Starting phenix.real_space_refine on Thu May 15 15:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_27385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_27385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_27385.map" model { file = "/net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_27385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de6_27385/05_2025/8de6_27385.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13243 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "B" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "C" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "G" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.23, per 1000 atoms: 0.62 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.71 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: 3.55 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3630 1.33 - 1.46: 3616 1.46 - 1.59: 6121 1.59 - 1.72: 0 1.72 - 1.85: 134 Bond restraints: 13501 Sorted by residual: bond pdb=" C2 BMA C 602 " pdb=" O2 BMA C 602 " ideal model delta sigma weight residual 1.402 1.461 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 BMA G 603 " pdb=" C2 BMA G 603 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C ALA G 399 " pdb=" N PRO G 400 " ideal model delta sigma weight residual 1.328 1.298 0.030 1.25e-02 6.40e+03 5.61e+00 bond pdb=" C2 BMA C 602 " pdb=" C3 BMA C 602 " ideal model delta sigma weight residual 1.544 1.501 0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" CA ASP B 91 " pdb=" CB ASP B 91 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.66e+00 ... (remaining 13496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 16764 1.58 - 3.15: 1312 3.15 - 4.73: 115 4.73 - 6.31: 26 6.31 - 7.89: 8 Bond angle restraints: 18225 Sorted by residual: angle pdb=" C ARG C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta sigma weight residual 121.54 127.22 -5.68 1.91e+00 2.74e-01 8.85e+00 angle pdb=" N THR I 26 " pdb=" CA THR I 26 " pdb=" C THR I 26 " ideal model delta sigma weight residual 110.97 114.14 -3.17 1.09e+00 8.42e-01 8.48e+00 angle pdb=" N LEU G 407 " pdb=" CA LEU G 407 " pdb=" C LEU G 407 " ideal model delta sigma weight residual 110.28 114.47 -4.19 1.48e+00 4.57e-01 8.01e+00 angle pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sigma weight residual 113.24 105.35 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C1 BMA C 602 " pdb=" O5 BMA C 602 " pdb=" C5 BMA C 602 " ideal model delta sigma weight residual 118.82 111.11 7.71 3.00e+00 1.11e-01 6.60e+00 ... (remaining 18220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 7966 22.75 - 45.51: 271 45.51 - 68.26: 31 68.26 - 91.01: 37 91.01 - 113.76: 24 Dihedral angle restraints: 8329 sinusoidal: 3547 harmonic: 4782 Sorted by residual: dihedral pdb=" O4 BMA A 602 " pdb=" C4 BMA A 602 " pdb=" C5 BMA A 602 " pdb=" O5 BMA A 602 " ideal model delta sinusoidal sigma weight residual 288.71 174.95 113.76 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O4 BMA A 603 " pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sinusoidal sigma weight residual 288.71 175.65 113.06 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" O4 BMA G 603 " pdb=" C4 BMA G 603 " pdb=" C5 BMA G 603 " pdb=" O5 BMA G 603 " ideal model delta sinusoidal sigma weight residual 288.71 177.12 111.59 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 8326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1498 0.067 - 0.135: 420 0.135 - 0.202: 55 0.202 - 0.270: 1 0.270 - 0.337: 6 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C2 BMA C 603 " pdb=" C1 BMA C 603 " pdb=" C3 BMA C 603 " pdb=" O2 BMA C 603 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 603 " pdb=" C4 BMA C 603 " pdb=" C6 BMA C 603 " pdb=" O5 BMA C 603 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1977 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 58 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 59 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 59 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 59 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 260 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ASP G 260 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP G 260 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL G 261 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 54 " -0.001 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP F 54 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP F 54 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 54 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP F 54 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 54 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 54 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 54 " 0.019 2.00e-02 2.50e+03 