Starting phenix.real_space_refine on Wed Mar 4 11:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de6_27385/03_2026/8de6_27385.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.144 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 101 5.16 5 C 8256 2.51 5 N 2271 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s 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: 13243 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "B" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "C" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "G" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.44, per 1000 atoms: 0.18 Number of scatterers: 13243 At special positions: 0 Unit cell: (149.8, 119, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 101 16.00 O 2612 8.00 N 2271 7.00 C 8256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 114 " distance=2.02 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 67 " distance=2.05 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 104 " distance=2.05 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 113 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 462 " distance=2.02 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.00 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 107 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 57 " distance=2.04 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 91 " distance=2.05 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 113 " distance=2.05 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 460 " distance=2.04 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 462 " distance=2.01 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 57 " distance=2.04 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 67 " distance=2.04 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 73 " distance=2.02 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 86 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 113 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 160 " distance=2.03 Simple disulfide: pdb=" SG CYS G 444 " - pdb=" SG CYS G 460 " distance=2.02 Simple disulfide: pdb=" SG CYS G 447 " - pdb=" SG CYS G 462 " distance=2.02 Simple disulfide: pdb=" SG CYS G 464 " - pdb=" SG CYS G 473 " distance=2.03 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 Atom "HETATM13167 O5 BMA A 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Links applied NAG-THR " NAG A 601 " - " THR A 452 " " NAG C 601 " - " THR C 452 " " NAG G 601 " - " THR G 452 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 479.7 milliseconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 28 sheets defined 18.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.586A pdb=" N VAL E 50 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR E 51 " --> pdb=" O LEU E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.693A pdb=" N ASP E 108 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 109' Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.834A pdb=" N ASP A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.614A pdb=" N GLU A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 removed outlier: 4.450A pdb=" N PHE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 411 through 414 removed outlier: 3.523A pdb=" N VAL A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.596A pdb=" N LYS A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.899A pdb=" N VAL B 50 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 removed outlier: 3.695A pdb=" N LYS B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'I' and resid 98 through 102 removed outlier: 3.721A pdb=" N VAL I 102 " --> pdb=" O GLN I 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 109 through 113 removed outlier: 4.045A pdb=" N ASP C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 129 through 134 removed outlier: 4.086A pdb=" N THR C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.516A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 396 removed outlier: 4.438A pdb=" N PHE C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 420 through 438 Processing helix chain 'C' and resid 440 through 444 removed outlier: 3.546A pdb=" N LYS C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 109 through 113 removed outlier: 4.091A pdb=" N ASP G 112 " --> pdb=" O ASP G 109 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS G 113 " --> pdb=" O GLU G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 130 through 134 removed outlier: 3.949A pdb=" N THR G 134 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 279 through 291 Processing helix chain 'G' and resid 369 through 381 removed outlier: 3.834A pdb=" N ARG G 380 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY G 381 " --> pdb=" O LYS G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 396 removed outlier: 4.500A pdb=" N PHE G 389 " --> pdb=" O ASP G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 399 No H-bonds generated for 'chain 'G' and resid 397 through 399' Processing helix chain 'G' and resid 411 through 414 Processing helix chain 'G' and resid 420 through 438 Processing helix chain 'G' and resid 440 through 444 Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.809A pdb=" N VAL E 31 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 53 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N MET E 69 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.415A pdb=" N LEU F 30 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 67 " --> pdb=" O TRP F 54 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN F 56 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU F 65 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS F 58 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU F 63 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 38 through 43 removed outlier: 3.705A pdb=" N ASP F 89 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.909A pdb=" N ARG A 23 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 43 Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 128 removed outlier: 6.689A pdb=" N GLU A 127 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AB1, first strand: chain 'A' and resid 178 through 199 removed outlier: 6.002A pdb=" N VAL A 255 