Starting phenix.real_space_refine on Wed Mar 4 08:24:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7up9_26658/03_2026/7up9_26658.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7698 2.51 5 N 1981 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "G" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12168 At special positions: 0 Unit cell: (100.32, 102.96, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2416 8.00 N 1981 7.00 C 7698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.04 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG B 1 " - " ASN G 67 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 99 " " NAG G 502 " - " ASN G 414 " " NAG G 503 " - " ASN G 464 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 519.9 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 36.5% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.954A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 5.727A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.750A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.804A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.544A pdb=" N ALA A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.890A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.664A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.794A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.934A pdb=" N ASP A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.572A pdb=" N THR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 5.372A pdb=" N GLU A 361 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.587A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.940A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.560A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.709A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.923A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.556A pdb=" N MET D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.653A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.765A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.781A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 4.223A pdb=" N ASP D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.533A pdb=" N LYS D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.627A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 475 removed outlier: 3.704A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.825A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 6.267A pdb=" N GLN G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS G 71 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.658A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.883A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 145 removed outlier: 4.091A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.739A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.711A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.549A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.569A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 475 removed outlier: 3.675A pdb=" N SER G 457 " --> pdb=" O LYS G 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.848A pdb=" N LYS H 64 " --> pdb=" O SER H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.522A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 11.035A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LYS A 49 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLU A 287 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 51 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 285 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 53 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A 55 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 281 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 57 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 279 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 59 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 277 " --> pdb=" O ILE A 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.108A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 277 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 59 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 279 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 57 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 281 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A 55 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 53 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 285 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 51 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLU A 287 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LYS A 49 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 323 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.527A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS G 392 " --> pdb=" O ILE G 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.476A pdb=" N CYS A 392 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.701A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.180A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 323 through 326 Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 303 removed outlier: 6.313A pdb=" N ARG D 365 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 401 removed outlier: 4.556A pdb=" N CYS D 392 