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 556 2.72 - 3.26: 12048 3.26 - 3.81: 18695 3.81 - 4.35: 23607 4.35 - 4.90: 42554 Nonbonded interactions: 97460 Sorted by model distance: nonbonded pdb=" OD2 ASP G 270 " pdb=" OH TYR G 290 " model vdw 2.169 3.040 nonbonded pdb=" OD2 ASP A 270 " pdb=" OH TYR A 290 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP G 109 " pdb="CA CA G 604 " model vdw 2.203 2.510 nonbonded pdb=" OG1 THR A 452 " pdb=" N2 NAG A 601 " model vdw 2.256 2.496 nonbonded pdb=" OG1 THR G 452 " pdb=" N2 NAG G 601 " model vdw 2.268 2.496 ... (remaining 97455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 1.350 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 13544 Z= 0.535 Angle : 0.931 7.885 18299 Z= 0.522 Chirality : 0.061 0.337 1980 Planarity : 0.007 0.058 2359 Dihedral : 14.683 113.764 5167 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 6.76 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.008 TRP C 30 HIS 0.018 0.005 HIS G 244 PHE 0.024 0.006 PHE A 389 TYR 0.026 0.006 TYR G 290 ARG 0.021 0.004 ARG G 95 Details of bonding type rmsd hydrogen bonds : bond 0.25970 ( 372) hydrogen bonds : angle 8.17558 ( 984) SS BOND : bond 0.01272 ( 34) SS BOND : angle 1.24028 ( 68) link_NAG-THR : bond 0.01170 ( 3) link_NAG-THR : angle 3.28575 ( 6) covalent geometry : bond 0.01021 (13501) covalent geometry : angle 0.92818 (18225) Misc. bond : bond 0.00416 ( 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 : 1.560 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: 0.8317 (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: 0.6843 (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: 0.7526 (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: 0.7514 (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: 0.2954 time to fit residues: 137.0484 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 : 1.563 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN F 25 GLN A 32 GLN A 153 ASN A 177 ASN A 199 GLN A 258 ASN B 20 GLN C 39 GLN C 177 ASN C 293 HIS C 354 ASN C 448 GLN C 449 ASN G 85 GLN G 157 ASN G 177 ASN G 449 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113442 restraints weight = 16210.707| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.48 r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13544 Z= 0.114 Angle : 0.527 6.044 18299 Z= 0.274 Chirality : 0.042 0.157 1980 Planarity : 0.004 0.051 2359 Dihedral : 11.660 72.863 2038 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.60 % Allowed : 10.38 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1633 helix: 0.74 (0.33), residues: 228 sheet: -0.19 (0.22), residues: 572 loop : -0.79 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 66 HIS 0.002 0.001 HIS I 46 PHE 0.009 0.001 PHE C 439 TYR 0.012 0.001 TYR G 294 ARG 0.004 0.000 ARG A 368 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 372) hydrogen bonds : angle 5.43785 ( 984) SS BOND : bond 0.00380 ( 34) SS BOND : angle 0.86296 ( 68) link_NAG-THR : bond 0.00154 ( 3) link_NAG-THR : angle 2.21498 ( 6) covalent geometry : bond 0.00251 (13501) covalent geometry : angle 0.52354 (18225) Misc. bond : bond 0.00096 ( 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 269 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 GLN cc_start: 0.8958 (mt0) cc_final: 0.8748 (mt0) REVERT: E 100 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7783 (mmmm) REVERT: F 26 THR cc_start: 0.8535 (p) cc_final: 0.8102 (p) REVERT: A 56 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7510 (ptp-110) REVERT: A 77 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7625 (pm20) REVERT: A 192 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8207 (ttm110) REVERT: A 234 TYR cc_start: 0.7497 (t80) cc_final: 0.7205 (t80) REVERT: A 250 HIS cc_start: 0.8757 (m-70) cc_final: 0.7980 (t70) REVERT: A 369 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8190 (tttp) REVERT: A 406 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8320 (ttmm) REVERT: A 433 GLU cc_start: 0.8232 (tt0) cc_final: 0.7667 (mt-10) REVERT: A 456 MET cc_start: 0.8371 (mmm) cc_final: 0.8042 (mmm) REVERT: B 82 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8547 (pp) REVERT: B 91 ASP cc_start: 0.7175 (t0) cc_final: 0.6602 (t70) REVERT: B 100 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7272 (mmmt) REVERT: B 108 ASP cc_start: 0.7964 (m-30) cc_final: 0.7655 (m-30) REVERT: B 132 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7779 (tp-100) REVERT: I 23 MET cc_start: 0.8848 (mmm) cc_final: 0.8301 (mmm) REVERT: C 24 MET cc_start: 0.9093 (mtp) cc_final: 0.8885 (mmm) REVERT: C 101 ASP cc_start: 0.7447 (m-30) cc_final: 0.7215 (m-30) REVERT: C 182 ILE cc_start: 0.8808 (mt) cc_final: 0.8505 (tt) REVERT: C 192 ARG cc_start: 0.7674 (ttm170) cc_final: 0.6517 (mmp80) REVERT: C 240 