Starting phenix.real_space_refine on Fri Jul 3 09:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de6_27385/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.map" model { file = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2026/8de6_27385.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-6108/lib/python3.11/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 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 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 chiralities: 3 Time building chain proxies: 2.68, per 1000 atoms: 0.20 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: 0.95 Conformation dependent library (CDL) restraints added in 573.4 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: 0.37 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: 2.17 Time building geometry restraints manager: 1.25 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 - 16.10: 7551 16.10 - 32.20: 506 32.20 - 48.30: 77 48.30 - 64.40: 16 64.40 - 80.51: 2 Dihedral angle restraints: 8152 sinusoidal: 3370 harmonic: 4782 Sorted by residual: dihedral pdb=" CA THR F 70 " pdb=" C THR F 70 " pdb=" N SER F 71 " pdb=" CA SER F 71 " ideal model delta harmonic sigma weight residual 180.00 163.68 16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA SER E 124 " pdb=" C SER E 124 " pdb=" N ALA E 125 " pdb=" CA ALA E 125 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP F 60 " pdb=" CB ASP F 60 " pdb=" CG ASP F 60 " pdb=" OD1 ASP F 60 " ideal model delta sinusoidal sigma weight residual -30.00 -84.77 54.77 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 8149 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: 1.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.860 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 10.743 80.506 4990 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/Z covalent geometry : bond 0.01021 / 0.54 (13501) covalent geometry : angle 0.92818 / 0.52 (18225) SS BOND : bond 0.01272 / 0.85 ( 34) SS BOND : angle 1.24028 / 0.80 ( 68) hydrogen bonds : bond 0.25970 / 17.39 ( 372) hydrogen bonds : angle 8.17558 / 5.71 ( 984) Misc. bond : bond 0.00416 / 0.21 ( 6) link_NAG-THR : bond 0.01170 / 0.56 ( 3) link_NAG-THR : angle 3.28575 / 2.43 ( 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 : 0.564 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: 0.1329 time to fit residues: 62.5730 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 : 0.510 ------------------------------------------------------------------------------- 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... E 96 GLN F 25 GLN A 32 GLN A 153 ASN A 177 ASN A 199 GLN A 258 ASN A 293 HIS 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 244 HIS G 449 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113310 restraints weight = 16248.676| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.49 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1615 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 : 0.521 6.233 18299 Z= 0.277 Chirality : 0.042 0.184 1980 Planarity : 0.004 0.053 2359 Dihedral : 5.193 58.575 1861 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.73 % Allowed : 10.72 % Favored : 86.54 % 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: -0.60 (0.20), residues: 1633 helix: 0.70 (0.32), residues: 228 sheet: -0.19 (0.22), 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 C 411 PHE 0.009 0.001 PHE F 106 TRP 0.009 0.001 TRP E 66 HIS 0.003 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13501) covalent geometry : angle 0.51748 / 0.28 (18225) SS BOND : bond 0.00315 / 0.21 ( 34) SS BOND : angle 0.95420 / 0.59 ( 68) hydrogen bonds : bond 0.04712 / 3.15 ( 372) hydrogen bonds : angle 5.52333 / 3.84 ( 984) Misc. bond : bond 0.00056 / 0.03 ( 6) link_NAG-THR : bond 0.00160 / 0.08 ( 3) link_NAG-THR : angle 2.30006 / 1.70 ( 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 272 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.506 Fit side-chains 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: 0.8744 (mt0) REVERT: E 100 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7783 (mmmm) REVERT: F 24 THR cc_start: 0.8759 (p) cc_final: 0.8559 (p) REVERT: F 26 THR cc_start: 0.8546 (p) cc_final: 0.8186 (p) REVERT: A 56 ARG cc_start: 0.7859 (ptp90) cc_final: 0.7512 (ptp-110) REVERT: A 77 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7660 (pm20) REVERT: A 192 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8165 (ttm110) REVERT: A 234 TYR cc_start: 0.7522 (t80) cc_final: 0.7229 (t80) REVERT: A 250 HIS cc_start: 0.8761 (m-70) cc_final: 0.7983 (t70) REVERT: A 369 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8191 (tttp) REVERT: A 406 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8349 (ttmm) REVERT: A 433 GLU cc_start: 0.8236 (tt0) cc_final: 0.7668 (mt-10) REVERT: B 82 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 91 ASP cc_start: 0.7303 (t0) cc_final: 0.6720 (t70) REVERT: B 100 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7269 (mmmt) REVERT: B 108 ASP cc_start: 0.7968 (m-30) cc_final: 0.7635 (m-30) REVERT: I 23 MET cc_start: 0.8852 (mmm) cc_final: 0.8313 (mmm) REVERT: C 24 MET cc_start: 0.9117 (mtp) cc_final: 0.8799 (mmm) REVERT: C 101 ASP cc_start: 0.7414 (m-30) cc_final: 0.7179 (m-30) REVERT: C 182 ILE cc_start: 0.8816 (mt) cc_final: 0.8509 (tt) REVERT: C 192 ARG cc_start: 0.7596 (ttm170) cc_final: 0.6616 (mmp80) REVERT: C 198 GLU cc_start: 0.6898 (mp0) cc_final: 0.6489 (tt0) REVERT: C 240 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8196 (mmtp) REVERT: C 272 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8132 (tttm) REVERT: G 19 HIS cc_start: 0.6254 (p-80) cc_final: 0.6046 (p90) REVERT: G 56 ARG cc_start: 0.7654 (ptp90) cc_final: 0.7320 (ptm160) REVERT: G 85 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7533 (tp40) REVERT: G 282 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7950 (mm-30) REVERT: G 376 GLU cc_start: 0.7573 (tp30) cc_final: 0.6841 (tt0) REVERT: G 453 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7630 (p) outliers start: 40 outliers final: 22 residues processed: 261 average time/residue: 0.1391 time to fit residues: 50.1336 Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 C residue 83 ASP 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 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 Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN C 412 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108455 restraints weight = 16562.394| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.49 r_work: 0.3091 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13544 Z= 0.171 Angle : 0.544 7.792 18299 Z= 0.288 Chirality : 0.043 0.154 1980 Planarity : 0.004 0.052 2359 Dihedral : 5.146 59.993 1852 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.42 % Allowed : 12.23 % Favored : 84.36 % 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: -0.70 (0.20), residues: 1633 helix: 0.73 (0.33), residues: 228 sheet: -0.09 (0.22), residues: 522 loop : -1.00 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 23 TYR 0.019 0.002 TYR G 137 PHE 0.014 0.002 PHE C 439 TRP 0.011 0.002 TRP E 130 HIS 0.006 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (13501) covalent geometry : angle 0.54121 / 0.29 (18225) SS BOND : bond 0.00361 / 0.24 ( 34) SS BOND : angle 0.90528 / 0.56 ( 68) hydrogen bonds : bond 0.04820 / 3.20 ( 372) hydrogen bonds : angle 4.91579 / 3.36 ( 984) Misc. bond : bond 0.00082 / 0.04 ( 6) link_NAG-THR : bond 0.00257 / 0.13 ( 3) link_NAG-THR : angle 2.20849 / 1.63 ( 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 254 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7747 (mmmm) REVERT: F 43 ARG cc_start: 0.7506 (ptp-170) cc_final: 0.7094 (ptp-170) REVERT: A 77 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7634 (pm20) REVERT: A 149 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9260 (p) REVERT: A 192 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8253 (ttm110) REVERT: A 234 TYR cc_start: 0.7717 (t80) cc_final: 0.7458 (t80) REVERT: A 241 MET cc_start: 0.8844 (ttp) cc_final: 0.8583 (ttp) REVERT: A 250 HIS cc_start: 0.8799 (m-70) cc_final: 0.7942 (t70) REVERT: A 260 ASP cc_start: 0.8725 (t0) cc_final: 0.8502 (t0) REVERT: A 369 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8221 (tttp) REVERT: A 433 GLU cc_start: 0.8273 (tt0) cc_final: 0.7703 (mt-10) REVERT: B 82 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 91 ASP cc_start: 0.7168 (t0) cc_final: 0.6561 (t70) REVERT: B 100 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7132 (mmmt) REVERT: B 132 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7867 (tp-100) REVERT: I 23 MET cc_start: 0.9010 (mmm) cc_final: 0.7981 (mmm) REVERT: I 69 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: I 123 LEU cc_start: 0.8135 (tp) cc_final: 0.7815 (tt) REVERT: C 101 ASP cc_start: 0.7398 (m-30) cc_final: 0.7151 (m-30) REVERT: C 182 ILE cc_start: 0.8687 (mt) cc_final: 0.8227 (tt) REVERT: C 188 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7793 (mt-10) REVERT: C 192 ARG cc_start: 0.7671 (ttm170) cc_final: 0.6917 (mmp80) REVERT: C 197 GLU cc_start: 0.8197 (pt0) cc_final: 0.7959 (mt-10) REVERT: C 240 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8178 (mmtp) REVERT: C 243 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8216 (mm) REVERT: G 56 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7287 (ptm160) REVERT: G 85 