optimal weight: 0.0040 chunk 258 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 227 ASN B 302 GLN C 444 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4055 r_free = 0.4055 target = 0.152054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107333 restraints weight = 36945.344| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.02 r_work: 0.3294 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20781 Z= 0.257 Angle : 0.722 12.706 28232 Z= 0.371 Chirality : 0.048 0.381 3286 Planarity : 0.005 0.054 3579 Dihedral : 6.068 84.105 2874 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 4.56 % Allowed : 17.80 % Favored : 77.64 % 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: -0.68 (0.17), residues: 2610 helix: 1.12 (0.26), residues: 417 sheet: -0.49 (0.17), residues: 903 loop : -0.88 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 65 TYR 0.022 0.002 TYR D 52A PHE 0.022 0.002 PHE D 67 TRP 0.019 0.002 TRP E 35 HIS 0.006 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00591 (20744) covalent geometry : angle 0.71773 (28157) SS BOND : bond 0.00675 ( 36) SS BOND : angle 1.64269 ( 72) hydrogen bonds : bond 0.03337 ( 900) hydrogen bonds : angle 5.62006 ( 2403) link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 3.39553 ( 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: 107 poor density : 366 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8235 (tttm) REVERT: A 338 ASP cc_start: 0.8721 (t0) cc_final: 0.8229 (t0) REVERT: A 448 ASP cc_start: 0.7843 (t0) cc_final: 0.7525 (t0) REVERT: A 510 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7490 (p0) REVERT: B 338 ASP cc_start: 0.8875 (t0) cc_final: 0.8319 (t0) REVERT: B 462 GLN cc_start: 0.8722 (tp40) cc_final: 0.8453 (tp-100) REVERT: C 49 ARG cc_start: 0.8625 (ttp80) cc_final: 0.7825 (ttp80) REVERT: C 363 ASN cc_start: 0.8647 (t0) cc_final: 0.8143 (t0) REVERT: C 448 ASP cc_start: 0.7520 (t0) cc_final: 0.7054 (t0) REVERT: F 36 TRP cc_start: 0.9383 (m100) cc_final: 0.9083 (m100) REVERT: F 43 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8934 (mmtp) REVERT: F 47 TRP cc_start: 0.9209 (t60) cc_final: 0.8849 (t60) REVERT: F 58 TYR cc_start: 0.8390 (m-80) cc_final: 0.7715 (m-10) REVERT: F 72 ASP cc_start: 0.8199 (t0) cc_final: 0.7816 (t0) REVERT: F 75 LYS cc_start: 0.8225 (mptt) cc_final: 0.7768 (mmtp) REVERT: F 176 TYR cc_start: 0.7362 (m-80) cc_final: 0.7022 (m-80) REVERT: G 4 MET cc_start: 0.6975 (ttt) cc_final: 0.6716 (ttt) REVERT: G 91 TYR cc_start: 0.9160 (p90) cc_final: 0.8505 (p90) REVERT: H 47 TRP cc_start: 0.8900 (t60) cc_final: 0.8552 (t60) REVERT: H 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7931 (t0) REVERT: H 76 ASN cc_start: 0.8553 (t0) cc_final: 0.8312 (t0) REVERT: H 83 ARG cc_start: 0.8303 (mpt-90) cc_final: 0.7869 (mpt-90) REVERT: H 91 TYR cc_start: 0.8659 (m-80) cc_final: 0.8444 (m-10) REVERT: H 96 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8446 (ttp80) REVERT: H 100 TYR cc_start: 0.8737 (m-10) cc_final: 0.7443 (m-80) REVERT: H 100 TYR cc_start: 0.8488 (m-80) cc_final: 0.8170 (m-80) REVERT: H 176 TYR cc_start: 0.6208 (m-80) cc_final: 0.5816 (m-80) REVERT: I 35 TRP cc_start: 0.9435 (m100) cc_final: 0.8341 (m100) REVERT: I 55 GLU cc_start: 0.8637 (tp30) cc_final: 0.8356 (tp30) REVERT: I 91 TYR cc_start: 0.9043 (p90) cc_final: 0.8651 (p90) REVERT: D 36 TRP cc_start: 0.9254 (m100) cc_final: 0.8729 (m100) REVERT: D 47 TRP cc_start: 0.9105 (t60) cc_final: 0.8175 (t60) REVERT: D 72 ASP cc_start: 0.8264 (t0) cc_final: 0.7902 (t0) REVERT: D 75 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8138 (mmtt) REVERT: D 76 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (t0) REVERT: D 81 GLN cc_start: 0.7712 (tt0) cc_final: 0.7456 (tp40) REVERT: D 83 ARG cc_start: 0.8235 (mpt-90) cc_final: 0.7915 (mpt-90) REVERT: D 100 ASP cc_start: 0.8936 (t0) cc_final: 0.8568 (t70) REVERT: D 100 TYR cc_start: 0.8700 (m-80) cc_final: 0.8305 (m-80) outliers start: 107 outliers final: 80 residues processed: 438 average time/residue: 0.1348 time to fit residues: 93.0481 Evaluate side-chains 426 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 343 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 415 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 79 ILE 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 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 C residue 36 THR Chi-restraints excluded: chain C residue 79 ILE 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 171 