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8187 (mmtp) REVERT: C 243 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8247 (mm) REVERT: C 272 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8144 (tttm) REVERT: G 19 HIS cc_start: 0.6230 (p-80) cc_final: 0.6018 (p90) REVERT: G 56 ARG cc_start: 0.7665 (ptp90) cc_final: 0.7339 (ptm160) REVERT: G 85 GLN cc_start: 0.7818 (tp40) cc_final: 0.7531 (tp40) REVERT: G 282 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7923 (mm-30) REVERT: G 376 GLU cc_start: 0.7551 (tp30) cc_final: 0.6819 (tt0) REVERT: G 453 VAL cc_start: 0.8020 (t) cc_final: 0.7629 (p) outliers start: 38 outliers final: 20 residues processed: 259 average time/residue: 0.3056 time to fit residues: 107.8802 Evaluate side-chains 232 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 12 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 293 HIS C 412 ASN G 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106956 restraints weight = 16433.909| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.48 r_work: 0.3054 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13544 Z= 0.207 Angle : 0.595 7.640 18299 Z= 0.312 Chirality : 0.045 0.160 1980 Planarity : 0.004 0.053 2359 Dihedral : 8.539 59.716 2026 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.62 % Allowed : 12.09 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1633 helix: 0.59 (0.33), residues: 225 sheet: -0.16 (0.22), residues: 540 loop : -1.09 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 27 HIS 0.004 0.001 HIS C 293 PHE 0.015 0.002 PHE C 191 TYR 0.022 0.002 TYR G 137 ARG 0.006 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 372) hydrogen bonds : angle 4.96360 ( 984) SS BOND : bond 0.00430 ( 34) SS BOND : angle 1.02497 ( 68) link_NAG-THR : bond 0.00294 ( 3) link_NAG-THR : angle 2.42722 ( 6) covalent geometry : bond 0.00499 (13501) covalent geometry : angle 0.59175 (18225) Misc. bond : bond 0.00096 ( 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 256 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7767 (mmmm) REVERT: A 77 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7627 (pm20) REVERT: A 149 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9229 (p) REVERT: A 192 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8282 (ttm110) REVERT: A 234 TYR cc_start: 0.7850 (t80) cc_final: 0.7597 (t80) REVERT: A 241 MET cc_start: 0.8864 (ttp) cc_final: 0.8550 (ttp) REVERT: A 250 HIS cc_start: 0.8777 (m-70) cc_final: 0.7950 (t70) REVERT: A 260 ASP cc_start: 0.8742 (t0) cc_final: 0.8507 (t0) REVERT: A 369 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8204 (tttm) REVERT: A 406 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8182 (ttmm) REVERT: A 433 GLU cc_start: 0.8294 (tt0) cc_final: 0.7724 (mt-10) REVERT: A 456 MET cc_start: 0.8559 (mmm) cc_final: 0.8305 (mmm) REVERT: B 82 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8533 (pp) REVERT: B 91 ASP cc_start: 0.7202 (t0) cc_final: 0.6590 (t70) REVERT: B 100 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7107 (mmmt) REVERT: B 132 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7765 (tp-100) REVERT: I 23 MET cc_start: 0.9038 (mmm) cc_final: 0.7911 (mmm) REVERT: I 69 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: C 101 ASP cc_start: 0.7431 (m-30) cc_final: 0.7183 (m-30) REVERT: C 192 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6951 (mmt-90) REVERT: C 240 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8199 (mmtp) REVERT: C 243 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8293 (mm) REVERT: G 56 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7319 (ptm160) REVERT: G 376 GLU cc_start: 0.7687 (tp30) cc_final: 0.7109 (tt0) REVERT: G 406 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7654 (tmtt) REVERT: G 453 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (p) REVERT: G 456 MET cc_start: 0.7609 (mmm) cc_final: 0.7403 (mmm) REVERT: G 477 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5659 (tppt) outliers start: 53 outliers final: 29 residues processed: 242 average time/residue: 0.3048 time to fit residues: 100.8929 Evaluate side-chains 225 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 A residue 237 LYS 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 185 THR Chi-restraints excluded: chain C residue 188 GLU 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 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 453 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 14 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN G 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108877 restraints weight = 16188.270| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.46 r_work: 0.3084 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13544 Z= 0.117 