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7790 (tp40) REVERT: G 376 GLU cc_start: 0.7728 (tp30) cc_final: 0.6961 (tt0) REVERT: G 453 VAL cc_start: 0.8131 (t) cc_final: 0.7797 (p) REVERT: G 456 MET cc_start: 0.7687 (mmm) cc_final: 0.7436 (mtm) outliers start: 50 outliers final: 31 residues processed: 241 average time/residue: 0.1315 time to fit residues: 44.3452 Evaluate side-chains 225 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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 139 ILE 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 85 GLN 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 405 GLN Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 140 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN C 412 ASN G 85 GLN G 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106480 restraints weight = 16462.113| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.47 r_work: 0.3024 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13544 Z= 0.184 Angle : 0.547 8.178 18299 Z= 0.291 Chirality : 0.043 0.152 1980 Planarity : 0.004 0.051 2359 Dihedral : 5.210 59.003 1848 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.89 % Allowed : 12.77 % Favored : 83.33 % 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: 0.62 (0.33), residues: 228 sheet: -0.21 (0.22), residues: 552 loop : -1.20 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 43 TYR 0.020 0.002 TYR B 113 PHE 0.013 0.002 PHE C 191 TRP 0.012 0.002 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (13501) covalent geometry : angle 0.54433 / 0.29 (18225) SS BOND : bond 0.00372 / 0.24 ( 34) SS BOND : angle 0.92709 / 0.58 ( 68) hydrogen bonds : bond 0.04648 / 3.07 ( 372) hydrogen bonds : angle 4.79238 / 3.27 ( 984) Misc. bond : bond 0.00075 / 0.04 ( 6) link_NAG-THR : bond 0.00198 / 0.10 ( 3) link_NAG-THR : angle 1.99604 / 1.45 ( 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 255 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7727 (mmmm) REVERT: F 43 ARG cc_start: 0.7462 (ptp-170) cc_final: 0.7118 (ptp-170) REVERT: A 77 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7632 (pm20) REVERT: A 192 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8359 (ttm110) REVERT: A 234 TYR cc_start: 0.7927 (t80) cc_final: 0.7633 (t80) REVERT: A 260 ASP cc_start: 0.8704 (t0) cc_final: 0.8457 (t0) REVERT: A 369 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8195 (tttm) REVERT: A 433 GLU cc_start: 0.8259 (tt0) cc_final: 0.7681 (mt-10) REVERT: B 62 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7398 (mmtm) REVERT: B 82 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8518 (pp) REVERT: B 91 ASP cc_start: 0.7211 (t0) cc_final: 0.6531 (t70) REVERT: B 100 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7091 (mmmt) REVERT: B 132 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7741 (tp-100) REVERT: I 98 GLU cc_start: 0.7634 (tp30) cc_final: 0.7064 (tp30) REVERT: C 101 ASP cc_start: 0.7404 (m-30) cc_final: 0.7142 (m-30) REVERT: C 124 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6821 (mmp-170) REVERT: C 169 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8498 (tp) REVERT: C 182 ILE cc_start: 0.8703 (mt) cc_final: 0.8229 (tt) REVERT: C 192 ARG cc_start: 0.7728 (ttm170) cc_final: 0.6937 (mmp80) REVERT: C 243 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8111 (mm) REVERT: G 56 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7389 (ptm160) REVERT: G 376 GLU cc_start: 0.7792 (tp30) cc_final: 0.7194 (tt0) REVERT: G 384 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6153 (tt) REVERT: G 453 VAL cc_start: 0.8181 (t) cc_final: 0.7851 (p) REVERT: G 456 MET cc_start: 0.7932 (mmm) cc_final: 0.7671 (mmm) outliers start: 57 outliers final: 37 residues processed: 238 average time/residue: 0.1242 time to fit residues: 41.1762 Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 THR 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 170 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 34 SER 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 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 169 LEU 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 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 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 384 ILE 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: 1.