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 162 removed outlier: 11.165A pdb=" N THR G 168 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP G 56 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 334 Processing sheet with id=AB5, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.871A pdb=" N LEU H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.118A pdb=" N TYR H 102 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.755A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3874 1.34 - 1.46: 2706 1.46 - 1.59: 5672 1.59 - 1.71: 0 1.71 - 1.83: 106 Bond restraints: 12358 Sorted by residual: bond pdb=" C ILE A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N ILE G 36 " pdb=" CA ILE G 36 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.88e+00 bond pdb=" N GLN A 393 " pdb=" CA GLN A 393 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" N LYS A 362 " pdb=" CA LYS A 362 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 7.96e+00 bond pdb=" N CYS A 363 " pdb=" CA CYS A 363 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.74e+00 ... (remaining 12353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 16114 1.40 - 2.80: 559 2.80 - 4.20: 80 4.20 - 5.61: 25 5.61 - 7.01: 1 Bond angle restraints: 16779 Sorted by residual: angle pdb=" N THR A 415 " pdb=" CA THR A 415 " pdb=" C THR A 415 " ideal model delta sigma weight residual 112.89 105.88 7.01 1.24e+00 6.50e-01 3.19e+01 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 113.12 108.09 5.03 1.25e+00 6.40e-01 1.62e+01 angle pdb=" N ILE A 36 " pdb=" CA ILE A 36 " pdb=" C ILE A 36 " ideal model delta sigma weight residual 113.07 107.75 5.32 1.37e+00 5.33e-01 1.51e+01 angle pdb=" CA GLN A 342 " pdb=" C GLN A 342 " pdb=" O GLN A 342 " ideal model delta sigma weight residual 121.40 117.42 3.98 1.13e+00 7.83e-01 1.24e+01 angle pdb=" C PRO A 191 " pdb=" CA PRO A 191 " pdb=" CB PRO A 191 " ideal model delta sigma weight residual 111.56 107.09 4.47 1.27e+00 6.20e-01 1.24e+01 ... (remaining 16774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 7167 17.58 - 35.15: 440 35.15 - 52.73: 102 52.73 - 70.31: 32 70.31 - 87.88: 10 Dihedral angle restraints: 7751 sinusoidal: 3212 harmonic: 4539 Sorted by residual: dihedral pdb=" CB CYS A 394 " pdb=" SG CYS A 394 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 160.52 -67.52 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -151.19 65.19 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 363 " pdb=" CB CYS A 363 " ideal model delta sinusoidal sigma weight residual -86.00 -136.51 50.51 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 7748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1695 0.059 - 0.118: 323 0.118 - 0.178: 32 0.178 - 0.237: 5 0.237 - 0.296: 1 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA ILE A 339 " pdb=" N ILE A 339 " pdb=" C ILE A 339 " pdb=" CB ILE A 339 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA GLN A 342 " pdb=" N GLN A 342 " pdb=" C GLN A 342 " pdb=" CB GLN A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA CYS A 392 " pdb=" N CYS A 392 " pdb=" C CYS A 392 " pdb=" CB CYS A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2053 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 390 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A 390 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 390 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 179 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ILE G 179 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE G 179 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN G 180 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 446 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO G 447 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 447 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 447 " -0.019 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 539 2.73 - 3.28: 11648 3.28 - 3.82: 18613 3.82 - 4.36: 23633 4.36 - 4.90: 40814 Nonbonded interactions: 95247 Sorted by model distance: nonbonded pdb=" O SER H 98 " pdb=" OG1 THR H 99 " model vdw 2.192 3.040 nonbonded pdb=" OG SER G 359 " pdb=" OE2 GLU G 361 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU D 152 " pdb=" OG SER D 273 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP G 103 " pdb=" OH TYR G 135 " model vdw 2.261 3.040 nonbonded pdb=" NZ LYS A 148 " pdb=" OG SER A 273 " model vdw 2.272 3.120 ... (remaining 95242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 503) selection = (chain 'D' and resid 27 through 503) selection = chain 'G' } 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: 15.550 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12392 Z= 0.200 Angle : 0.627 11.297 16861 Z= 0.361 Chirality : 0.047 0.296 2056 Planarity : 0.004 0.034 2104 Dihedral : 12.629 87.883 4769 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.51 % Allowed : 0.58 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1540 helix: 0.90 (0.25), residues: 423 sheet: 0.58 (0.26), residues: 400 loop : -0.66 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 244 TYR 0.008 0.001 TYR L 49 PHE 0.008 0.001 PHE D 301 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00338 (12358) covalent geometry : angle 0.60713 (16779) SS BOND : bond 0.00383 ( 20) SS BOND : angle 1.55592 ( 40) hydrogen bonds : bond 0.22248 ( 481) hydrogen bonds : angle 7.34165 ( 1356) link_BETA1-4 : bond 0.01065 ( 2) link_BETA1-4 : angle 6.53211 ( 6) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 1.67160 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 160 average time/residue: 0.6826 time to fit residues: 117.1570 Evaluate side-chains 116 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN G 372 HIS H 16 GLN H 73 ASN L 6 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089826 restraints weight = 17241.684| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.09 r_work: 0.2988 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12392 Z= 0.140 Angle : 0.571 8.881 16861 Z= 0.297 Chirality : 0.047 0.220 2056 Planarity : 0.004 0.035 2104 Dihedral : 5.835 53.936 1949 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.23 % Allowed : 7.83 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1540 helix: 1.59 (0.26), residues: 426 sheet: 0.58 (0.26), residues: 397 loop : -0.76 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.020 0.001 TYR L 49 PHE 0.014 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.010 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00336 (12358) covalent geometry : angle 0.55008 (16779) SS BOND : bond 0.00374 ( 20) SS BOND : angle 1.77970 ( 40) hydrogen bonds : bond 0.05262 ( 481) hydrogen bonds : angle 5.29465 ( 1356) link_BETA1-4 : bond 0.00954 ( 2) link_BETA1-4 : angle 5.28828 ( 6) link_NAG-ASN : bond 0.00329 ( 12) link_NAG-ASN : angle 1.91682 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.456 Fit side-chains REVERT: G 290 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8345 (mp-120) outliers start: 17 outliers final: 4 residues processed: 132 average time/residue: 0.6819 time to fit residues: 96.5087 Evaluate side-chains 111 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain H residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN H 16 GLN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.083361 restraints weight = 17772.112| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.98 r_work: 0.2854 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12392 Z= 0.130 Angle : 0.549 10.424 16861 Z= 0.283 Chirality : 0.046 0.252 2056 Planarity : 0.004 0.036 2104 Dihedral : 5.483 54.010 1949 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.59 % Allowed : 10.00 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1540 helix: 1.79 (0.26), residues: 426 sheet: 0.48 (0.26), residues: 400 loop : -0.76 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 336 TYR 0.025 0.001 TYR L 49 PHE 0.014 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00314 (12358) covalent geometry : angle 0.52650 (16779) SS BOND : bond 0.00307 ( 20) SS BOND : angle 1.86308 ( 40) hydrogen bonds : bond 0.04531 ( 481) hydrogen bonds : angle 4.92657 ( 1356) link_BETA1-4 : bond 0.01004 ( 2) link_BETA1-4 : angle 5.07664 ( 6) link_NAG-ASN : bond 0.00338 ( 12) link_NAG-ASN : angle 1.97019 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9089 (mtp) REVERT: D 197 LEU cc_start: 0.8382 (tp) cc_final: 0.7612 (mt) REVERT: G 290 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8361 (mp-120) REVERT: H 75 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7949 (mmtp) outliers start: 22 outliers final: 12 residues processed: 133 average time/residue: 0.6653 time to fit residues: 95.0899 Evaluate side-chains 123 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 131 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 303 ASN H 3 GLN H 16 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088782 restraints weight = 17088.665| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.01 r_work: 0.3004 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12392 Z= 0.101 Angle : 0.510 10.571 16861 Z= 0.262 Chirality : 0.045 0.218 2056 Planarity : 0.004 0.034 2104 Dihedral : 5.102 54.006 1949 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 11.45 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1540 helix: 2.01 (0.26), residues: 426 sheet: 0.54 (0.26), residues: 400 loop : -0.71 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 336 TYR 0.025 0.001 TYR L 49 PHE 0.013 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00233 (12358) covalent geometry : angle 0.48827 (16779) SS BOND : bond 0.00237 ( 20) SS BOND : angle 1.74431 ( 40) hydrogen bonds : bond 0.03689 ( 481) hydrogen bonds : angle 4.62366 ( 1356) link_BETA1-4 : bond 0.01047 ( 2) link_BETA1-4 : angle 4.92217 ( 6) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 1.85606 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.449 Fit side-chains REVERT: A 61 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9079 (mtp) REVERT: A 114 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7463 (m) REVERT: D 197 LEU cc_start: 0.8283 (tp) cc_final: 0.7543 (mt) REVERT: L 74 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6950 (mtmt) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.6540 time to fit residues: 96.5750 Evaluate side-chains 123 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089822 restraints weight = 17297.659| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.02 r_work: 0.3001 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12392 Z= 0.102 Angle : 0.512 10.571 16861 Z= 0.261 Chirality : 0.045 0.208 2056 Planarity : 0.004 0.035 2104 Dihedral : 4.938 53.900 1949 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.96 % Allowed : 12.39 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1540 helix: 2.16 (0.26), residues: 426 sheet: 0.52 (0.24), residues: 445 loop : -0.76 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 336 TYR 0.026 0.001 TYR L 49 PHE 0.014 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00236 (12358) covalent geometry : angle 0.48911 (16779) SS BOND : bond 0.00278 ( 20) SS BOND : angle 1.85579 ( 40) hydrogen bonds : bond 0.03625 ( 481) hydrogen bonds : angle 4.47581 ( 1356) link_BETA1-4 : bond 0.01082 ( 2) link_BETA1-4 : angle 4.85513 ( 6) link_NAG-ASN : bond 0.00324 ( 12) link_NAG-ASN : angle 1.84963 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9019 (mtp) REVERT: A 114 CYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7540 (m) REVERT: D 197 LEU cc_start: 0.8302 (tp) cc_final: 0.7671 (mt) outliers start: 27 outliers final: 12 residues processed: 138 average time/residue: 0.6249 time to fit residues: 92.9408 Evaluate side-chains 124 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088406 restraints weight = 17219.796| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.01 r_work: 0.2983 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12392 Z= 0.127 Angle : 0.530 9.685 16861 Z= 0.271 Chirality : 0.046 0.178 2056 Planarity : 0.004 0.037 2104 Dihedral : 4.914 53.979 1949 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.46 % Allowed : 12.46 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1540 helix: 2.16 (0.27), residues: 423 sheet: 0.51 (0.24), residues: 445 loop : -0.82 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.025 0.001 TYR L 49 PHE 0.015 0.001 PHE A 330 TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00308 (12358) covalent geometry : angle 0.50833 (16779) SS BOND : bond 0.00302 ( 20) SS BOND : angle 1.70866 ( 40) hydrogen bonds : bond 0.04032 ( 481) hydrogen bonds : angle 4.51525 ( 1356) link_BETA1-4 : bond 0.01089 ( 2) link_BETA1-4 : angle 4.86449 ( 6) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 1.94412 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.433 Fit side-chains REVERT: A 61 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9029 (mtp) REVERT: A 114 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7574 (m) REVERT: A 471 LYS cc_start: 0.7381 (mtpt) cc_final: 0.7116 (ttmt) REVERT: D 197 LEU cc_start: 0.8371 (tp) cc_final: 0.7685 (mt) REVERT: G 410 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9090 (mp) REVERT: H 75 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7998 (mmtp) REVERT: L 74 LYS cc_start: 0.7226 (mtmt) cc_final: 0.7023 (mtmt) outliers start: 34 outliers final: 14 residues processed: 135 average time/residue: 0.6048 time to fit residues: 88.4652 Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087425 restraints weight = 17119.332| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.05 r_work: 0.2944 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12392 Z= 0.174 Angle : 0.580 8.696 16861 Z= 0.296 Chirality : 0.048 0.180 2056 Planarity : 0.004 0.042 2104 Dihedral : 5.150 53.931 1949 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.25 % Allowed : 12.90 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1540 helix: 1.83 (0.26), residues: 441 sheet: 0.49 (0.26), residues: 400 loop : -0.82 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.024 0.001 TYR L 49 PHE 0.016 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS L 27D Details of bonding type rmsd covalent geometry : bond 0.00438 (12358) covalent geometry : angle 0.55801 (16779) SS BOND : bond 0.00425 ( 20) SS BOND : angle 1.81162 ( 40) hydrogen bonds : bond 0.04840 ( 481) hydrogen bonds : angle 4.67666 ( 1356) link_BETA1-4 : bond 0.01099 ( 2) link_BETA1-4 : angle 4.97834 ( 6) link_NAG-ASN : bond 0.00342 ( 12) link_NAG-ASN : angle 2.14888 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.475 Fit side-chains REVERT: A 114 CYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7618 (m) REVERT: A 471 LYS cc_start: 0.7491 (mtpt) cc_final: 0.7219 (ttmt) REVERT: D 197 LEU cc_start: 0.8448 (tp) cc_final: 0.7726 (mt) REVERT: H 75 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8093 (mmtp) REVERT: L 74 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6957 (mtmt) outliers start: 31 outliers final: 18 residues processed: 128 average time/residue: 0.6440 time to fit residues: 88.8730 Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088439 restraints weight = 17214.099| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.97 r_work: 0.2989 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12392 Z= 0.136 Angle : 0.539 8.424 16861 Z= 0.276 Chirality : 0.046 0.163 2056 Planarity : 0.004 0.039 2104 Dihedral : 5.037 54.187 1949 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 13.77 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1540 helix: 2.08 (0.26), residues: 423 sheet: 0.49 (0.26), residues: 400 loop : -0.91 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.023 0.001 TYR L 49 PHE 0.014 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00335 (12358) covalent geometry : angle 0.51720 (16779) SS BOND : bond 0.00326 ( 20) SS BOND : angle 1.63854 ( 40) hydrogen bonds : bond 0.04250 ( 481) hydrogen bonds : angle 