Angle : 0.491 6.455 18299 Z= 0.259 Chirality : 0.041 0.148 1980 Planarity : 0.003 0.050 2359 Dihedral : 6.974 59.933 2023 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.48 % Allowed : 12.91 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1633 helix: 0.79 (0.34), residues: 228 sheet: -0.10 (0.22), residues: 552 loop : -1.06 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 27 HIS 0.003 0.001 HIS A 293 PHE 0.011 0.001 PHE C 267 TYR 0.015 0.001 TYR B 113 ARG 0.005 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 372) hydrogen bonds : angle 4.68049 ( 984) SS BOND : bond 0.00256 ( 34) SS BOND : angle 0.66370 ( 68) link_NAG-THR : bond 0.00143 ( 3) link_NAG-THR : angle 1.88133 ( 6) covalent geometry : bond 0.00273 (13501) covalent geometry : angle 0.48913 (18225) Misc. bond : bond 0.00032 ( 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 245 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7695 (pm20) REVERT: A 192 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8270 (ttm110) REVERT: A 234 TYR cc_start: 0.7734 (t80) cc_final: 0.7456 (t80) REVERT: A 250 HIS cc_start: 0.8737 (m-70) cc_final: 0.8494 (m90) REVERT: A 260 ASP cc_start: 0.8759 (t0) cc_final: 0.8479 (t0) REVERT: A 369 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8207 (tttm) REVERT: A 433 GLU cc_start: 0.8226 (tt0) cc_final: 0.7638 (mt-10) REVERT: B 82 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8533 (pp) REVERT: B 91 ASP cc_start: 0.7138 (t0) cc_final: 0.6462 (t70) REVERT: B 100 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7128 (mmmt) REVERT: B 132 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7638 (tp-100) REVERT: I 23 MET cc_start: 0.8949 (mmm) cc_final: 0.8469 (mmm) REVERT: I 69 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: I 98 GLU cc_start: 0.7738 (tp30) cc_final: 0.7210 (tp30) REVERT: I 122 LYS cc_start: 0.8595 (tppt) cc_final: 0.8363 (ttmm) REVERT: C 101 ASP cc_start: 0.7407 (m-30) cc_final: 0.7095 (m-30) REVERT: C 124 ARG cc_start: 0.6974 (mmp-170) cc_final: 0.6722 (mmp-170) REVERT: C 182 ILE cc_start: 0.8674 (mt) cc_final: 0.8232 (tt) REVERT: C 192 ARG cc_start: 0.7582 (ttm170) cc_final: 0.6650 (mmp80) REVERT: C 240 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8241 (mmtp) REVERT: G 56 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7399 (ptm160) REVERT: G 376 GLU cc_start: 0.7668 (tp30) cc_final: 0.7110 (tt0) REVERT: G 384 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6350 (tt) REVERT: G 453 VAL cc_start: 0.8163 (t) cc_final: 0.7828 (p) REVERT: G 456 MET cc_start: 0.7914 (mmm) cc_final: 0.7674 (mmm) outliers start: 51 outliers final: 35 residues processed: 232 average time/residue: 0.2844 time to fit residues: 92.0113 Evaluate side-chains 224 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TYR Chi-restraints excluded: chain 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 188 GLU 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 40 MET 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 251 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 405 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102506 restraints weight = 16650.927| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.47 r_work: 0.3007 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 13544 Z= 0.318 Angle : 0.671 7.179 18299 Z= 0.355 Chirality : 0.048 0.157 1980 Planarity : 0.005 0.054 2359 Dihedral : 7.426 59.489 2021 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.17 % Allowed : 13.87 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1633 helix: 0.20 (0.34), residues: 225 sheet: -0.41 (0.22), residues: 534 loop : -1.43 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 27 HIS 0.006 0.002 HIS A 293 PHE 0.021 0.003 PHE C 191 TYR 0.026 0.003 TYR B 113 ARG 0.007 0.001 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 372) hydrogen bonds : angle 4.99926 ( 984) SS BOND : bond 0.00535 ( 34) SS BOND : angle 1.33878 ( 68) link_NAG-THR : bond 0.00235 ( 3) link_NAG-THR : angle 2.22425 ( 6) covalent geometry : bond 0.00774 (13501) covalent geometry : angle 0.66609 (18225) Misc. bond : bond 0.00081 ( 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 251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7723 (mp10) cc_final: 0.7480 (mp10) REVERT: A 234 TYR cc_start: 0.8056 (t80) cc_final: 0.7832 (t80) REVERT: A 353 GLU cc_start: 0.7997 (mp0) cc_final: 0.7496 (mp0) REVERT: B 62 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7328 (mmtm) REVERT: B 82 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (pp) REVERT: B 91 ASP cc_start: 0.7270 (t0) cc_final: 0.6615 (t70) REVERT: B 100 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7076 (mmmt) REVERT: B 132 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7827 (tp-100) REVERT: I 98 GLU