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 46 HIS A 199 GLN C 412 ASN G 244 HIS 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 = 0.138593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105640 restraints weight = 16533.268| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.48 r_work: 0.3039 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13544 Z= 0.195 Angle : 0.552 7.064 18299 Z= 0.293 Chirality : 0.043 0.146 1980 Planarity : 0.004 0.051 2359 Dihedral : 5.250 57.891 1846 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.96 % Allowed : 13.66 % Favored : 82.38 % 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: -1.03 (0.20), residues: 1633 helix: 0.59 (0.34), residues: 225 sheet: -0.31 (0.22), residues: 546 loop : -1.27 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 43 TYR 0.020 0.002 TYR B 113 PHE 0.013 0.002 PHE G 466 TRP 0.012 0.002 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (13501) covalent geometry : angle 0.54817 / 0.29 (18225) SS BOND : bond 0.00387 / 0.26 ( 34) SS BOND : angle 1.03078 / 0.72 ( 68) hydrogen bonds : bond 0.04742 / 3.14 ( 372) hydrogen bonds : angle 4.75905 / 3.24 ( 984) Misc. bond : bond 0.00084 / 0.05 ( 6) link_NAG-THR : bond 0.00170 / 0.08 ( 3) link_NAG-THR : angle 1.88917 / 1.38 ( 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 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7615 (mp10) cc_final: 0.7383 (mp10) REVERT: F 43 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.7110 (ptp-170) REVERT: F 46 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.7565 (m90) REVERT: A 77 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7640 (pm20) REVERT: A 234 TYR cc_start: 0.7983 (t80) cc_final: 0.7695 (t80) REVERT: A 241 MET cc_start: 0.8816 (ttm) cc_final: 0.8570 (ttp) REVERT: A 353 GLU cc_start: 0.7992 (mp0) cc_final: 0.7224 (mp0) REVERT: A 369 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8208 (tttp) REVERT: A 433 GLU cc_start: 0.8266 (tt0) cc_final: 0.7689 (mt-10) REVERT: B 82 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8575 (pp) REVERT: B 91 ASP cc_start: 0.7196 (t0) cc_final: 0.6538 (t70) REVERT: B 100 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7104 (mmmt) REVERT: B 132 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7744 (tp-100) REVERT: I 123 LEU cc_start: 0.8211 (tp) cc_final: 0.7843 (tt) REVERT: C 101 ASP cc_start: 0.7282 (m-30) cc_final: 0.7037 (m-30) REVERT: C 124 ARG cc_start: 0.7078 (mmp-170) cc_final: 0.6807 (mmp-170) REVERT: C 162 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8114 (ptm160) REVERT: C 192 ARG cc_start: 0.7767 (ttm170) cc_final: 0.6967 (mmp80) REVERT: C 243 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8067 (mm) REVERT: C 442 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8091 (mtm110) REVERT: G 56 ARG cc_start: 0.7774 (ptp90) cc_final: 0.7409 (ptm160) REVERT: G 376 GLU cc_start: 0.7807 (tp30) cc_final: 0.7256 (tt0) REVERT: G 384 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6514 (tt) REVERT: G 456 MET cc_start: 0.7915 (mmm) cc_final: 0.7595 (mmm) REVERT: G 477 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5550 (tppt) outliers start: 58 outliers final: 41 residues processed: 232 average time/residue: 0.1302 time to fit residues: 42.6583 Evaluate side-chains 234 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 120 TYR Chi-restraints excluded: chain F residue 46 HIS 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 182 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL 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 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 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 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 250 HIS Chi-restraints excluded: chain G residue 265 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 46 HIS A 199 GLN C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107784 restraints weight = 16422.485| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.48 r_work: 0.3070 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2842 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= 0.101 Angle : 0.478 6.668 18299 Z= 0.255 Chirality : 0.040 0.145 1980 Planarity : 0.003 0.049 2359 Dihedral : 4.973 59.786 1846 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.35 % Allowed : 14.96 % Favored : 81.69 % 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: 0.80 (0.34), residues: 228 sheet: -0.18 (0.22), residues: 552 loop : -1.21 (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 0.009 0.001 PHE C 267 TRP 0.010 0.001 TRP G 27 HIS 0.011 0.001 HIS F 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (13501) covalent geometry : angle 0.47613 / 0.25 (18225) SS BOND : bond 0.00246 / 0.17 ( 34) SS BOND : angle 0.67411 / 0.46 ( 68) hydrogen bonds : bond 0.03697 / 2.45 ( 372) hydrogen bonds : angle 4.55518 / 3.12 ( 984) Misc. bond : bond 0.00042 / 0.02 ( 6) link_NAG-THR : bond 0.00119 / 0.06 ( 3) link_NAG-THR : angle 1.65914 / 1.23 ( 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 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7152 (mttm) REVERT: E 107 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7931 (t70) REVERT: F 43 ARG cc_start: 0.7411 (ptp-170) cc_final: 0.7006 (ptp-170) REVERT: A 77 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7634 (pm20) REVERT: A 199 GLN cc_start: 0.7876 (mt0) cc_final: 0.7528 (mt0) REVERT: A 234 TYR cc_start: 0.7841 (t80) cc_final: 0.7552 (t80) REVERT: A 250 HIS cc_start: 0.8726 (m-70) cc_final: 0.8498 (m90) REVERT: A 353 GLU cc_start: 0.7985 (mp0) cc_final: 0.7275 (mp0) REVERT: A 369 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8236 (tttm) REVERT: A 433 GLU cc_start: 0.8188 (tt0) cc_final: 0.7593 (mt-10) REVERT: B 82 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8556 (pp) REVERT: B 91 ASP cc_start: 0.7071 (t0) cc_final: 0.6458 (t0) REVERT: B 100 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7074 (mmmt) REVERT: B 132 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7655 (tp-100) REVERT: I 69 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: I 122 LYS cc_start: 0.8536 (tppt) cc_final: 0.8270 (ttmm) REVERT: I 123 LEU cc_start: 0.8164 (tp) cc_final: 0.7798 (tt) REVERT: C 101 ASP cc_start: 0.7365 (m-30) cc_final: 0.7057 (m-30) REVERT: C 124 ARG cc_start: 0.7101 (mmp-170) cc_final: 0.6809 (mmp-170) REVERT: C 162 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8055 (ptm160) REVERT: C 182 ILE cc_start: 0.8861 (mt) cc_final: 0.8440 (tt) REVERT: C 192 ARG cc_start: 0.7689 (ttm170) cc_final: 0.6837 (mmp80) REVERT: C 243 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8383 (tp) REVERT: C 442 ARG cc_start: 0.8364 (mtm110) cc_final: 0.8072 (mtm110) REVERT: G 56 ARG cc_start: 0.7746 (ptp90) cc_final: 0.7396 (ptm160) REVERT: G 376 GLU cc_start: 0.7736 (tp30) cc_final: 0.7469 (tt0) REVERT: G 453 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7856 (p) REVERT: G 456 MET cc_start: 0.7883 (mmm) cc_final: 0.7595 (mmm) outliers start: 49 outliers final: 39 residues processed: 235 average time/residue: 0.1249 time to fit residues: 41.6559 Evaluate side-chains 240 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 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 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 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 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 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 106 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 132 GLN C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102564 restraints weight = 16534.408| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.52 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13544 Z= 0.157 Angle : 0.520 7.557 18299 Z= 0.275 Chirality : 0.042 0.142 1980 Planarity : 0.004 0.050 2359 Dihedral : 5.051 59.084 1846 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.89 % Allowed : 15.37 % Favored : 80.74 % 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: -0.96 (0.20), residues: 1633 helix: 0.71 (0.34), residues: 225 sheet: -0.25 (0.22), residues: 546 loop : -1.25 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 43 TYR 0.017 0.002 TYR B 113 PHE 0.010 0.001 PHE C 191 TRP 0.012 0.001 TRP G 27 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13501) covalent geometry : angle 0.51755 / 0.27 (18225) SS BOND : bond 0.00326 / 0.22 ( 34) SS BOND : angle 0.84423 / 0.56 ( 68) hydrogen bonds : bond 0.04301 / 2.85 ( 372) hydrogen bonds : angle 4.59242 / 3.13 ( 984) Misc. bond : bond 0.00073 / 0.04 ( 6) link_NAG-THR : bond 0.00147 / 0.07 ( 3) link_NAG-THR : angle 1.76311 / 1.30 ( 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 254 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8181 (p0) REVERT: F 43 ARG cc_start: 0.7332 (ptp-170) cc_final: 0.7037 (ptp-170) REVERT: A 77 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7664 (pm20) REVERT: A 199 GLN cc_start: 0.7985 (mt0) cc_final: 0.7607 (mt0) REVERT: A 234 TYR cc_start: 0.7955 (t80) cc_final: 0.7647 (t80) REVERT: A 250 HIS cc_start: 0.8632 (m-70) cc_final: 0.8407 (m90) REVERT: A 353 GLU cc_start: 0.7955 (mp0) cc_final: 0.7386 (mp0) REVERT: A 433 GLU cc_start: 0.8170 (tt0) cc_final: 0.7571 (mt-10) REVERT: B 62 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7377 (mmtm) REVERT: B 82 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 91 ASP cc_start: 0.7093 (t0) cc_final: 0.6455 (t0) REVERT: B 100 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7037 (mmmt) REVERT: B 132 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7738 (tp-100) REVERT: I 98 GLU cc_start: 0.7622 (tp30) cc_final: 0.7287 (tp30) REVERT: I 123 LEU cc_start: 0.8199 (tp) cc_final: 0.7820 (tt) REVERT: C 101 ASP cc_start: 0.7325 (m-30) cc_final: 0.7065 (m-30) REVERT: C 124 ARG cc_start: 0.7120 (mmp-170) cc_final: 0.6911 (mmp80) REVERT: C 162 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8055 (ptm160) REVERT: C 182 ILE cc_start: 0.8696 (mt) cc_final: 0.8198 (tt) REVERT: C 192 ARG cc_start: 0.7732 (ttm170) cc_final: 0.6900 (mmp80) REVERT: C 243 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8038 (mm) REVERT: G 56 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7391 (ptm160) REVERT: G 376 GLU cc_start: 0.7863 (tp30) cc_final: 0.7570 (tt0) REVERT: G 384 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6212 (tt) REVERT: G 406 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7702 (tmtt) REVERT: G 456 MET cc_start: 0.7897 (mmm) cc_final: 0.7567 (mmm) REVERT: G 477 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.5727 (tppt) outliers start: 57 outliers final: 46 residues processed: 240 average time/residue: 0.1226 time to fit residues: 41.5254 Evaluate side-chains 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 182 ILE Chi-restraints excluded: chain A residue 184 GLU 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 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 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 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 250 HIS Chi-restraints excluded: chain G residue 265 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 453 VAL 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: 2.9990 chunk 147 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102538 restraints weight = 16528.936| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.52 r_work: 0.3030 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3034 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= 0.157 Angle : 0.518 7.327 18299 Z= 0.275 Chirality : 0.042 0.142 1980 Planarity : 0.004 0.049 2359 Dihedral : 5.031 58.450 1846 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.10 % Allowed : 15.78 % Favored : 80.12 % 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: 0.68 (0.34), residues: 225 sheet: -0.28 (0.22), residues: 546 loop : -1.28 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 43 TYR 0.017 0.002 TYR B 113 PHE 0.010 0.001 PHE A 155 TRP 0.011 0.001 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13501) covalent geometry : angle 0.51582 / 0.27 (18225) SS BOND : bond 0.00312 / 0.21 ( 34) SS BOND : angle 0.80107 / 0.53 ( 68) hydrogen bonds : bond 0.04204 / 2.78 ( 372) hydrogen bonds : angle 4.57987 / 3.12 ( 984) Misc. bond : bond 0.00064 / 0.03 ( 6) link_NAG-THR : bond 0.00120 / 0.06 ( 3) link_NAG-THR : angle 1.67726 / 1.24 ( 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 251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LEU cc_start: 0.9280 (mm) cc_final: 0.8951 (mm) REVERT: E 100 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7169 (mttm) REVERT: E 107 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8200 (p0) REVERT: F 43 ARG cc_start: 0.7331 (ptp-170) cc_final: 0.7055 (ptp-170) REVERT: A 77 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7610 (pm20) REVERT: A 199 GLN cc_start: 0.8017 (mt0) cc_final: 0.7654 (mt0) REVERT: A 234 TYR cc_start: 0.8006 (t80) cc_final: 0.7684 (t80) REVERT: A 250 HIS cc_start: 0.8755 (m-70) cc_final: 0.8551 (m90) REVERT: A 353 GLU cc_start: 0.7974 (mp0) cc_final: 0.7411 (mp0) REVERT: A 433 GLU cc_start: 0.8207 (tt0) cc_final: 0.7610 (mt-10) REVERT: B 62 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7437 (mmtm) REVERT: B 82 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8589 (pp) REVERT: B 91 ASP cc_start: 0.7080 (t0) cc_final: 0.6450 (t0) REVERT: B 100 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7050 (mmmt) REVERT: B 105 GLN cc_start: 0.8159 (mt0) cc_final: 0.7728 (mp-120) REVERT: B 132 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7795 (tp-100) REVERT: I 58 LYS cc_start: 0.7970 (ptpt) cc_final: 0.7758 (ptpp) REVERT: I 98 GLU cc_start: 0.7351 (tp30) cc_final: 0.7032 (tp30) REVERT: I 123 LEU cc_start: 0.8263 (tp) cc_final: 0.7873 (tt) REVERT: C 101 ASP cc_start: 0.7354 (m-30) cc_final: 0.7092 (m-30) REVERT: C 124 ARG cc_start: 0.7135 (mmp-170) cc_final: 0.6922 (mmp80) REVERT: C 192 ARG cc_start: 0.7752 (ttm170) cc_final: 0.6942 (mmp80) REVERT: C 243 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8086 (mm) REVERT: G 56 ARG cc_start: 0.7794 (ptp90) cc_final: 0.7377 (ptm160) REVERT: G 376 GLU cc_start: 0.7893 (tp30) cc_final: 0.7616 (tt0) REVERT: G 406 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7704 (tmtt) REVERT: G 456 MET cc_start: 0.7927 (mmm) cc_final: 0.7643 (mmm) REVERT: G 477 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5722 (tppt) outliers start: 60 outliers final: 50 residues processed: 236 average time/residue: 0.1179 time to fit