4.58110 ( 1356) link_BETA1-4 : bond 0.00970 ( 2) link_BETA1-4 : angle 4.98581 ( 6) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 2.02022 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.462 Fit side-chains REVERT: A 114 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7605 (m) REVERT: A 471 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7239 (ttmt) REVERT: D 197 LEU cc_start: 0.8391 (tp) cc_final: 0.7685 (mt) REVERT: H 16 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: H 75 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (mmtp) REVERT: L 74 LYS cc_start: 0.7216 (mtmt) cc_final: 0.6981 (mtmt) outliers start: 27 outliers final: 17 residues processed: 127 average time/residue: 0.6130 time to fit residues: 84.2673 Evaluate side-chains 126 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 113 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088466 restraints weight = 17151.889| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.97 r_work: 0.2988 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12392 Z= 0.136 Angle : 0.539 8.342 16861 Z= 0.275 Chirality : 0.046 0.164 2056 Planarity : 0.004 0.039 2104 Dihedral : 5.015 54.117 1949 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.96 % Allowed : 13.84 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1540 helix: 1.91 (0.26), residues: 441 sheet: 0.48 (0.26), residues: 400 loop : -0.85 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 244 TYR 0.023 0.001 TYR L 49 PHE 0.016 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00334 (12358) covalent geometry : angle 0.51798 (16779) SS BOND : bond 0.00320 ( 20) SS BOND : angle 1.58164 ( 40) hydrogen bonds : bond 0.04223 ( 481) hydrogen bonds : angle 4.56744 ( 1356) link_BETA1-4 : bond 0.01101 ( 2) link_BETA1-4 : angle 4.97515 ( 6) link_NAG-ASN : bond 0.00311 ( 12) link_NAG-ASN : angle 2.00957 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.434 Fit side-chains REVERT: A 114 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7587 (m) REVERT: A 471 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7234 (ttmt) REVERT: D 197 LEU cc_start: 0.8383 (tp) cc_final: 0.7685 (mt) REVERT: G 290 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: H 75 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8079 (mmtp) REVERT: L 74 LYS cc_start: 0.7218 (mtmt) cc_final: 0.6955 (mtmt) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.6491 time to fit residues: 85.8846 Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 133 optimal weight: 0.0270 chunk 138 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090668 restraints weight = 17169.342| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.06 r_work: 0.2995 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12392 Z= 0.095 Angle : 0.497 8.351 16861 Z= 0.255 Chirality : 0.044 0.158 2056 Planarity : 0.004 0.036 2104 Dihedral : 4.795 54.200 1949 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.16 % Allowed : 14.64 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.22), residues: 1540 helix: 2.25 (0.27), residues: 423 sheet: 0.49 (0.25), residues: 445 loop : -0.90 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 244 TYR 0.022 0.001 TYR L 49 PHE 0.014 0.001 PHE A 330 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.000 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00213 (12358) covalent geometry : angle 0.47715 (16779) SS BOND : bond 0.00253 ( 20) SS BOND : angle 1.37983 ( 40) hydrogen bonds : bond 0.03426 ( 481) hydrogen bonds : angle 4.40810 ( 1356) link_BETA1-4 : bond 0.00984 ( 2) link_BETA1-4 : angle 4.90346 ( 6) link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 1.81702 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.446 Fit side-chains REVERT: A 114 CYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7543 (m) REVERT: D 197 LEU cc_start: 0.8389 (tp) cc_final: 0.7642 (mt) REVERT: D 335 LYS cc_start: 0.8757 (tppt) cc_final: 0.8493 (tttm) REVERT: G 290 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8133 (mp10) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.6188 time to fit residues: 85.5156 Evaluate side-chains 122 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089851 restraints weight = 17157.207| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.06 r_work: 0.2984 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12392 Z= 0.112 Angle : 0.512 8.176 16861 Z= 0.261 Chirality : 0.045 0.160 2056 Planarity : 0.004 0.048 2104 Dihedral : 4.793 54.074 1949 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.30 % Allowed : 14.64 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1540 helix: 2.27 (0.27), residues: 423 sheet: 0.49 (0.25), residues: 445 loop : -0.89 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 244 TYR 0.025 0.001 TYR L 49 PHE 0.011 0.001 PHE A 330 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00269 (12358) covalent geometry : angle 0.49233 (16779) SS BOND : bond 0.00282 ( 20) SS BOND : angle 1.41208 ( 40) hydrogen bonds : bond 0.03707 ( 481) hydrogen bonds : angle 4.43231 ( 1356) link_BETA1-4 : bond 0.01005 ( 2) link_BETA1-4 : angle 4.88866 ( 6) link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 1.87369 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.67 seconds wall clock time: 62 minutes 58.91 seconds (3778.91 seconds total)