cc_start: 0.7589 (tp30) cc_final: 0.7223 (tp30) REVERT: I 122 LYS cc_start: 0.8591 (tppt) cc_final: 0.8357 (ttmm) REVERT: I 123 LEU cc_start: 0.8319 (tp) cc_final: 0.7977 (tt) REVERT: C 101 ASP cc_start: 0.7296 (m-30) cc_final: 0.7044 (m-30) REVERT: C 124 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6890 (mmp-170) REVERT: C 192 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7008 (mmt-90) REVERT: G 56 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7427 (ptm160) REVERT: G 376 GLU cc_start: 0.7861 (tp30) cc_final: 0.7571 (tt0) REVERT: G 456 MET cc_start: 0.7853 (mmm) cc_final: 0.7547 (mmm) REVERT: G 477 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5387 (tppt) outliers start: 61 outliers final: 47 residues processed: 237 average time/residue: 0.2800 time to fit residues: 92.4346 Evaluate side-chains 237 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 100 LYS Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 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 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 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 265 THR 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 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 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 161 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 113 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3650 r_free = 0.3650 target = 0.139249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106075 restraints weight = 16539.368| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.51 r_work: 0.3033 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13544 Z= 0.107 Angle : 0.491 6.893 18299 Z= 0.260 Chirality : 0.041 0.147 1980 Planarity : 0.004 0.060 2359 Dihedral : 6.332 56.660 2021 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.83 % Allowed : 14.75 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1633 helix: 0.61 (0.34), residues: 228 sheet: -0.28 (0.22), residues: 552 loop : -1.30 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 27 HIS 0.002 0.001 HIS A 293 PHE 0.010 0.001 PHE C 267 TYR 0.015 0.001 TYR B 113 ARG 0.006 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 372) hydrogen bonds : angle 4.64480 ( 984) SS BOND : bond 0.00272 ( 34) SS BOND : angle 0.72019 ( 68) link_NAG-THR : bond 0.00096 ( 3) link_NAG-THR : angle 1.76260 ( 6) covalent geometry : bond 0.00244 (13501) covalent geometry : angle 0.48907 (18225) Misc. bond : bond 0.00033 ( 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 248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLN cc_start: 0.7517 (mp10) cc_final: 0.7191 (mp10) REVERT: E 107 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7925 (t70) REVERT: F 46 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.7577 (m90) REVERT: A 77 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7643 (pm20) REVERT: A 199 GLN cc_start: 0.8040 (mt0) cc_final: 0.7671 (mt0) REVERT: A 234 TYR cc_start: 0.7889 (t80) cc_final: 0.7571 (t80) REVERT: A 250 HIS cc_start: 0.8771 (m-70) cc_final: 0.8515 (m90) REVERT: A 353 GLU cc_start: 0.7986 (mp0) cc_final: 0.7263 (mp0) REVERT: A 469 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: B 82 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8622 (pp) REVERT: B 91 ASP cc_start: 0.7059 (t0) cc_final: 0.6374 (t70) REVERT: B 100 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7037 (mmmt) REVERT: B 132 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7756 (tp-100) REVERT: I 69 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: I 98 GLU cc_start: 0.7617 (tp30) cc_final: 0.7335 (tp30) REVERT: I 122 LYS cc_start: 0.8558 (tppt) cc_final: 0.8325 (ttmm) REVERT: C 101 ASP cc_start: 0.7365 (m-30) cc_final: 0.7037 (m-30) REVERT: C 124 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6822 (mmp-170) REVERT: C 162 ARG cc_start: 0.8290 (ptm160) cc_final: 0.8028 (ptm-80) REVERT: C 182 ILE cc_start: 0.8690 (mt) cc_final: 0.8216 (tt) REVERT: C 192 ARG cc_start: 0.7695 (ttm170) cc_final: 0.6833 (mmp80) REVERT: G 56 ARG cc_start: 0.7752 (ptp90) cc_final: 0.7380 (ptm160) REVERT: G 376 GLU cc_start: 0.7781 (tp30) cc_final: 0.7498 (tt0) REVERT: G 406 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7677 (tmtt) REVERT: G 453 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7868 (p) REVERT: G 456 MET cc_start: 0.7924 (mmm) cc_final: 0.7639 (mmm) outliers start: 56 outliers final: 42 residues processed: 235 average time/residue: 0.2821 time to fit residues: 92.6209 Evaluate side-chains 243 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TYR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 ARG 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 188 GLU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 HIS Chi-restraints excluded: chain G residue 265 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 30 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS I 50 ASN C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105854 restraints weight = 16504.268| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.47 r_work: 0.3089 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3065 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= 0.182 Angle : 0.536 7.623 18299 Z= 0.285 Chirality : 0.043 0.143 1980 Planarity : 0.004 0.063 2359 Dihedral : 6.285 57.921 2021 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.76 % Allowed : 16.