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 266 ILE 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 398 SER 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 455 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 211 VAL 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 H residue 86 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 108 THR 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 83 ILE 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 E residue 46 LEU Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 361 GLN B 227 ASN C 302 GLN C 444 ASN C 454 ASN I 53 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4038 r_free = 0.4038 target = 0.150629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105571 restraints weight = 37068.057| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.01 r_work: 0.3276 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20781 Z= 0.232 Angle : 0.702 11.808 28232 Z= 0.357 Chirality : 0.047 0.379 3286 Planarity : 0.005 0.052 3579 Dihedral : 6.030 80.060 2874 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.25 % Favored : 94.60 % Rotamer: Outliers : 4.77 % Allowed : 18.82 % Favored : 76.41 % 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: -0.76 (0.17), residues: 2610 helix: 1.08 (0.26), residues: 417 sheet: -0.60 (0.17), residues: 881 loop : -0.89 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 65 TYR 0.024 0.002 TYR D 52A PHE 0.024 0.002 PHE F 67 TRP 0.013 0.002 TRP E 35 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00539 (20744) covalent geometry : angle 0.69814 (28157) SS BOND : bond 0.00544 ( 36) SS BOND : angle 1.46604 ( 72) hydrogen bonds : bond 0.03181 ( 900) hydrogen bonds : angle 5.63081 ( 2403) link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 3.59212 ( 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 487 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 375 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8277 (tttm) REVERT: A 338 ASP cc_start: 0.8770 (t0) cc_final: 0.8320 (t0) REVERT: A 361 GLN cc_start: 0.9046 (tp40) cc_final: 0.8747 (mm110) REVERT: A 448 ASP cc_start: 0.7943 (t0) cc_final: 0.7628 (t0) REVERT: A 462 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8531 (tp-100) REVERT: A 505 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 510 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (p0) REVERT: B 78 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 251 MET cc_start: 0.9136 (ttm) cc_final: 0.8846 (ttm) REVERT: B 338 ASP cc_start: 0.8838 (t0) cc_final: 0.8239 (t0) REVERT: B 417 TYR cc_start: 0.8887 (m-80) cc_final: 0.8492 (m-10) REVERT: C 49 ARG cc_start: 0.8630 (ttp80) cc_final: 0.7793 (ttp80) REVERT: C 264 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8916 (ptm) REVERT: C 363 ASN cc_start: 0.8540 (t0) cc_final: 0.8108 (t0) REVERT: F 34 MET cc_start: 0.8731 (mmt) cc_final: 0.8387 (mmm) REVERT: F 36 TRP cc_start: 0.9382 (m100) cc_final: 0.9102 (m100) REVERT: F 43 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8861 (mmtp) REVERT: F 47 TRP cc_start: 0.9211 (t60) cc_final: 0.8810 (t60) REVERT: F 58 TYR cc_start: 0.8460 (m-80) cc_final: 0.7716 (m-10) REVERT: F 72 ASP cc_start: 0.8241 (t0) cc_final: 0.8003 (t0) REVERT: F 176 TYR cc_start: 0.7390 (m-80) cc_final: 0.7064 (m-80) REVERT: G 35 TRP cc_start: 0.9417 (m100) cc_final: 0.9061 (m100) REVERT: G 50 ASP cc_start: 0.8965 (m-30) cc_final: 0.8716 (m-30) REVERT: G 116 PHE cc_start: 0.1450 (OUTLIER) cc_final: -0.0191 (m-80) REVERT: H 43 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8557 (mmtp) REVERT: H 47 TRP cc_start: 0.8961 (t60) cc_final: 0.8214 (t60) REVERT: H 72 ASP cc_start: 0.8218 (t0) cc_final: 0.7819 (t0) REVERT: H 76 ASN cc_start: 0.8549 (t0) cc_final: 0.8322 (t0) REVERT: H 83 ARG cc_start: 0.8307 (mpt-90) cc_final: 0.7898 (mpt-90) REVERT: H 96 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8441 (ttp80) REVERT: H 100 ASP cc_start: 0.9020 (t0) cc_final: 0.8203 (t70) REVERT: H 100 TYR cc_start: 0.8746 (m-10) cc_final: 0.7130 (m-80) REVERT: H 100 TYR cc_start: 0.8451 (m-80) cc_final: 0.8213 (m-80) REVERT: H 100 TYR cc_start: 0.8662 (m-80) cc_final: 0.7686 (m-80) REVERT: H 176 TYR cc_start: 0.6111 (m-80) cc_final: 0.5697 (m-80) REVERT: I 55 GLU cc_start: 0.8491 (tp30) cc_final: 0.8245 (tp30) REVERT: I 91 TYR cc_start: 0.8933 (p90) cc_final: 0.8386 (p90) REVERT: D 36 TRP cc_start: 0.9285 (m100) cc_final: 0.8739 (m100) REVERT: D 47 TRP cc_start: 0.9122 (t60) cc_final: 