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 181 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG A 253 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR A 183 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 251 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N THR A 185 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE A 249 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLY A 187 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLY A 247 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS A 189 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL A 245 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N PHE A 191 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LEU A 243 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR A 193 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N MET A 241 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N HIS A 195 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLU A 239 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N GLU A 197 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LYS A 237 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 239 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 308 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 247 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 300 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 253 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY A 298 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 315 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 350 " --> pdb=" O ARG A 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 364 current: chain 'C' and resid 234 through 256 removed outlier: 3.882A pdb=" N LYS C 237 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 247 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 304 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 300 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG C 253 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY C 298 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 362 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 315 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 352 " --> pdb=" O MET C 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 351 through 364 current: chain 'G' and resid 237 through 256 removed outlier: 3.788A pdb=" N TYR G 308 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 247 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 300 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG G 253 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 298 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 303 " --> pdb=" O ARG G 364 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET G 315 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 352 " --> pdb=" O MET G 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.649A pdb=" N GLN B 96 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.695A pdb=" N VAL B 31 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 110 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 53 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET B 69 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.271A pdb=" N LEU I 30 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 38 through 43 removed outlier: 3.656A pdb=" N ASP I 89 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 72 through 73 removed outlier: 3.752A pdb=" N THR I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 58 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS I 64 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP I 54 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU I 52 " --> pdb=" O TYR I 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.898A pdb=" N ARG C 23 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.554A pdb=" N ARG C 42 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.665A pdb=" N GLY C 50 " --> pdb=" O CYS C 460 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N CYS C 462 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.813A pdb=" N GLU C 127 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 170 " --> pdb=" O ASP C 165 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AC5, first strand: chain 'G' and resid 23 through 24 removed outlier: 6.862A pdb=" N ARG G 23 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 43 Processing sheet with id=AC7, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'G' and resid 127 through 128 removed outlier: 6.618A pdb=" N GLU G 127 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR G 170 " --> pdb=" O ASP G 165 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 138 through 139 Processing sheet with id=AD1, first strand: chain 'G' and resid 452 through 455 372 hydrogen bonds defined for protein. 984 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: 2.12 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3630 1.33 - 1.46: 3616 1.46 - 1.59: 6121 1.59 - 1.72: 0 1.72 - 1.85: 134 Bond restraints: 13501 Sorted by residual: bond pdb=" C2 BMA C 602 " pdb=" O2 BMA C 602 " ideal model delta sigma weight residual 1.402 1.461 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 BMA G 603 " pdb=" C2 BMA G 603 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C ALA G 399 " pdb=" N PRO G 400 " ideal model delta sigma weight residual 1.328 1.298 0.030 1.25e-02 6.40e+03 5.61e+00 bond pdb=" C2 BMA C 602 " pdb=" C3 BMA C 602 " ideal model delta sigma weight residual 1.544 1.501 0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" CA ASP B 91 " pdb=" CB ASP B 91 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.66e+00 ... (remaining 13496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 16764 1.58 - 3.15: 1312 3.15 - 4.73: 115 4.73 - 6.31: 26 6.31 - 7.89: 8 Bond angle restraints: 18225 Sorted by residual: angle pdb=" C ARG C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta sigma weight residual 121.54 127.22 -5.68 1.91e+00 2.74e-01 8.85e+00 angle pdb=" N THR I 26 " pdb=" CA THR I 26 " pdb=" C THR I 26 " ideal model delta sigma weight residual 110.97 114.14 -3.17 1.09e+00 8.42e-01 8.48e+00 angle pdb=" N LEU G 407 " pdb=" CA LEU G 407 " pdb=" C LEU G 407 " ideal model delta sigma weight residual 110.28 114.47 -4.19 1.48e+00 4.57e-01 8.01e+00 