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1633 helix: 0.56 (0.35), residues: 225 sheet: -0.32 (0.22), residues: 546 loop : -1.34 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 27 HIS 0.010 0.001 HIS F 46 PHE 0.014 0.002 PHE G 466 TYR 0.019 0.002 TYR B 113 ARG 0.006 0.001 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 372) hydrogen bonds : angle 4.67071 ( 984) SS BOND : bond 0.00347 ( 34) SS BOND : angle 0.89326 ( 68) link_NAG-THR : bond 0.00116 ( 3) link_NAG-THR : angle 1.82039 ( 6) covalent geometry : bond 0.00438 (13501) covalent geometry : angle 0.53364 (18225) Misc. bond : bond 0.00037 ( 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 243 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7170 (mttm) REVERT: A 77 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7682 (pm20) REVERT: A 234 TYR cc_start: 0.8021 (t80) cc_final: 0.7694 (t80) REVERT: A 250 HIS cc_start: 0.8610 (m-70) cc_final: 0.8362 (m90) REVERT: A 353 GLU cc_start: 0.7983 (mp0) cc_final: 0.7473 (mp0) REVERT: A 469 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6013 (pm20) REVERT: B 62 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7390 (mmtm) REVERT: B 82 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8651 (pp) REVERT: B 91 ASP cc_start: 0.7134 (t0) cc_final: 0.6490 (t70) REVERT: B 100 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7040 (mmmt) REVERT: B 132 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7720 (tp-100) REVERT: I 98 GLU cc_start: 0.7564 (tp30) cc_final: 0.7311 (tp30) REVERT: I 100 GLU cc_start: 0.7996 (pm20) cc_final: 0.7770 (pm20) REVERT: I 122 LYS cc_start: 0.8526 (tppt) cc_final: 0.8293 (ttmm) REVERT: I 123 LEU cc_start: 0.8244 (tp) cc_final: 0.7877 (tt) REVERT: C 101 ASP cc_start: 0.7330 (m-30) cc_final: 0.7085 (m-30) REVERT: C 124 ARG cc_start: 0.7011 (mmp-170) cc_final: 0.6698 (mmp-170) REVERT: C 192 ARG cc_start: 0.7745 (ttm170) cc_final: 0.6957 (mmp80) REVERT: G 56 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7440 (ptm160) REVERT: G 376 GLU cc_start: 0.7882 (tp30) cc_final: 0.7613 (tt0) REVERT: G 384 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6249 (tt) REVERT: G 406 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7776 (tmtt) REVERT: G 456 MET cc_start: 0.7863 (mmm) cc_final: 0.7553 (mmm) REVERT: G 477 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.5751 (tppt) outliers start: 55 outliers final: 42 residues processed: 230 average time/residue: 0.2845 time to fit residues: 91.4501 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 : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 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 184 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 351 THR 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 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107805 restraints weight = 16417.649| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.48 r_work: 0.3068 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3090 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= 0.104 Angle : 0.475 7.433 18299 Z= 0.251 Chirality : 0.040 0.145 1980 Planarity : 0.003 0.055 2359 Dihedral : 5.701 57.880 2021 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.55 % Allowed : 16.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1633 helix: 0.72 (0.34), residues: 228 sheet: -0.19 (0.22), residues: 546 loop : -1.27 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 27 HIS 0.002 0.000 HIS I 46 PHE 0.010 0.001 PHE C 267 TYR 0.013 0.001 TYR B 113 ARG 0.007 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 372) hydrogen bonds : angle 4.49605 ( 984) SS BOND : bond 0.00233 ( 34) SS BOND : angle 0.63554 ( 68) link_NAG-THR : bond 0.00093 ( 3) link_NAG-THR : angle 1.65834 ( 6) covalent geometry : bond 0.00241 (13501) covalent geometry : angle 0.47304 (18225) Misc. bond : bond 0.00026 ( 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 248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7933 (t70) REVERT: A 77 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7581 (pm20) REVERT: A 199 GLN cc_start: 0.7912 (mt0) cc_final: 0.7583 (mt0) REVERT: A 234 TYR cc_start: 