0.8178 (t60) REVERT: D 72 ASP cc_start: 0.8150 (t0) cc_final: 0.7812 (t0) REVERT: D 75 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8333 (mptt) REVERT: D 76 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8036 (t0) REVERT: D 83 ARG cc_start: 0.8341 (mpt-90) cc_final: 0.7983 (mpt-90) REVERT: D 100 TYR cc_start: 0.8733 (m-80) cc_final: 0.8376 (m-80) REVERT: D 100 MET cc_start: 0.9019 (mpp) cc_final: 0.8403 (mpp) REVERT: E 27 GLN cc_start: 0.8787 (pp30) cc_final: 0.8372 (pp30) REVERT: E 106 ILE cc_start: 0.7501 (mm) cc_final: 0.7052 (mm) REVERT: E 164 THR cc_start: 0.6469 (p) cc_final: 0.6241 (t) outliers start: 112 outliers final: 85 residues processed: 453 average time/residue: 0.1370 time to fit residues: 97.4816 Evaluate side-chains 432 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 340 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 227 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 MET 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 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 A residue 510 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 ILE 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 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 334 LEU 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 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 B residue 505 PHE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 79 ILE 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 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 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 398 SER 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 454 ASN 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 211 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 86 ASP 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 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 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 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: 5.9990 chunk 155 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN I 147 GLN ** 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 = 0.4085 r_free = 0.4085 target = 0.154551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109620 restraints weight = 36986.677| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.10 r_work: 0.3349 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20781 Z= 0.137 Angle : 0.673 14.918 28232 Z= 0.338 Chirality : 0.046 0.385 3286 Planarity : 0.005 0.051 3579 Dihedral : 5.738 74.345 2874 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 3.45 % Allowed : 21.25 % Favored : 75.30 % 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: -0.63 (0.17), residues: 2610 helix: 1.29 (0.26), residues: 417 sheet: -0.47 (0.17), residues: 904 loop : -0.88 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 235 TYR 0.026 0.001 TYR D 52A PHE 0.028 0.002 PHE F 67 TRP 0.014 0.001 TRP I 35 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00317 (20744) covalent geometry : angle 0.66983 (28157) SS BOND : bond 0.00491 ( 36) SS BOND : angle 1.32398 ( 72) hydrogen bonds : bond 0.02937 ( 900) hydrogen bonds : angle 5.44952 ( 2403) link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 3.89203 ( 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 463 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 382 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7990 (p90) cc_final: 0.7564 (m-80) REVERT: A 156 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8172 (tttm) REVERT: A 338 ASP cc_start: 0.8737 (t0) cc_final: 0.8370 (t0) REVERT: A 448 ASP cc_start: 0.7833 (t0) cc_final: 0.7468 (t0) REVERT: A 505 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7618 (t80) REVERT: A 510 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7519 (p0) REVERT: B 338 ASP cc_start: 0.8740 (t0) cc_final: 0.8278 (t0) REVERT: B 363 ASN cc_start: 0.8477 (t0) cc_final: 0.8232 (t0) REVERT: B 417 TYR cc_start: 0.8809 (m-80) cc_final: 0.8550 (m-10) REVERT: C 49 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7809 (ttp80) REVERT: C 75 LYS cc_start: 0.9266 (mttt) cc_final: 0.8893 (mttp) REVERT: C 363 ASN cc_start: 0.8455 (t0) cc_final: 0.8015 (t0) REVERT: C 440 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7924 (t0) REVERT: C 462 GLN cc_start: 0.8716 (tp40) cc_final: 0.8509 (tp-100) REVERT: F 34 MET cc_start: 0.8639 (mmt) cc_final: 0.8374 (mmm) REVERT: F 43 LYS cc_start: 0.9057 (mmtm) cc_final: 0.8851 (mmtp) REVERT: F 47 TRP cc_start: 