angle pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sigma weight residual 113.24 105.35 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C1 BMA C 602 " pdb=" O5 BMA C 602 " pdb=" C5 BMA C 602 " ideal model delta sigma weight residual 118.82 111.11 7.71 3.00e+00 1.11e-01 6.60e+00 ... (remaining 18220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 7966 22.75 - 45.51: 271 45.51 - 68.26: 31 68.26 - 91.01: 37 91.01 - 113.76: 24 Dihedral angle restraints: 8329 sinusoidal: 3547 harmonic: 4782 Sorted by residual: dihedral pdb=" O4 BMA A 602 " pdb=" C4 BMA A 602 " pdb=" C5 BMA A 602 " pdb=" O5 BMA A 602 " ideal model delta sinusoidal sigma weight residual 288.71 174.95 113.76 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O4 BMA A 603 " pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sinusoidal sigma weight residual 288.71 175.65 113.06 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" O4 BMA G 603 " pdb=" C4 BMA G 603 " pdb=" C5 BMA G 603 " pdb=" O5 BMA G 603 " ideal model delta sinusoidal sigma weight residual 288.71 177.12 111.59 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 8326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1498 0.067 - 0.135: 420 0.135 - 0.202: 55 0.202 - 0.270: 1 0.270 - 0.337: 6 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C2 BMA C 603 " pdb=" C1 BMA C 603 " pdb=" C3 BMA C 603 " pdb=" O2 BMA C 603 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 603 " pdb=" C4 BMA C 603 " pdb=" C6 BMA C 603 " pdb=" O5 BMA C 603 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1977 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 58 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 59 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 59 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 59 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 260 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ASP G 260 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP G 260 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL G 261 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 54 " -0.001 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP F 54 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP F 54 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 54 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP F 54 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 54 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 54 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 54 " 0.019 2.00e-02 2.50e+03 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 556 2.72 - 3.26: 12048 3.26 - 3.81: 18695 3.81 - 4.35: 23607 4.35 - 4.90: 42554 Nonbonded interactions: 97460 Sorted by model distance: nonbonded pdb=" OD2 ASP G 270 " pdb=" OH TYR G 290 " model vdw 2.169 3.040 nonbonded pdb=" OD2 ASP A 270 " pdb=" OH TYR A 290 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP G 109 " pdb="CA CA G 604 " model vdw 2.203 2.510 nonbonded pdb=" OG1 THR A 452 " pdb=" N2 NAG A 601 " model vdw 2.256 2.496 nonbonded pdb=" OG1 THR G 452 " pdb=" N2 NAG G 601 " model vdw 2.268 2.496 ... (remaining 97455 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'F' 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: 1.240 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.010 0.071 13544 Z= 0.535 Angle : 0.931 7.885 18299 Z= 0.522 Chirality : 0.061 0.337 1980 Planarity : 0.007 0.058 2359 Dihedral : 14.683 113.764 5167 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 6.76 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.86 (0.20), residues: 1633 helix: -0.06 (0.30), residues: 219 sheet: -0.28 (0.22), residues: 512 loop : -0.83 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.004 ARG G 95 TYR 0.026 0.006 TYR G 290 PHE 0.024 0.006 PHE A 389 TRP 0.027 0.008 TRP C 30 HIS 0.018 0.005 HIS G 244 Details of bonding type rmsd covalent geometry : bond 0.01021 (13501) covalent geometry : angle 0.92818 (18225) SS BOND : bond 0.01272 ( 34) SS BOND : angle 1.24028 ( 68) hydrogen bonds : bond 0.25970 ( 372) hydrogen bonds : angle 8.17558 ( 984) Misc. bond : bond 0.00416 ( 6) link_NAG-THR : bond 0.01170 ( 3) link_NAG-THR : angle 3.28575 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 GLN cc_start: 0.8830 (pt0) cc_final: 0.8275 (pt0) REVERT: E 96 GLN cc_start: 0.9015 (mt0) cc_final: 0.8814 (mt0) REVERT: E 100 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7666 (mmmm) REVERT: F 43 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7051 (mtm110) REVERT: A 56 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7455 (ptp-110) REVERT: A 77 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7662 (pm20) REVERT: A 234 TYR cc_start: 0.7316 (t80) cc_final: 0.7076 (t80) REVERT: A 241 MET cc_start: 0.8640 (ttm) cc_final: 0.8380 (ttp) REVERT: A 250 HIS cc_start: 0.8653 (m-70) cc_final: 0.7784 (t70) REVERT: A 269 ASP cc_start: 0.8576 (m-30) cc_final: 0.8122 (m-30) REVERT: A 406 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8316 (ttmm) REVERT: A 433 GLU cc_start: 0.7711 (tt0) cc_final: 0.7130 (mt-10) REVERT: A 456 MET cc_start: 0.8051 (mmm) cc_final: 0.7791 (mmm) REVERT: B 62 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7156 (mmtm) REVERT: B 91 ASP cc_start: 0.7310 (t0) cc_final: 0.6844 (t70) REVERT: B 100 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6960 (mmtt) REVERT: B 108 ASP cc_start: 0.7820 (m-30) cc_final: 0.7560 (m-30) REVERT: I 23 MET cc_start: 0.8661 (mmm) cc_final: 0.8418 (mmm) REVERT: I 82 SER cc_start: 0.7802 (m) cc_final: 0.7527 (p) REVERT: I 96 ASN cc_start: 0.7923 (m110) cc_final: 0.7701 (m110) REVERT: I 123 LEU cc_start: 0.7649 (tp) cc_final: 0.7427 (tt) REVERT: C 23 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.8017 (ttp80) REVERT: C 101 ASP cc_start: 0.7324 (m-30) cc_final: 0.7080 (m-30) REVERT: C 107 PHE cc_start: 0.7059 (m-80) cc_final: 0.6851 (m-80) REVERT: C 171 TYR cc_start: 0.8195 (m-80) cc_final: 0.7969 (m-80) REVERT: C 182 ILE cc_start: 0.8512 (mt) cc_final: 0.8086 (mp) REVERT: C 185 THR cc_start: 0.8177 (m) cc_final: 0.7917 (p) REVERT: C 192 ARG cc_start: 0.6929 (ttm170) cc_final: 0.6351 (mmp80) REVERT: C 240 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7668 (mmtp) REVERT: C 251 LEU cc_start: 0.8401 (tp) cc_final: 0.8129 (tp) REVERT: C 