0.7929 (t80) cc_final: 0.7595 (t80) REVERT: A 250 HIS cc_start: 0.8586 (m-70) cc_final: 0.8340 (m90) REVERT: A 353 GLU cc_start: 0.7955 (mp0) cc_final: 0.7495 (mp0) REVERT: A 469 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5792 (pm20) REVERT: B 62 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7445 (mmtm) REVERT: B 82 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8607 (pp) REVERT: B 91 ASP cc_start: 0.7017 (t0) cc_final: 0.6400 (t0) REVERT: B 100 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7056 (mmmt) REVERT: B 132 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7657 (tp-100) REVERT: I 122 LYS cc_start: 0.8584 (tppt) cc_final: 0.8359 (ttmm) REVERT: C 101 ASP cc_start: 0.7340 (m-30) cc_final: 0.7009 (m-30) REVERT: C 124 ARG cc_start: 0.7169 (mmp-170) cc_final: 0.6946 (mmp80) REVERT: C 182 ILE cc_start: 0.8825 (mt) cc_final: 0.8394 (tt) REVERT: C 192 ARG cc_start: 0.7691 (ttm170) cc_final: 0.6844 (mmp80) REVERT: G 56 ARG cc_start: 0.7789 (ptp90) cc_final: 0.7388 (ptm160) REVERT: G 376 GLU cc_start: 0.7857 (tp30) cc_final: 0.7597 (tt0) REVERT: G 453 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7920 (p) REVERT: G 456 MET cc_start: 0.7985 (mmm) cc_final: 0.7718 (mmm) REVERT: G 477 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.5826 (tppt) outliers start: 52 outliers final: 43 residues processed: 236 average time/residue: 0.2817 time to fit residues: 92.8570 Evaluate side-chains 238 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 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 A residue 469 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 131 LEU 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 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 186 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105578 restraints weight = 16336.799| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.46 r_work: 0.3036 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13544 Z= 0.180 Angle : 0.544 7.162 18299 Z= 0.289 Chirality : 0.042 0.143 1980 Planarity : 0.004 0.054 2359 Dihedral : 5.898 57.992 2021 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.83 % Allowed : 16.39 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1633 helix: 0.59 (0.35), residues: 225 sheet: -0.30 (0.22), residues: 546 loop : -1.31 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 27 HIS 0.004 0.001 HIS I 46 PHE 0.011 0.002 PHE G 389 TYR 0.018 0.002 TYR B 113 ARG 0.007 0.001 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 372) hydrogen bonds : angle 4.59483 ( 984) SS BOND : bond 0.00345 ( 34) SS BOND : angle 0.86865 ( 68) link_NAG-THR : bond 0.00147 ( 3) link_NAG-THR : angle 1.74103 ( 6) covalent geometry : bond 0.00434 (13501) covalent geometry : angle 0.54127 (18225) Misc. bond : bond 0.00039 ( 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 245 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7437 (m90) REVERT: A 77 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7589 (pm20) REVERT: A 199 GLN cc_start: 0.8027 (mt0) cc_final: 0.7679 (mt0) REVERT: A 234 TYR cc_start: 0.7981 (t80) cc_final: 0.7712 (t80) REVERT: A 250 HIS cc_start: 0.8614 (m-70) cc_final: 0.8372 (m90) REVERT: A 353 GLU cc_start: 0.7977 (mp0) cc_final: 0.7440 (mp0) REVERT: A 469 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: B 82 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8620 (pp) REVERT: B 91 ASP cc_start: 0.7089 (t0) cc_final: 0.6469 (t0) REVERT: B 100 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: B 105 GLN cc_start: 0.8168 (mt0) cc_final: 0.7728 (mp-120) REVERT: B 132 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7735 (tp-100) REVERT: I 122 LYS cc_start: 0.8556 (tppt) cc_final: 0.8335 (ttmm) REVERT: C 101 ASP cc_start: 0.7303 (m-30) cc_final: 0.7051 (m-30) REVERT: C 124 ARG cc_start: 0.7116 (mmp-170) cc_final: 0.6898 (mmp80) REVERT: C 182 ILE cc_start: 0.8850 (mt) cc_final: 0.8408 (tt) REVERT: C 192 ARG cc_start: 0.7699 (ttm170) cc_final: 0.6910 (mmp80) REVERT: G 56 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7431 (ptm160) REVERT: G 376 GLU cc_start: 0.7920 (tp30) cc_final: 0.7646 (tt0) REVERT: G 384 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6330 (tt) REVERT: G 406 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7759 (tmtt) REVERT: G 453 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7917 (p) REVERT: G 456 MET cc_start: 0.7870 (mmm) cc_final: 0.7557 (mmm) REVERT: G 477 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.5741 (tppt) outliers start: 56 outliers final: 44 residues processed: 230 average time/residue: 0.2811 time to fit residues: 90.1404 Evaluate side-chains 240 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 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 A residue 405 