0.9126 (t60) cc_final: 0.8801 (t60) REVERT: F 58 TYR cc_start: 0.8484 (m-80) cc_final: 0.7942 (m-10) REVERT: F 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: F 144 ASP cc_start: 0.6695 (m-30) cc_final: 0.6358 (m-30) REVERT: F 176 TYR cc_start: 0.7418 (m-80) cc_final: 0.7089 (m-80) REVERT: G 35 TRP cc_start: 0.9370 (m100) cc_final: 0.9078 (m100) REVERT: G 50 ASP cc_start: 0.8943 (m-30) cc_final: 0.8697 (m-30) REVERT: G 91 TYR cc_start: 0.9064 (p90) cc_final: 0.8441 (p90) REVERT: G 116 PHE cc_start: 0.1229 (OUTLIER) cc_final: -0.0254 (m-80) REVERT: H 43 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8583 (mmtp) REVERT: H 47 TRP cc_start: 0.8801 (t60) cc_final: 0.8115 (t60) REVERT: H 58 TYR cc_start: 0.8606 (m-80) cc_final: 0.6979 (m-80) REVERT: H 59 TYR cc_start: 0.8789 (m-80) cc_final: 0.8581 (m-80) REVERT: H 72 ASP cc_start: 0.8258 (t0) cc_final: 0.7847 (t0) REVERT: H 76 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8185 (t0) REVERT: H 83 ARG cc_start: 0.8256 (mpt-90) cc_final: 0.7915 (mpt-90) REVERT: H 96 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8209 (ttt-90) REVERT: H 100 ASP cc_start: 0.8990 (t0) cc_final: 0.8682 (t0) REVERT: H 100 TYR cc_start: 0.8659 (m-10) cc_final: 0.7133 (m-80) REVERT: H 100 TYR cc_start: 0.8342 (m-80) cc_final: 0.7581 (m-80) REVERT: H 176 TYR cc_start: 0.6169 (m-80) cc_final: 0.5768 (m-80) REVERT: I 91 TYR cc_start: 0.8762 (p90) cc_final: 0.8435 (p90) REVERT: D 36 TRP cc_start: 0.9255 (m100) cc_final: 0.8730 (m100) REVERT: D 47 TRP cc_start: 0.9113 (t60) cc_final: 0.8089 (t60) REVERT: D 58 TYR cc_start: 0.8680 (m-80) cc_final: 0.6990 (m-80) REVERT: D 72 ASP cc_start: 0.8047 (t0) cc_final: 0.7694 (t0) REVERT: D 75 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8263 (mptt) REVERT: D 76 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7990 (t0) REVERT: D 83 ARG cc_start: 0.8366 (mpt-90) cc_final: 0.7916 (mpt-90) REVERT: D 100 TYR cc_start: 0.8659 (m-80) cc_final: 0.7811 (m-80) REVERT: E 27 GLN cc_start: 0.8690 (pp30) cc_final: 0.8337 (pp30) REVERT: E 106 ILE cc_start: 0.7500 (mm) cc_final: 0.7055 (mm) outliers start: 81 outliers final: 55 residues processed: 432 average time/residue: 0.1368 time to fit residues: 93.0138 Evaluate side-chains 413 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 351 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 367 CYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 510 ASP 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 365 VAL 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 79 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 171 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 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 422 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 VAL 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 76 ASN Chi-restraints excluded: chain H residue 86 ASP 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 D residue 77 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 179 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 0.0040 chunk 251 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 227 ASN C 454 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 = 0.4040 r_free = 0.4040 target = 0.150838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105841 restraints weight = 36995.292| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.05 r_work: 0.3284 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20781 Z= 0.211 Angle : 0.708 15.791 28232 Z= 0.357 Chirality : 0.046 0.392 3286 Planarity : 0.005 0.057 3579 Dihedral : 5.830 70.551 2874 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 4.26 % Allowed : 21.64 % Favored : 74.11 % 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: -0.68 (0.17), residues: 2610 helix: 1.21 (0.26), residues: 417 sheet: -0.49 (0.17), residues: 907 loop : -0.93 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 235 TYR 0.036 0.002 TYR F 52A PHE 0.030 0.002 PHE F 67 TRP 0.013 0.002 TRP H 36 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00492 (20744) covalent geometry : angle 0.70376 (28157) SS BOND : bond 0.00584 ( 36) SS BOND : angle 1.42351 ( 72) hydrogen bonds : bond 0.03128 ( 900) hydrogen bonds : angle 5.54024 ( 2403) link_NAG-ASN : bond 0.00040 ( 1) link_NAG-ASN : angle 4.20530 ( 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 465 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 365 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7837 (tmm) cc_final: 0.7595 (tmm) REVERT: A 156 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8270 (tttm) REVERT: A 338 ASP cc_start: 0.8777 (t0) cc_final: 0.8370 (t0) REVERT: A 448 ASP cc_start: 0.7967 (t0) cc_final: 0.7633 (t0) REVERT: A 505 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7669 (t80) REVERT: A 510 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7517 (p0) REVERT: B 334 LEU cc_start: 0.8870 (tt) cc_final: 0.8423 (tp) REVERT: B 338 ASP cc_start: 0.8717 (t0) cc_final: 0.8236 (t0) REVERT: B 417 TYR cc_start: 0.8903 (m-80) cc_final: 0.8469 (m-10) REVERT: C 49 ARG cc_start: 0.8579 (ttp80) cc_final: 0.7820 (ttp80) REVERT: C 75 LYS cc_start: 0.9195 (mttt) cc_final: 0.8932 (mttp) REVERT: C 363 ASN cc_start: 0.8532 (t0) cc_final: 0.8074 (t0) REVERT: C 440 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8063 (t0) REVERT: C 462 GLN cc_start: 0.8817 (tp40) cc_final: 0.8601 (tp-100) REVERT: F 16 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7366 (ttp-110) REVERT: F 34 MET cc_start: 0.8679 (mmt) cc_final: 0.8414 (mmm) REVERT: F 47 TRP cc_start: 0.9113 (t60) cc_final: 0.8784 (t60) REVERT: F 58 TYR cc_start: 0.8612 (m-80) cc_final: 0.7995 (m-80) REVERT: F 72 ASP cc_start: 0.8240 (t0) cc_final: 0.7956 (t0) REVERT: F 86 ASP cc_start: 0.8856 (t0) cc_final: 0.8038 (t70) REVERT: F 100 TYR cc_start: 0.8727 (m-80) cc_final: 0.8335 (m-80) REVERT: G 35 TRP cc_start: 0.9409 (m100) cc_final: 0.9025 (m100) REVERT: G 50 ASP cc_start: 0.8947 (m-30) cc_final: 0.8679 (m-30) REVERT: G 116 PHE cc_start: 0.1467 (OUTLIER) cc_final: -0.0221 (m-80) REVERT: H 43 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8713 (mmtp) REVERT: H 47 TRP cc_start: 0.8950 (t60) cc_final: 0.8252 (t60) REVERT: H 59 TYR cc_start: 0.8814 (m-80) cc_final: 0.8604 (m-80) REVERT: H 72 ASP cc_start: 0.8324 (t0) cc_final: 0.7963 (t0) REVERT: H 76 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8198 (t0) REVERT: H 83 ARG cc_start: 0.8292 (mpt-90) cc_final: 0.8084 (mpt-90) REVERT: H 96 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8274 (ttt-90) REVERT: H 100 TYR cc_start: 0.8717 (m-10) cc_final: 0.7397 (m-80) REVERT: H 100 TYR cc_start: 0.8440 (m-80) cc_final: 0.8238 (m-80) REVERT: H 176 TYR cc_start: 0.6237 (m-80) cc_final: 0.5835 (m-80) REVERT: I 91 TYR cc_start: 0.9087 (p90) cc_final: 0.8886 (p90) REVERT: D 36 TRP cc_start: 0.9286 (m100) cc_final: 0.8697 (m100) REVERT: D 47 TRP cc_start: 0.9157 (t60) cc_final: 0.8140 (t60) REVERT: D 75 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8467 (mmtt) REVERT: D 76 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7940 (t0) REVERT: D 83 ARG cc_start: 0.8401 (mpt-90) cc_final: 0.7924 (mpt-90) REVERT: D 100 ASP cc_start: 0.8927 (t0) cc_final: 0.8714 (t70) REVERT: D 100 TYR cc_start: 0.8728 (m-80) cc_final: 0.8435 (m-80) REVERT: D 100 MET cc_start: 0.8970 (mpp) cc_final: 0.8319 (mpp) REVERT: E 27 GLN cc_start: 0.8815 (pp30) cc_final: 0.8380 (pp30) REVERT: E 106 ILE cc_start: 0.7530 (mm) cc_final: 0.7083 (mm) REVERT: E 164 THR cc_start: 0.6453 (p) cc_final: 0.6161 (t) outliers start: 100 outliers final: 75 residues processed: 432 average time/residue: 0.1373 time to fit residues: 93.5961 Evaluate side-chains 429 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 347 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 367 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 510 ASP 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 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 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 454 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 79 ILE 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 239 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 258 LEU 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 377 SER 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 C residue 485 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 67 PHE 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 46 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 86 ASP 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 77 THR 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 97 THR 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: 9.9990 chunk 203 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN C 460 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.153848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109080 restraints weight = 36833.636| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.08 