272 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7869 (mtpp) REVERT: G 19 HIS cc_start: 0.6191 (p-80) cc_final: 0.5979 (p90) REVERT: G 45 SER cc_start: 0.7802 (t) cc_final: 0.7524 (p) REVERT: G 56 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6902 (ptm160) REVERT: G 79 ASP cc_start: 0.7531 (m-30) cc_final: 0.7263 (p0) REVERT: G 269 ASP cc_start: 0.8023 (m-30) cc_final: 0.7515 (m-30) REVERT: G 270 ASP cc_start: 0.7994 (m-30) cc_final: 0.7711 (m-30) REVERT: G 315 MET cc_start: 0.7638 (ttp) cc_final: 0.7357 (tmm) REVERT: G 379 LEU cc_start: 0.8084 (tp) cc_final: 0.7741 (tp) REVERT: G 406 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7949 (tmtt) REVERT: G 459 LYS cc_start: 0.7790 (tttm) cc_final: 0.7378 (tttt) outliers start: 37 outliers final: 20 residues processed: 339 average time/residue: 0.1279 time to fit residues: 59.8718 Evaluate side-chains 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN F 25 GLN A 32 GLN A 153 ASN A 177 ASN A 199 GLN A 258 ASN B 20 GLN C 39 GLN C 177 ASN C 293 HIS C 354 ASN C 448 GLN C 449 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN G 177 ASN G 449 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112991 restraints weight = 16262.657| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.49 r_work: 0.3176 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13544 Z= 0.120 Angle : 0.532 6.006 18299 Z= 0.277 Chirality : 0.042 0.167 1980 Planarity : 0.004 0.052 2359 Dihedral : 11.730 73.526 2038 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.66 % Allowed : 10.52 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.62 (0.20), residues: 1633 helix: 0.70 (0.32), residues: 228 sheet: -0.22 (0.21), residues: 572 loop : -0.81 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 122 TYR 0.012 0.001 TYR A 283 PHE 0.009 0.001 PHE C 439 TRP 0.010 0.001 TRP E 66 HIS 0.003 0.001 HIS I 46 Details of bonding type rmsd covalent geometry : bond 0.00266 (13501) covalent geometry : angle 0.52895 (18225) SS BOND : bond 0.00555 ( 34) SS BOND : angle 0.79228 ( 68) hydrogen bonds : bond 0.04528 ( 372) hydrogen bonds : angle 5.44819 ( 984) Misc. bond : bond 0.00094 ( 6) link_NAG-THR : bond 0.00152 ( 3) link_NAG-THR : angle 2.22076 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.386 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: E 96 GLN cc_start: 0.8962 (mt0) cc_final: 0.8753 (mt0) REVERT: E 100 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7780 (mmmm) REVERT: F 26 THR cc_start: 0.8537 (p) cc_final: 0.8106 (p) REVERT: F 43 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7336 (ptp90) REVERT: A 56 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7526 (ptp-110) REVERT: A 77 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7624 (pm20) REVERT: A 192 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8211 (ttm110) REVERT: A 234 TYR cc_start: 0.7524 (t80) cc_final: 0.7231 (t80) REVERT: A 250 HIS cc_start: 0.8764 (m-70) cc_final: 0.7976 (t70) REVERT: A 369 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8203 (tttm) REVERT: A 406 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8318 (ttmm) REVERT: A 433 GLU cc_start: 0.8228 (tt0) cc_final: 0.7661 (mt-10) REVERT: A 456 MET cc_start: 0.8370 (mmm) cc_final: 0.8044 (mmm) REVERT: B 82 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8548 (pp) REVERT: B 91 ASP cc_start: 0.7205 (t0) cc_final: 0.6598 (t70) REVERT: B 100 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7262 (mmmt) REVERT: B 108 ASP cc_start: 0.7973 (m-30) cc_final: 0.7676 (m-30) REVERT: B 132 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7794 (tp-100) REVERT: I 23 MET cc_start: 0.8861 (mmm) cc_final: 0.8286 (mmm) REVERT: C 24 MET cc_start: 0.9105 (mtp) cc_final: 0.8876 (mmm) REVERT: C 101 ASP cc_start: 0.7439 (m-30) cc_final: 0.7207 (m-30) REVERT: C 182 ILE cc_start: 0.8811 (mt) cc_final: 0.8496 (tt) REVERT: C 192 ARG cc_start: 0.7619 (ttm170) cc_final: 0.6610 (mmp80) REVERT: C 240 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8174 (mmtp) REVERT: C 243 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (mm) REVERT: C 272 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8137 (tttm) REVERT: G 19 HIS cc_start: 0.6259 (p-80) cc_final: 0.6040 (p90) REVERT: G 56 ARG cc_start: 0.7672 (ptp90) cc_final: 0.7341 (ptm160) REVERT: G 85 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7551 (tp40) REVERT: G 282 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7926 (mm-30) REVERT: G 376 GLU cc_start: 0.7561 (tp30) cc_final: 0.6825 (tt0) REVERT: G 453 VAL cc_start: 0.8024 (t) cc_final: 0.7633 (p) outliers start: 39 outliers final: 20 residues processed: 257 average time/residue: 0.1252 time to fit residues: 44.3820 Evaluate side-chains 231 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 139 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN ** G 85 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 = 0.3708 r_free = 0.3708 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110469 restraints weight = 16534.150| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.51 r_work: 0.3133 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13544 Z= 0.124 Angle : 0.505 7.079 18299 Z= 0.263 Chirality : 0.042 0.155 1980 Planarity : 0.003 0.051 2359 Dihedral : 8.047 58.931 2026 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.14 % Allowed : 12.30 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.56 (0.20), residues: 1633 helix: 0.92 (0.33), residues: 228 sheet: -0.07 (0.22), residues: 559 loop : -0.91 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 43 TYR 0.015 0.001 TYR B 113 PHE 0.010 0.001 PHE C 439 TRP 0.009 0.001 TRP E 66 HIS 0.002 0.001 HIS I 46 Details of bonding type rmsd covalent geometry : bond 0.00290 (13501) covalent geometry : angle 0.50264 (18225) SS BOND : bond 0.00290 ( 34) SS BOND : angle 0.72478 ( 68) hydrogen bonds : bond 0.04199 ( 372) hydrogen bonds : angle 4.81768 ( 984) Misc. bond : bond 0.00065 ( 6) link_NAG-THR : bond 0.00202 ( 3) link_NAG-THR : angle 2.17112 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 THR cc_start: 0.8489 (p) cc_final: 0.8155 (p) REVERT: A 77 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7640 (pm20) REVERT: A 149 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9223 (p) REVERT: A 234 