GLN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 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 131 LEU 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 188 GLU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 186 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 56 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108486 restraints weight = 16270.714| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.48 r_work: 0.3077 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13544 Z= 0.088 Angle : 0.480 7.397 18299 Z= 0.256 Chirality : 0.040 0.144 1980 Planarity : 0.004 0.052 2359 Dihedral : 5.531 58.612 2021 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.14 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1633 helix: 1.31 (0.35), residues: 210 sheet: -0.43 (0.21), residues: 603 loop : -1.27 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 27 HIS 0.005 0.001 HIS F 46 PHE 0.010 0.001 PHE G 466 TYR 0.013 0.001 TYR A 137 ARG 0.008 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 372) hydrogen bonds : angle 4.44040 ( 984) SS BOND : bond 0.00215 ( 34) SS BOND : angle 0.55553 ( 68) link_NAG-THR : bond 0.00091 ( 3) link_NAG-THR : angle 1.59930 ( 6) covalent geometry : bond 0.00191 (13501) covalent geometry : angle 0.47888 (18225) Misc. bond : bond 0.00021 ( 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 235 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7582 (pm20) REVERT: A 199 GLN cc_start: 0.8019 (mt0) cc_final: 0.7709 (mt0) REVERT: A 234 TYR cc_start: 0.7917 (t80) cc_final: 0.7580 (t80) REVERT: A 250 HIS cc_start: 0.8581 (m-70) cc_final: 0.8334 (m90) REVERT: A 353 GLU cc_start: 0.7989 (mp0) cc_final: 0.7492 (mp0) REVERT: A 406 LYS cc_start: 0.8816 (tttm) cc_final: 0.8273 (ttmm) REVERT: A 469 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5771 (pm20) REVERT: B 62 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7433 (mmtm) REVERT: B 82 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8613 (pp) REVERT: B 91 ASP cc_start: 0.6943 (t0) cc_final: 0.6284 (t70) REVERT: B 100 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7056 (mmmt) REVERT: B 105 GLN cc_start: 0.7908 (mt0) cc_final: 0.7283 (mp-120) REVERT: B 132 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7655 (tp-100) REVERT: I 122 LYS cc_start: 0.8551 (tppt) cc_final: 0.8329 (ttmm) REVERT: C 101 ASP cc_start: 0.7309 (m-30) cc_final: 0.7004 (m-30) REVERT: C 182 ILE cc_start: 0.8840 (mt) cc_final: 0.8426 (tt) REVERT: C 192 ARG cc_start: 0.7617 (ttm170) cc_final: 0.6726 (mmp80) REVERT: G 29 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: G 56 ARG cc_start: 0.7947 (ptp90) cc_final: 0.7542 (ptm160) REVERT: G 376 GLU cc_start: 0.7867 (tp30) cc_final: 0.7597 (tt0) REVERT: G 453 VAL cc_start: 0.8249 (t) cc_final: 0.7970 (p) REVERT: G 456 MET cc_start: 0.7968 (mmm) cc_final: 0.7684 (mmm) REVERT: G 477 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5800 (tppt) outliers start: 46 outliers final: 39 residues processed: 224 average time/residue: 0.2910 time to fit residues: 90.5983 Evaluate side-chains 230 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 SER 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 A residue 405 GLN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 38 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 127 GLU Chi-restraints excluded: chain C residue 131 LEU 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 271 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 186 LYS 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 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 51 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107624 restraints weight = 16427.088| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.49 r_work: 0.3064 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13544 Z= 0.113 Angle : 0.488 7.169 18299 Z= 0.259 Chirality : 0.041 0.143 1980 Planarity : 0.004 0.051 2359 Dihedral : 5.507 59.434 2020 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.55 % Allowed : 17.21 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1633 helix: 1.29 (0.35), residues: 210 sheet: -0.17 (0.22), residues: 546 loop : -1.17 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 27 HIS 0.003 0.001 HIS I 46 PHE 0.009 0.001 PHE C 267 TYR 0.014 0.001 TYR B 113 ARG 0.008 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 372) hydrogen bonds : angle 4.41186 ( 984) SS BOND : bond 0.00245 ( 34) SS BOND : angle 0.63612 ( 68) link_NAG-THR : bond 0.00106 ( 3) link_NAG-THR : angle 1.58841 ( 6) covalent geometry : bond 0.00265 (13501) covalent geometry : angle 0.48674 (18225) Misc. bond : bond 0.00019 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6979.25 seconds wall clock time: 121 minutes 30.65 seconds (7290.65 seconds total)