residues: 39.3647 Evaluate side-chains 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 107 ASP Chi-restraints excluded: chain E residue 109 THR 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 182 ILE 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 B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER 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 86 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 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 250 HIS 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 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: 2.9990 chunk 151 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105778 restraints weight = 16500.717| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.48 r_work: 0.3054 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13544 Z= 0.166 Angle : 0.535 7.264 18299 Z= 0.284 Chirality : 0.042 0.142 1980 Planarity : 0.004 0.050 2359 Dihedral : 5.089 57.623 1846 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.10 % Allowed : 16.26 % Favored : 79.64 % 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: -1.05 (0.20), residues: 1633 helix: 0.64 (0.34), residues: 225 sheet: -0.31 (0.22), residues: 546 loop : -1.32 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 43 TYR 0.017 0.002 TYR B 113 PHE 0.010 0.001 PHE G 389 TRP 0.011 0.001 TRP G 27 HIS 0.004 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13501) covalent geometry : angle 0.53227 / 0.28 (18225) SS BOND : bond 0.00326 / 0.22 ( 34) SS BOND : angle 0.83596 / 0.55 ( 68) hydrogen bonds : bond 0.04320 / 2.86 ( 372) hydrogen bonds : angle 4.58587 / 3.12 ( 984) Misc. bond : bond 0.00066 / 0.03 ( 6) link_NAG-THR : bond 0.00126 / 0.06 ( 3) link_NAG-THR : angle 1.68928 / 1.26 ( 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 251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LEU cc_start: 0.9293 (mm) cc_final: 0.8950 (mm) REVERT: E 100 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7169 (mttm) REVERT: E 107 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7957 (t70) REVERT: F 43 ARG cc_start: 0.7465 (ptp-170) cc_final: 0.7236 (ptp-170) REVERT: A 77 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7549 (pm20) REVERT: A 199 GLN cc_start: 0.8026 (mt0) cc_final: 0.7676 (mt0) REVERT: A 234 TYR cc_start: 0.7961 (t80) cc_final: 0.7699 (t80) REVERT: A 250 HIS cc_start: 0.8613 (m-70) cc_final: 0.8400 (m90) REVERT: A 353 GLU cc_start: 0.7959 (mp0) cc_final: 0.7392 (mp0) REVERT: A 433 GLU cc_start: 0.8221 (tt0) cc_final: 0.7631 (mt-10) REVERT: B 82 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 91 ASP cc_start: 0.7094 (t0) cc_final: 0.6474 (t0) REVERT: B 100 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7025 (mmmt) REVERT: B 105 GLN cc_start: 0.8194 (mt0) cc_final: 0.7758 (mp-120) REVERT: B 132 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7852 (tp-100) REVERT: I 98 GLU cc_start: 0.7415 (tp30) cc_final: 0.7187 (tp30) REVERT: I 123 LEU cc_start: 0.8289 (tp) cc_final: 0.7894 (tt) REVERT: C 101 ASP cc_start: 0.7339 (m-30) cc_final: 0.7072 (m-30) REVERT: C 124 ARG cc_start: 0.7140 (mmp-170) cc_final: 0.6913 (mmp80) REVERT: C 162 ARG cc_start: 0.8323 (ptm160) cc_final: 0.8122 (ptm160) REVERT: C 192 ARG cc_start: 0.7737 (ttm170) cc_final: 0.6979 (mmp80) REVERT: C 197 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: C 243 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8115 (mm) REVERT: G 56 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7467 (ptm160) REVERT: G 376 GLU cc_start: 0.7900 (tp30) cc_final: 0.7628 (tt0) REVERT: G 384 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6327 (tt) REVERT: G 406 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7743 (tmtt) REVERT: G 456 MET cc_start: 0.7951 (mmm) cc_final: 0.7640 (mmm) REVERT: G 477 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5733 (tppt) outliers start: 60 outliers final: 48 residues processed: 235 average time/residue: 0.1172 time to fit residues: 38.8340 Evaluate side-chains 244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU 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 182 ILE 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 B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER 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 38 VAL 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 197 GLU 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 250 HIS Chi-restraints excluded: chain G residue 265 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 97 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106508 restraints weight = 16426.390| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.49 r_work: 0.3076 