TYR cc_start: 0.7562 (t80) cc_final: 0.7287 (t80) REVERT: A 250 HIS cc_start: 0.8750 (m-70) cc_final: 0.7952 (t70) REVERT: A 369 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8204 (tttp) REVERT: A 433 GLU cc_start: 0.8220 (tt0) cc_final: 0.7650 (mt-10) REVERT: B 82 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8539 (pp) REVERT: B 91 ASP cc_start: 0.7083 (t0) cc_final: 0.6471 (t70) REVERT: B 100 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7166 (mmmt) REVERT: B 132 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7654 (tp-100) REVERT: I 23 MET cc_start: 0.8959 (mmm) cc_final: 0.8085 (mmm) REVERT: I 69 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: C 101 ASP cc_start: 0.7420 (m-30) cc_final: 0.7107 (m-30) REVERT: C 182 ILE cc_start: 0.8665 (mt) cc_final: 0.8266 (tt) REVERT: C 188 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7761 (mt-10) REVERT: C 192 ARG cc_start: 0.7506 (ttm170) cc_final: 0.6591 (mmp80) REVERT: C 240 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8187 (mmtp) REVERT: C 243 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8155 (mm) REVERT: G 56 ARG cc_start: 0.7746 (ptp90) cc_final: 0.7392 (ptm160) REVERT: G 85 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7649 (tp40) REVERT: G 376 GLU cc_start: 0.7642 (tp30) cc_final: 0.6879 (tt0) REVERT: G 453 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7703 (p) outliers start: 46 outliers final: 32 residues processed: 236 average time/residue: 0.1295 time to fit residues: 42.3294 Evaluate side-chains 231 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TYR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 405 GLN Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 140 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN ** G 85 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 = 0.3645 r_free = 0.3645 target = 0.138865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105368 restraints weight = 16486.209| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.52 r_work: 0.3048 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13544 Z= 0.172 Angle : 0.538 8.102 18299 Z= 0.284 Chirality : 0.042 0.150 1980 Planarity : 0.004 0.051 2359 Dihedral : 7.007 59.688 2025 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.62 % Allowed : 12.43 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.75 (0.20), residues: 1633 helix: 0.76 (0.34), residues: 228 sheet: -0.12 (0.22), residues: 552 loop : -1.08 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 43 TYR 0.020 0.002 TYR B 113 PHE 0.012 0.002 PHE C 191 TRP 0.012 0.001 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd covalent geometry : bond 0.00411 (13501) covalent geometry : angle 0.53537 (18225) SS BOND : bond 0.00364 ( 34) SS BOND : angle 0.84196 ( 68) hydrogen bonds : bond 0.04520 ( 372) hydrogen bonds : angle 4.73300 ( 984) Misc. bond : bond 0.00043 ( 6) link_NAG-THR : bond 0.00215 ( 3) link_NAG-THR : angle 2.17198 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.7175 (ptp-170) REVERT: A 77 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7642 (pm20) REVERT: A 149 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9262 (p) REVERT: A 234 TYR cc_start: 0.7831 (t80) cc_final: 0.7566 (t80) REVERT: A 369 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8202 (tttm) REVERT: A 433 GLU cc_start: 0.8270 (tt0) cc_final: 0.7705 (mt-10) REVERT: B 82 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8458 (pp) REVERT: B 91 ASP cc_start: 0.7202 (t0) cc_final: 0.6532 (t70) REVERT: B 100 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7129 (mmmt) REVERT: B 132 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7713 (tp-100) REVERT: I 23 MET cc_start: 0.9033 (mmm) cc_final: 0.8447 (mmm) REVERT: I 98 GLU cc_start: 0.7608 (tp30) cc_final: 0.7105 (tp30) REVERT: C 101 ASP cc_start: 0.7415 (m-30) cc_final: 0.7146 (m-30) REVERT: C 124 ARG cc_start: 0.7026 (mmp-170) cc_final: 0.6776 (mmp-170) REVERT: C 182 ILE cc_start: 0.8665 (mt) cc_final: 0.8225 (tt) REVERT: C 188 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7508 (tt0) REVERT: C 192 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6947 (mmp80) REVERT: C 198 GLU cc_start: 0.6974 (mp0) cc_final: 0.6747 (tt0) REVERT: C 240 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8226 (mmtp) REVERT: C 243 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8483 (tp) REVERT: G 56 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7321 (ptm160) REVERT: G 376 GLU cc_start: 0.7689 (tp30) cc_final: 0.7104 (tt0) REVERT: G 453 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7854 (p) outliers start: 53 outliers final: 33 residues processed: 241 average time/residue: 0.1178 time to fit residues: 39.6110 Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN G 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103659 restraints weight = 16618.509| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.48 r_work: 0.3011 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13544 Z= 0.259 Angle : 0.624 9.828 18299 Z= 0.329 Chirality : 0.045 0.153 1980 Planarity : 0.005 0.064 2359 Dihedral : 7.217 59.705 2023 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.62 % Allowed : 13.59 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.13 (0.20), residues: 1633 helix: 0.43 (0.34), residues: 225 sheet: -0.37 (0.22), residues: 552 loop : -1.32 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 44 TYR 0.024 0.002 TYR B 113 PHE 0.016 0.002 PHE C 191 TRP 0.014 0.002 TRP G 27 HIS 0.006 0.002 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00627 (13501) covalent geometry : angle 0.61988 (18225) SS BOND : bond 0.00463 ( 34) SS BOND : angle 1.15488 ( 68) hydrogen bonds : bond 0.05403 ( 372) hydrogen bonds : angle 4.89660 ( 984) Misc. bond : bond 0.00058 ( 6) link_NAG-THR : bond 0.00198 ( 3) link_NAG-THR : angle 2.01803 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7653 (mp10) cc_final: 0.7410 (mp10) REVERT: F 43 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.7124 (ptp-170) REVERT: A 149 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9268 (p) REVERT: A 234 TYR cc_start: 0.8060 (t80) cc_final: 0.7765 (t80) REVERT: A 353 GLU cc_start: 0.7983 (mp0) cc_final: 0.7234 (mp0) REVERT: A 433 GLU cc_start: 0.8284 (tt0) cc_final: 