r_work: 0.3351 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20781 Z= 0.145 Angle : 0.686 14.984 28232 Z= 0.344 Chirality : 0.046 0.384 3286 Planarity : 0.005 0.054 3579 Dihedral : 5.652 65.449 2874 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 3.58 % Allowed : 22.27 % Favored : 74.15 % 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: -0.59 (0.17), residues: 2610 helix: 1.30 (0.26), residues: 417 sheet: -0.44 (0.17), residues: 900 loop : -0.86 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 235 TYR 0.038 0.002 TYR F 52A PHE 0.027 0.002 PHE F 67 TRP 0.022 0.002 TRP F 36 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00337 (20744) covalent geometry : angle 0.68256 (28157) SS BOND : bond 0.00499 ( 36) SS BOND : angle 1.19150 ( 72) hydrogen bonds : bond 0.02962 ( 900) hydrogen bonds : angle 5.46044 ( 2403) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 4.39473 ( 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 459 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9167 (mttt) cc_final: 0.8953 (mttm) REVERT: A 97 MET cc_start: 0.7760 (tmm) cc_final: 0.7541 (tmm) REVERT: A 140 PHE cc_start: 0.7819 (p90) cc_final: 0.7451 (m-80) REVERT: A 156 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8210 (tttm) REVERT: A 338 ASP cc_start: 0.8673 (t0) cc_final: 0.8303 (t0) REVERT: A 448 ASP cc_start: 0.7803 (t0) cc_final: 0.7435 (t0) REVERT: A 505 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 510 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 75 LYS cc_start: 0.9218 (mttt) cc_final: 0.8833 (mttp) REVERT: B 334 LEU cc_start: 0.8799 (tt) cc_final: 0.8466 (tp) REVERT: B 338 ASP cc_start: 0.8677 (t0) cc_final: 0.8268 (t0) REVERT: B 363 ASN cc_start: 0.8520 (t0) cc_final: 0.8258 (t0) REVERT: B 417 TYR cc_start: 0.8819 (m-80) cc_final: 0.8491 (m-10) REVERT: B 419 LYS cc_start: 0.8647 (ptmt) cc_final: 0.8258 (mttt) REVERT: C 49 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7818 (ttp80) REVERT: C 75 LYS cc_start: 0.9190 (mttt) cc_final: 0.8946 (mttp) REVERT: C 363 ASN cc_start: 0.8526 (t0) cc_final: 0.8075 (t0) REVERT: C 417 TYR cc_start: 0.8608 (m-10) cc_final: 0.8152 (m-10) REVERT: C 440 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8099 (t0) REVERT: F 16 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7228 (ttp-110) REVERT: F 34 MET cc_start: 0.8599 (mmt) cc_final: 0.8367 (mmm) REVERT: F 47 TRP cc_start: 0.9100 (t60) cc_final: 0.8748 (t60) REVERT: F 58 TYR cc_start: 0.8595 (m-80) cc_final: 0.7901 (m-80) REVERT: F 72 ASP cc_start: 0.8232 (t0) cc_final: 0.7950 (t0) REVERT: F 74 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8487 (t) REVERT: F 86 ASP cc_start: 0.8893 (t0) cc_final: 0.8218 (t70) REVERT: F 100 ASP cc_start: 0.9055 (t0) cc_final: 0.8718 (t0) REVERT: F 100 TYR cc_start: 0.8695 (m-80) cc_final: 0.8013 (m-80) REVERT: G 35 TRP cc_start: 0.9350 (m100) cc_final: 0.9089 (m100) REVERT: G 50 ASP cc_start: 0.8936 (m-30) cc_final: 0.8655 (m-30) REVERT: G 91 TYR cc_start: 0.9156 (p90) cc_final: 0.8550 (p90) REVERT: G 116 PHE cc_start: 0.1400 (OUTLIER) cc_final: -0.0116 (m-80) REVERT: H 43 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8604 (mmtp) REVERT: H 47 TRP cc_start: 0.8871 (t60) cc_final: 0.8217 (t60) REVERT: H 58 TYR cc_start: 0.8625 (m-80) cc_final: 0.7086 (m-80) REVERT: H 59 TYR cc_start: 0.8823 (m-80) cc_final: 0.8603 (m-80) REVERT: H 72 ASP cc_start: 0.8296 (t0) cc_final: 0.7938 (t0) REVERT: H 76 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8114 (t0) REVERT: H 100 TYR cc_start: 0.8680 (m-10) cc_final: 0.7518 (m-80) REVERT: H 100 TYR cc_start: 0.8397 (m-80) cc_final: 0.7721 (m-80) REVERT: H 176 TYR cc_start: 0.6186 (m-80) cc_final: 0.5693 (m-80) REVERT: I 88 CYS cc_start: 0.6981 (p) cc_final: 0.6733 (p) REVERT: D 36 TRP cc_start: 0.9259 (m100) cc_final: 0.8699 (m100) REVERT: D 47 TRP cc_start: 0.9122 (t60) cc_final: 0.8071 (t60) REVERT: D 58 TYR cc_start: 0.8738 (m-80) cc_final: 0.7055 (m-80) REVERT: D 64 LYS cc_start: 0.8768 (tppt) cc_final: 0.8431 (tptp) REVERT: D 75 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8459 (mmtp) REVERT: D 76 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7936 (t0) REVERT: D 83 ARG cc_start: 0.8434 (mpt-90) cc_final: 0.7952 (mpt-90) REVERT: D 100 ASP cc_start: 0.8926 (t0) cc_final: 0.8651 (t70) REVERT: D 100 TYR cc_start: 0.8673 (m-80) cc_final: 0.7856 (m-80) REVERT: D 100 MET cc_start: 0.8891 (mpp) cc_final: 0.8315 (mpp) REVERT: E 27 GLN cc_start: 0.8789 (pp30) cc_final: 0.8365 (pp30) REVERT: E 85 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8316 (p) REVERT: E 106 ILE cc_start: 0.7523 (mm) cc_final: 0.7082 (mm) REVERT: E 164 THR cc_start: 0.6316 (p) cc_final: 0.6025 (t) outliers start: 84 outliers final: 68 residues processed: 427 average time/residue: 0.1336 time to fit residues: 89.6665 Evaluate side-chains 436 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 359 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 367 CYS Chi-restraints excluded: chain A residue 377 SER 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 A residue 505 PHE Chi-restraints excluded: chain A residue 510 ASP 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 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 377 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 454 ASN 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 79 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 171 LEU 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 422 CYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 485 SER 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 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 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 86 ASP 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 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 85 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN C 460 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4068 r_free = 0.4068 target = 0.153283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108458 restraints weight = 37154.863| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.09 r_work: 0.3351 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20781 Z= 0.159 Angle : 0.698 15.663 28232 Z= 0.349 Chirality : 0.046 0.384 3286 Planarity : 0.005 0.052 3579 Dihedral : 5.562 60.586 2874 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.13 % Favored : 94.71 % Rotamer: Outliers : 3.75 % Allowed : 21.89 % 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: -0.61 (0.17), residues: 2610 helix: 1.31 (0.26), residues: 417 sheet: -0.45 (0.17), residues: 900 loop : -0.89 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 235 TYR 0.039 0.002 TYR H 52A PHE 0.028 0.002 PHE D 67 TRP 0.043 0.002 TRP F 36 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00375 (20744) covalent geometry : angle 0.69479 (28157) SS BOND : bond 0.00499 ( 36) SS BOND : angle 1.22473 ( 72) hydrogen bonds : bond 0.02987 ( 900) hydrogen bonds : angle 5.43885 ( 2403) link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 4.73108 ( 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 460 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7846 (p90) cc_final: 0.7418 (m-80) REVERT: A 156 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8258 (tttm) REVERT: A 338 ASP cc_start: 0.8609 (t0) cc_final: 0.8266 (t0) REVERT: A 448 ASP cc_start: 0.7827 (t0) cc_final: 0.7462 (t0) REVERT: A 510 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7389 (p0) REVERT: B 75 LYS cc_start: 0.9208 (mttt) cc_final: 0.8829 (mttp) REVERT: B 334 LEU cc_start: 0.8778 (tt) cc_final: 0.8446 (tp) REVERT: B 338 ASP cc_start: 0.8651 (t0) cc_final: 0.8248 (t0) REVERT: B 363 ASN cc_start: 0.8577 (t0) cc_final: 0.8307 (t0) REVERT: B 417 TYR cc_start: 0.8820 (m-80) cc_final: 0.8457 (m-10) REVERT: B 419 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8268 (mttt) REVERT: C 49 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7814 (ttp80) REVERT: C 75 LYS cc_start: 0.9211 (mttt) cc_final: 0.8969 (mttp) REVERT: C 363 ASN cc_start: 0.8522 (t0) cc_final: 0.8063 (t0) REVERT: C 417 TYR cc_start: 0.8697 (m-10) cc_final: 0.8229 (m-10) REVERT: F 16 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7331 (ttp-110) REVERT: F 34 MET cc_start: 0.8605 (mmt) cc_final: 0.8376 (mmm) REVERT: F 47 TRP cc_start: 0.9101 (t60) cc_final: 0.8739 (t60) REVERT: F 58 TYR cc_start: 0.8601 (m-80) cc_final: 0.7906 (m-80) REVERT: F 72 ASP cc_start: 0.8251 (t0) cc_final: 0.7970 (t0) REVERT: F 74 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8506 (t) REVERT: F 86 ASP cc_start: 0.8870 (t0) cc_final: 0.8213 (t70) REVERT: F 100 ASP cc_start: 0.9040 (t0) cc_final: 0.8507 (t0) REVERT: F 100 TYR cc_start: 0.8693 (m-80) cc_final: 0.7972 (m-80) REVERT: F 100 TYR cc_start: 0.8723 (m-80) cc_final: 0.8515 (m-80) REVERT: G 35 TRP cc_start: 0.9368 (m100) cc_final: 0.9099 (m100) REVERT: G 50 ASP cc_start: 0.8942 (m-30) cc_final: 0.8653 (m-30) REVERT: G 91 TYR cc_start: 0.9184 (p90) cc_final: 0.8615 (p90) REVERT: G 116 PHE cc_start: 0.1392 (OUTLIER) cc_final: -0.0114 (m-80) REVERT: H 3 GLN cc_start: 0.8538 (tt0) cc_final: 0.8178 (tt0) REVERT: H 43 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8513 (mmtp) REVERT: H 47 TRP cc_start: 0.8886 (t60) cc_final: 0.8239 (t60) REVERT: H 58 TYR cc_start: 0.8627 (m-80) cc_final: 0.7073 (m-80) REVERT: H 59 TYR cc_start: 0.8806 (m-80) cc_final: 0.8590 (m-80) REVERT: H 72 ASP cc_start: 0.8288 (t0) cc_final: 0.7933 (t0) REVERT: H 76 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8096 (t0) REVERT: H 82 MET cc_start: 0.6361 (mtm) cc_final: 0.5931 (mtm) REVERT: H 83 ARG cc_start: 0.8352 (mpt-90) cc_final: 0.7967 (mpt-90) REVERT: H 100 ASP cc_start: 0.8975 (t0) cc_final: 0.8738 (t0) REVERT: H 100 TYR cc_start: 0.8657 (m-10) cc_final: 0.7619 (m-80) REVERT: H 100 TYR cc_start: 0.8429 (m-80) cc_final: 0.7765 (m-80) REVERT: H 176 TYR cc_start: 0.6227 (m-80) cc_final: 0.5724 (m-80) REVERT: I 88 CYS cc_start: 0.7019 (p) cc_final: 0.6687 (p) REVERT: D 36 TRP cc_start: 0.9256 (m100) cc_final: 0.8755 (m100) REVERT: D 47 TRP cc_start: 0.9126 (t60) cc_final: 0.8098 (t60) REVERT: D 58 TYR cc_start: 0.8738 (m-80) cc_final: 0.7054 (m-80) REVERT: D 64 LYS cc_start: 0.8733 (tppt) cc_final: 0.8420 (tptp) REVERT: D 67 PHE cc_start: 0.7748 (m-80) cc_final: 0.7060 (m-80) REVERT: D 75 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8493 (mmtp) REVERT: D 76 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7924 (t0) REVERT: D 83 ARG cc_start: 0.8415 (mpt-90) cc_final: 0.7931 (mpt-90) REVERT: D 100 TYR cc_start: 0.8689 (m-80) cc_final: 0.7872 (m-80) REVERT: D 100 MET cc_start: 0.8880 (mpp) cc_final: 0.8344 (mpp) REVERT: E 27 GLN cc_start: 0.8815 (pp30) cc_final: 0.8358 (pp30) REVERT: E 85 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8333 (p) REVERT: E 89 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: E 106 ILE cc_start: 0.7521 (mm) cc_final: 0.7221 (mm) REVERT: E 164 THR cc_start: 0.6417 (p) cc_final: 0.6144 (t) outliers start: 88 outliers final: 75 residues processed: 427 average time/residue: 0.1352 time to fit residues: 90.2885 Evaluate side-chains 446 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 367 CYS Chi-restraints excluded: chain A residue 377 SER 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 A residue 510 ASP 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 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 365 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET 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 454 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 171 LEU 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 422 CYS Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 485 SER 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 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 78 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 76 ASN 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 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 85 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 202 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN D 3 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.145655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.100464 restraints weight = 37554.936| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.02 r_work: 0.3208 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 20781 Z= 0.357 Angle : 0.827 15.468 28232 Z= 0.423 Chirality : 0.050 0.394 3286 Planarity : 0.005 0.076 3579 Dihedral : 6.131 60.518 2874 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.37 % Rotamer: Outliers : 4.00 % Allowed : 21.89 % Favored : 74.11 % 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: -1.04 (0.16), residues: 2610 helix: 0.91 (0.26), residues: 414 sheet: -0.79 (0.17), residues: 925 loop : -1.07 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 235 TYR 0.040 0.003 TYR F 52A PHE 0.044 0.003 PHE D 67 TRP 0.069 0.003 TRP F 36 HIS 0.009 0.002 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00824 (20744) covalent geometry : angle 0.82167 (28157) SS BOND : bond 0.00768 ( 36) SS BOND : angle 1.69000 ( 72) hydrogen bonds : bond 0.03679 ( 900) hydrogen bonds : angle 5.89745 ( 2403) link_NAG-ASN : bond 0.00306 ( 1) link_NAG-ASN : angle 5.01306 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.67 seconds wall clock time: 96 minutes 12.24 seconds (5772.24 seconds total)