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13544 Z= 0.107 Angle : 0.493 7.287 18299 Z= 0.262 Chirality : 0.040 0.142 1980 Planarity : 0.003 0.048 2359 Dihedral : 4.909 58.911 1846 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.21 % Allowed : 17.42 % Favored : 79.37 % 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: -0.95 (0.20), residues: 1633 helix: 0.78 (0.34), residues: 228 sheet: -0.27 (0.21), residues: 573 loop : -1.28 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 43 TYR 0.014 0.001 TYR B 113 PHE 0.009 0.001 PHE C 267 TRP 0.010 0.001 TRP G 27 HIS 0.002 0.000 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13501) covalent geometry : angle 0.49169 / 0.26 (18225) SS BOND : bond 0.00249 / 0.17 ( 34) SS BOND : angle 0.63204 / 0.42 ( 68) hydrogen bonds : bond 0.03623 / 2.40 ( 372) hydrogen bonds : angle 4.47147 / 3.06 ( 984) Misc. bond : bond 0.00039 / 0.02 ( 6) link_NAG-THR : bond 0.00112 / 0.05 ( 3) link_NAG-THR : angle 1.55573 / 1.17 ( 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 243 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LEU cc_start: 0.9274 (mm) cc_final: 0.8936 (mm) REVERT: E 107 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.7951 (t70) REVERT: F 43 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7174 (ptp-170) REVERT: A 77 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7564 (pm20) REVERT: A 199 GLN cc_start: 0.7958 (mt0) cc_final: 0.7614 (mt0) REVERT: A 234 TYR cc_start: 0.7925 (t80) cc_final: 0.7601 (t80) REVERT: A 353 GLU cc_start: 0.7999 (mp0) cc_final: 0.7510 (mp0) REVERT: A 433 GLU cc_start: 0.8172 (tt0) cc_final: 0.7578 (mt-10) REVERT: B 62 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7441 (mmtm) REVERT: B 82 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8631 (pp) REVERT: B 91 ASP cc_start: 0.7003 (t0) cc_final: 0.6384 (t0) REVERT: B 100 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7071 (mmmt) REVERT: B 105 GLN cc_start: 0.8172 (mt0) cc_final: 0.7737 (mp-120) REVERT: B 132 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7820 (tp-100) REVERT: I 98 GLU cc_start: 0.7390 (tp30) cc_final: 0.7176 (tp30) REVERT: C 101 ASP cc_start: 0.7329 (m-30) cc_final: 0.7064 (m-30) REVERT: C 124 ARG cc_start: 0.6997 (mmp-170) cc_final: 0.6790 (mmp80) REVERT: C 162 ARG cc_start: 0.8351 (ptm160) cc_final: 0.8080 (ptm-80) REVERT: C 182 ILE cc_start: 0.8862 (mt) cc_final: 0.8420 (tt) REVERT: C 192 ARG cc_start: 0.7699 (ttm170) cc_final: 0.6865 (mmp80) REVERT: C 197 GLU cc_start: 0.8698 (pt0) cc_final: 0.8297 (mt-10) REVERT: G 56 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7532 (ptm160) REVERT: G 198 GLU cc_start: 0.6895 (mp0) cc_final: 0.6431 (tt0) REVERT: G 376 GLU cc_start: 0.7885 (tp30) cc_final: 0.7614 (tt0) REVERT: G 453 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8051 (p) REVERT: G 456 MET cc_start: 0.7895 (mmm) cc_final: 0.7586 (mmm) REVERT: G 477 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5808 (tppt) outliers start: 47 outliers final: 41 residues processed: 231 average time/residue: 0.1151 time to fit residues: 37.5816 Evaluate side-chains 239 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 359 VAL 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 169 LEU Chi-restraints excluded: chain C residue 185 THR 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 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE 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: 5.9990 chunk 54 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103047 restraints weight = 16560.411| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.51 r_work: 0.3006 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13544 Z= 0.199 Angle : 0.560 7.137 18299 Z= 0.298 Chirality : 0.043 0.143 1980 Planarity : 0.004 0.054 2359 Dihedral : 5.001 56.631 1844 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.55 % Allowed : 16.87 % Favored : 79.58 % 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: -1.12 (0.20), residues: 1633 helix: 0.58 (0.35), residues: 225 sheet: -0.41 (0.22), residues: 560 loop : -1.33 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 43 TYR 0.019 0.002 TYR B 113 PHE 0.012 0.002 PHE C 254 TRP 0.012 0.002 TRP G 27 HIS 0.005 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (13501) covalent geometry : angle 0.55792 / 0.30 (18225) SS BOND : bond 0.00365 / 0.24 ( 34) SS BOND : angle 0.92344 / 0.61 ( 68) hydrogen bonds : bond 0.04630 / 3.07 ( 372) hydrogen bonds : angle 4.62284 / 3.14 ( 984) Misc. bond : bond 0.00077 / 0.04 ( 6) link_NAG-THR : bond 0.00124 / 0.06 ( 3) link_NAG-THR : angle 1.64502 / 1.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3236.01 seconds wall clock time: 56 minutes 2.64 seconds (3362.64 seconds total)