0.7707 (mt-10) REVERT: B 62 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7304 (mmtm) REVERT: B 82 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 91 ASP cc_start: 0.7234 (t0) cc_final: 0.6578 (t70) REVERT: B 100 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7038 (mmmt) REVERT: B 132 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7860 (tp-100) REVERT: I 98 GLU cc_start: 0.7450 (tp30) cc_final: 0.7038 (tp30) REVERT: I 122 LYS cc_start: 0.8567 (tppt) cc_final: 0.8318 (ttmm) REVERT: I 123 LEU cc_start: 0.8225 (tp) cc_final: 0.7881 (tt) REVERT: C 101 ASP cc_start: 0.7302 (m-30) cc_final: 0.7048 (m-30) REVERT: C 124 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6852 (mmp-170) REVERT: C 162 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8216 (ptm160) REVERT: C 192 ARG cc_start: 0.7778 (ttm170) cc_final: 0.6997 (mmt-90) REVERT: C 243 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8195 (mm) REVERT: G 56 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7414 (ptm160) REVERT: G 376 GLU cc_start: 0.7905 (tp30) cc_final: 0.7362 (tt0) REVERT: G 384 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6473 (tt) REVERT: G 453 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7905 (p) REVERT: G 477 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5559 (tppt) outliers start: 53 outliers final: 37 residues processed: 236 average time/residue: 0.1217 time to fit residues: 40.1412 Evaluate side-chains 236 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN F 46 HIS A 199 GLN A 293 HIS C 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108317 restraints weight = 16367.808| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.48 r_work: 0.3073 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13544 Z= 0.095 Angle : 0.485 10.378 18299 Z= 0.255 Chirality : 0.040 0.146 1980 Planarity : 0.003 0.056 2359 Dihedral : 6.213 59.082 2023 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.28 % Allowed : 14.96 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.87 (0.20), residues: 1633 helix: 0.76 (0.34), residues: 228 sheet: -0.16 (0.22), residues: 552 loop : -1.22 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 43 TYR 0.013 0.001 TYR B 113 PHE 0.011 0.001 PHE C 267 TRP 0.009 0.001 TRP G 27 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00213 (13501) covalent geometry : angle 0.48343 (18225) SS BOND : bond 0.00234 ( 34) SS BOND : angle 0.64509 ( 68) hydrogen bonds : bond 0.03584 ( 372) hydrogen bonds : angle 4.57954 ( 984) Misc. bond : bond 0.00035 ( 6) link_NAG-THR : bond 0.00094 ( 3) link_NAG-THR : angle 1.69176 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7504 (mp10) cc_final: 0.7200 (mp10) REVERT: E 107 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7938 (t70) REVERT: F 43 ARG cc_start: 0.7293 (ptp-170) cc_final: 0.6957 (ptp-170) REVERT: F 46 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.7527 (m90) REVERT: A 77 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7637 (pm20) REVERT: A 199 GLN cc_start: 0.8011 (mt0) cc_final: 0.7642 (mt0) REVERT: A 234 TYR cc_start: 0.7828 (t80) cc_final: 0.7537 (t80) REVERT: A 250 HIS cc_start: 0.8579 (m-70) cc_final: 0.8339 (m90) REVERT: A 353 GLU cc_start: 0.7972 (mp0) cc_final: 0.7269 (mp0) REVERT: A 433 GLU cc_start: 0.8189 (tt0) cc_final: 0.7602 (mt-10) REVERT: B 62 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7432 (mmtm) REVERT: B 82 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8574 (pp) REVERT: B 91 ASP cc_start: 0.7062 (t0) cc_final: 0.6411 (t70) REVERT: B 100 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: B 132 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7726 (tp-100) REVERT: I 69 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: I 98 GLU cc_start: 0.7301 (tp30) cc_final: 0.7030 (tp30) REVERT: I 122 LYS cc_start: 0.8567 (tppt) cc_final: 0.8329 (ttmm) REVERT: C 101 ASP cc_start: 0.7383 (m-30) cc_final: 0.7053 (m-30) REVERT: C 182 ILE cc_start: 0.8822 (mt) cc_final: 0.8398 (tt) REVERT: C 192 ARG cc_start: 0.7654 (ttm170) cc_final: 0.6825 (mmp80) REVERT: C 243 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8380 (tp) REVERT: G 56 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7389 (ptm160) REVERT: G 316 LYS cc_start: 0.7371 (tmtt) cc_final: 0.7041 (tmtt) REVERT: G 376 GLU cc_start: 0.7731 (tp30) cc_final: 0.7471 (tt0) REVERT: G 453 VAL cc_start: 0.8190 (t) cc_final: 0.7913 (p) outliers start: 48 outliers final: 34 residues processed: 233 average time/residue: 0.1280 time to fit residues: 41.5203 Evaluate side-chains 228 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TYR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106422 restraints weight = 16367.342| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.50 r_work: 0.3053 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13544 Z= 0.115 Angle : 0.493 11.344 18299 Z= 0.258 Chirality : 0.041 0.143 1980 Planarity : 0.003 0.061 2359 Dihedral : 5.982 59.962 2023 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.62 % Allowed : 15.10 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.82 (0.20), residues: 1633 helix: 0.80 (0.34), residues: 228 sheet: -0.13 (0.22), residues: 552 loop : -1.19 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 43 TYR 0.014 0.001 TYR B 113 PHE 0.014 0.001 PHE G 466 TRP 0.010 0.001 TRP G 27 HIS 0.013 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00271 (13501) covalent geometry : angle 0.49113 (18225) SS BOND : bond 0.00266 ( 34) SS BOND : angle 0.67680 ( 68) hydrogen bonds : bond 0.03737 ( 372) hydrogen bonds : angle 4.50852 ( 984) Misc. bond : bond 0.00027 ( 6) link_NAG-THR : bond 0.00112 ( 3) link_NAG-THR : angle 1.74987 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7933 (t70) REVERT: F 43 ARG cc_start: 0.7398 (ptp-170) cc_final: 0.7043 (ptp-170) REVERT: A 77 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7588 (pm20) REVERT: A 199 GLN cc_start: 0.7865 (mt0) cc_final: 0.7512 (mt0) REVERT: A 234 TYR cc_start: 0.7857 (t80) cc_final: 0.7558 (t80) REVERT: A 250 HIS cc_start: 0.8604 (m-70) cc_final: 0.8366 (m90) REVERT: A 353 GLU cc_start: 0.7957 (mp0) cc_final: 0.7242 (mp0) REVERT: A 433 GLU cc_start: 0.8209 (tt0) cc_final: 0.7615 (mt-10) REVERT: A 469 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5777 (pm20) REVERT: B 62 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7416 (mmtm) REVERT: B 82 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8529 (pp) REVERT: B 91 ASP cc_start: 0.7051 (t0) cc_final: 0.6432 (t0) REVERT: B 100 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7042 (mmmt) REVERT: B 132 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7769 (tp-100) REVERT: I 98 GLU cc_start: 0.7468 (tp30) cc_final: 0.7248 (tp30) REVERT: I 122 LYS cc_start: 0.8522 (tppt) cc_final: 0.8285 (ttmm) REVERT: I 123 LEU cc_start: 0.8196 (tp) cc_final: 0.7836 (tt) REVERT: C 101 ASP cc_start: 0.7382 (m-30) cc_final: 0.7114 (m-30) REVERT: C 182 ILE cc_start: 0.8818 (mt) cc_final: 0.8390 (tt) REVERT: C 192 ARG cc_start: 0.7681 (ttm170) cc_final: 0.6828 (mmp80) REVERT: C 243 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (tp) REVERT: G 56 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7390 (ptm160) REVERT: G 316 LYS cc_start: 0.7373 (tmtt) cc_final: 0.6799 (tmtt) REVERT: G 376 GLU cc_start: 0.7771 (tp30) cc_final: 0.7494 (tt0) REVERT: G 406 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7645 (tmtt) REVERT: G 453 VAL cc_start: 0.8217 (t) cc_final: 0.7939 (p) outliers start: 53 outliers final: 41 residues processed: 236 average time/residue: 0.1235 time to fit residues: 41.0488 Evaluate side-chains 240 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 0.0270 chunk 147 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 GLN F 46 HIS I 50 ASN C 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105532 restraints weight = 16444.306| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.47 r_work: 0.3038 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13544 Z= 0.186 Angle : 0.555 12.188 18299 Z= 0.291 Chirality : 0.043 0.144 1980 Planarity : 0.004 0.062 2359 Dihedral : 6.132 58.372 2023 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.76 % Allowed : 15.10 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.00 (0.20), residues: 1633 helix: 0.62 (0.34), residues: 225 sheet: -0.27 (0.22), residues: 552 loop : -1.27 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 38 TYR 0.019 0.002 TYR B 113 PHE 0.012 0.002 PHE G 389 TRP 0.012 0.002 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd covalent geometry : bond 0.00448 (13501) covalent geometry : angle 0.55225 (18225) SS BOND : bond 0.00358 ( 34) SS BOND : angle 0.89948 ( 68) hydrogen bonds : bond 0.04569 ( 372) hydrogen bonds : angle 4.62381 ( 984) Misc. bond : bond 0.00038 ( 6) link_NAG-THR : bond 0.00144 ( 3) link_NAG-THR : angle 1.84567 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7791 (mp10) cc_final: 0.7553 (mp10) REVERT: E 107 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8200 (p0) REVERT: F 43 ARG cc_start: 0.7388 (ptp-170) cc_final: 0.7105 (ptp-170) REVERT: F 46 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7427 (m90) REVERT: A 77 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7561 (pm20) REVERT: A 234 TYR cc_start: 0.7949 (t80) cc_final: 0.7699 (t80) REVERT: A 353 GLU cc_start: 0.7955 (mp0) cc_final: 0.7392 (mp0) REVERT: A 433 GLU cc_start: 0.8239 (tt0) cc_final: 0.7648 (mt-10) REVERT: A 469 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5982 (pm20) REVERT: B 62 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7292 (mmtm) REVERT: B 82 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8587 (pp) REVERT: B 91 ASP cc_start: 0.7129 (t0) cc_final: 0.6511 (t0) REVERT: B 100 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7045 (mmmt) REVERT: B 105 GLN cc_start: 0.8133 (mt0) cc_final: 0.7570 (mp-120) REVERT: B 132 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7721 (tp-100) REVERT: I 122 LYS cc_start: 0.8515 (tppt) cc_final: 0.8278 (ttmm) REVERT: I 123 LEU cc_start: 0.8342 (tp) cc_final: 0.7982 (tt) REVERT: C 101 ASP cc_start: 0.7242 (m-30) cc_final: 0.6983 (m-30) REVERT: C 182 ILE cc_start: 0.8687 (mt) cc_final: 0.8209 (tt) REVERT: C 192 ARG cc_start: 0.7701 (ttm170) cc_final: 0.6901 (mmp80) REVERT: C 243 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8108 (mm) REVERT: G 56 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7461 (ptm160) REVERT: G 376 GLU cc_start: 0.7911 (tp30) cc_final: 0.7632 (tt0) REVERT: G 406 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: G 453 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7957 (p) REVERT: G 477 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.5702 (tppt) outliers start: 55 outliers final: 44 residues processed: 233 average time/residue: 0.1251 time to fit residues: 41.0310 Evaluate side-chains 242 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 151 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106596 restraints weight = 16486.792| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.48 r_work: 0.3063 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13544 Z= 0.135 Angle : 0.522 12.241 18299 Z= 0.273 Chirality : 0.041 0.143 1980 Planarity : 0.004 0.072 2359 Dihedral : 5.958 58.207 2023 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.69 % Allowed : 15.51 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.94 (0.20), residues: 1633 helix: 0.71 (0.35), residues: 225 sheet: -0.24 (0.22), residues: 552 loop : -1.25 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 43 TYR 0.016 0.001 TYR B 113 PHE 0.010 0.001 PHE A 155 TRP 0.011 0.001 TRP G 27 HIS 0.005 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00322 (13501) covalent geometry : angle 0.51969 (18225) SS BOND : bond 0.00302 ( 34) SS BOND : angle 0.74732 ( 68) hydrogen bonds : bond 0.04059 ( 372) hydrogen bonds : angle 4.55661 ( 984) Misc. bond : bond 0.00033 ( 6) link_NAG-THR : bond 0.00114 ( 3) link_NAG-THR : angle 1.76877 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7641 (mp10) cc_final: 0.7366 (mp10) REVERT: E 107 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8205 (p0) REVERT: F 43 ARG cc_start: 0.7334 (ptp-170) cc_final: 0.7083 (ptp-170) REVERT: A 77 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7569 (pm20) REVERT: A 199 GLN cc_start: 0.7943 (mt0) cc_final: 0.7590 (mt0) REVERT: A 234 TYR cc_start: 0.7988 (t80) cc_final: 0.7669 (t80) REVERT: A 250 HIS cc_start: 0.8605 (m-70) cc_final: 0.8387 (m90) REVERT: A 353 GLU cc_start: 0.7956 (mp0) cc_final: 0.7456 (mp0) REVERT: A 433 GLU cc_start: 0.8213 (tt0) cc_final: 0.7617 (mt-10) REVERT: A 469 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5849 (pm20) REVERT: B 62 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7449 (mmtm) REVERT: B 82 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8585 (pp) REVERT: B 91 ASP cc_start: 0.7081 (t0) cc_final: 0.6464 (t0) REVERT: B 100 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7060 (mmmt) REVERT: B 105 GLN cc_start: 0.8159 (mt0) cc_final: 0.7729 (mp-120) REVERT: B 132 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7712 (tp-100) REVERT: I 69 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: I 98 GLU cc_start: 0.7438 (tp30) cc_final: 0.7208 (tp30) REVERT: I 122 LYS cc_start: 0.8515 (tppt) cc_final: 0.8275 (ttmm) REVERT: I 123 LEU cc_start: 0.8338 (tp) cc_final: 0.7976 (tt) REVERT: C 101 ASP cc_start: 0.7338 (m-30) cc_final: 0.7077 (m-30) REVERT: C 182 ILE cc_start: 0.8845 (mt) cc_final: 0.8415 (tt) REVERT: C 192 ARG cc_start: 0.7663 (ttm170) cc_final: 0.6886 (mmp80) REVERT: C 243 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8102 (mm) REVERT: G 56 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7416 (ptm160) REVERT: G 316 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7010 (tmtt) REVERT: G 376 GLU cc_start: 0.7897 (tp30) cc_final: 0.7623 (tt0) REVERT: G 406 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7710 (tmtt) REVERT: G 453 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8016 (p) REVERT: G 477 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.5694 (tppt) outliers start: 54 outliers final: 44 residues processed: 236 average time/residue: 0.1194 time to fit residues: 39.6922 Evaluate side-chains 245 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TYR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103714 restraints weight = 16566.944| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.46 r_work: 0.3027 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13544 Z= 0.254 Angle : 0.625 12.977 18299 Z= 0.328 Chirality : 0.045 0.150 1980 Planarity : 0.005 0.067 2359 Dihedral : 6.390 59.940 2023 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.69 % Allowed : 15.85 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.20 (0.20), residues: 1633 helix: 0.81 (0.35), residues: 207 sheet: -0.46 (0.22), residues: 546 loop : -1.42 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 43 TYR 0.022 0.002 TYR B 113 PHE 0.015 0.002 PHE C 254 TRP 0.013 0.002 TRP G 27 HIS 0.006 0.001 HIS I 46 Details of bonding type rmsd covalent geometry : bond 0.00617 (13501) covalent geometry : angle 0.62235 (18225) SS BOND : bond 0.00440 ( 34) SS BOND : angle 1.08890 ( 68) hydrogen bonds : bond 0.05277 ( 372) hydrogen bonds : angle 4.78383 ( 984) Misc. bond : bond 0.00054 ( 6) link_NAG-THR : bond 0.00198 ( 3) link_NAG-THR : angle 1.81794 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LEU cc_start: 0.9309 (mm) cc_final: 0.8966 (mm) REVERT: E 105 GLN cc_start: 0.7747 (mp10) cc_final: 0.7458 (mp10) REVERT: E 107 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (p0) REVERT: F 43 ARG cc_start: 0.7402 (ptp-170) cc_final: 0.7154 (ptp-170) REVERT: F 46 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.7694 (m90) REVERT: A 234 TYR cc_start: 0.8094 (t80) cc_final: 0.7836 (t80) REVERT: A 250 HIS cc_start: 0.8622 (m-70) cc_final: 0.8407 (m90) REVERT: A 353 GLU cc_start: 0.7956 (mp0) cc_final: 0.7447 (mp0) REVERT: A 469 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6130 (pm20) REVERT: B 62 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7320 (mmtm) REVERT: B 82 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8646 (pp) REVERT: B 91 ASP cc_start: 0.7170 (t0) cc_final: 0.6557 (t0) REVERT: B 100 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7021 (mmmt) REVERT: B 105 GLN cc_start: 0.8283 (mt0) cc_final: 0.7783 (mp-120) REVERT: B 132 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7780 (tp-100) REVERT: I 58 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7908 (ptpp) REVERT: I 98 GLU cc_start: 0.7553 (tp30) cc_final: 0.7330 (tp30) REVERT: I 122 LYS cc_start: 0.8564 (tppt) cc_final: 0.8332 (ttmm) REVERT: I 123 LEU cc_start: 0.8397 (tp) cc_final: 0.8026 (tt) REVERT: C 101 ASP cc_start: 0.7241 (m-30) cc_final: 0.6987 (m-30) REVERT: C 192 ARG cc_start: 0.7727 (ttm170) cc_final: 0.6957 (mmt-90) REVERT: G 29 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: G 56 ARG cc_start: 0.7902 (ptp90) cc_final: 0.7447 (ptm160) REVERT: G 376 GLU cc_start: 0.7950 (tp30) cc_final: 0.7674 (tt0) REVERT: G 384 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6368 (tt) REVERT: G 406 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7799 (tmtt) REVERT: G 453 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8029 (p) REVERT: G 477 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.5596 (tppt) outliers start: 54 outliers final: 43 residues processed: 236 average time/residue: 0.1287 time to fit residues: 42.4354 Evaluate side-chains 245 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN F 46 HIS C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106387 restraints weight = 16398.761| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.50 r_work: 0.3084 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13544 Z= 0.100 Angle : 0.510 12.863 18299 Z= 0.267 Chirality : 0.041 0.146 1980 Planarity : 0.004 0.060 2359 Dihedral : 5.896 56.401 2023 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.01 % Allowed : 16.60 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.92 (0.20), residues: 1633 helix: 1.17 (0.35), residues: 210 sheet: -0.29 (0.22), residues: 552 loop : -1.27 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 162 TYR 0.015 0.001 TYR B 113 PHE 0.009 0.001 PHE C 267 TRP 0.009 0.001 TRP G 27 HIS 0.010 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00225 (13501) covalent geometry : angle 0.50911 (18225) SS BOND : bond 0.00251 ( 34) SS BOND : angle 0.62482 ( 68) hydrogen bonds : bond 0.03628 ( 372) hydrogen bonds : angle 4.54632 ( 984) Misc. bond : bond 0.00023 ( 6) link_NAG-THR : bond 0.00080 ( 3) link_NAG-THR : angle 1.61039 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.80 seconds wall clock time: 53 minutes 3.76 seconds (3183.76 seconds total)