Starting phenix.real_space_refine on Wed Jul 30 08:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_26658_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_26658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_26658.map" model { file = "/net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_26658_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7up9_26658/07_2025/7up9_26658_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.195 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.22, per 1000 atoms: 0.84 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.81 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: 4.56 Time building geometry restraints manager: 3.31 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 475 or resid 501 through 503)) selection = (chain 'D' and (resid 27 through 475 or resid 501 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: 18.450 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.270 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 PHE 0.008 0.001 PHE D 301 TYR 0.008 0.001 TYR L 49 ARG 0.004 0.000 ARG G 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 1.67160 ( 36) link_BETA1-4 : bond 0.01065 ( 2) link_BETA1-4 : angle 6.53211 ( 6) hydrogen bonds : bond 0.22248 ( 481) hydrogen bonds : angle 7.34165 ( 1356) SS BOND : bond 0.00383 ( 20) SS BOND : angle 1.55592 ( 40) covalent geometry : bond 0.00338 (12358) covalent geometry : angle 0.60713 (16779) *********************** 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 : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 160 average time/residue: 1.4903 time to fit residues: 257.6496 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 : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 372 HIS H 16 GLN H 73 ASN L 6 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090741 restraints weight = 17264.136| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.01 r_work: 0.3020 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12392 Z= 0.115 Angle : 0.546 9.459 16861 Z= 0.284 Chirality : 0.046 0.206 2056 Planarity : 0.004 0.036 2104 Dihedral : 5.756 54.470 1949 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.23 % Allowed : 7.17 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1540 helix: 1.68 (0.26), residues: 426 sheet: 0.60 (0.26), residues: 397 loop : -0.71 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.010 0.001 HIS G 372 PHE 0.013 0.001 PHE A 330 TYR 0.021 0.001 TYR L 49 ARG 0.006 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 1.81487 ( 36) link_BETA1-4 : bond 0.00942 ( 2) link_BETA1-4 : angle 5.20671 ( 6) hydrogen bonds : bond 0.04524 ( 481) hydrogen bonds : angle 5.22456 ( 1356) SS BOND : bond 0.00387 ( 20) SS BOND : angle 1.59083 ( 40) covalent geometry : bond 0.00250 (12358) covalent geometry : angle 0.52603 (16779) *********************** 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 145 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.487 Fit side-chains REVERT: G 290 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8372 (mp-120) outliers start: 17 outliers final: 4 residues processed: 140 average time/residue: 1.5719 time to fit residues: 237.2619 Evaluate side-chains 119 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 103 ASP 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 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN D 303 ASN G 393 GLN H 16 GLN H 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082046 restraints weight = 17716.348| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.97 r_work: 0.2832 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12392 Z= 0.163 Angle : 0.586 10.143 16861 Z= 0.301 Chirality : 0.048 0.264 2056 Planarity : 0.004 0.038 2104 Dihedral : 5.594 53.901 1949 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 9.86 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1540 helix: 1.74 (0.26), residues: 426 sheet: 0.48 (0.26), residues: 400 loop : -0.79 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS D 29 PHE 0.016 0.001 PHE A 330 TYR 0.024 0.001 TYR L 49 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 12) link_NAG-ASN : angle 2.08191 ( 36) link_BETA1-4 : bond 0.01166 ( 2) link_BETA1-4 : angle 5.06028 ( 6) hydrogen bonds : bond 0.05072 ( 481) hydrogen bonds : angle 5.01497 ( 1356) SS BOND : bond 0.00370 ( 20) SS BOND : angle 2.15108 ( 40) covalent geometry : bond 0.00409 (12358) covalent geometry : angle 0.56223 (16779) *********************** 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 142 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9105 (mtp) REVERT: D 190 ILE cc_start: 0.8331 (mm) cc_final: 0.8131 (tt) REVERT: D 197 LEU cc_start: 0.8456 (tp) cc_final: 0.7672 (mt) REVERT: G 290 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (mp-120) REVERT: H 75 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7963 (mmtp) outliers start: 25 outliers final: 12 residues processed: 134 average time/residue: 1.8323 time to fit residues: 264.9288 Evaluate side-chains 122 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 153 SER 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 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 63 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN G 303 ASN H 3 GLN H 16 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.082139 restraints weight = 17511.655| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.93 r_work: 0.2825 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12392 Z= 0.154 Angle : 0.567 9.026 16861 Z= 0.290 Chirality : 0.047 0.253 2056 Planarity : 0.004 0.040 2104 Dihedral : 5.395 54.008 1949 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.10 % Allowed : 11.59 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1540 helix: 1.80 (0.26), residues: 426 sheet: 0.45 (0.26), residues: 400 loop : -0.87 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS D 29 PHE 0.015 0.001 PHE A 330 TYR 0.025 0.001 TYR L 49 ARG 0.003 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 12) link_NAG-ASN : angle 2.08668 ( 36) link_BETA1-4 : bond 0.01116 ( 2) link_BETA1-4 : angle 5.04401 ( 6) hydrogen bonds : bond 0.04647 ( 481) hydrogen bonds : angle 4.82231 ( 1356) SS BOND : bond 0.00345 ( 20) SS BOND : angle 2.01168 ( 40) covalent geometry : bond 0.00383 (12358) covalent geometry : angle 0.54298 (16779) *********************** 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 144 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.466 Fit side-chains REVERT: A 61 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9076 (mtp) REVERT: A 114 CYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7502 (m) REVERT: D 197 LEU cc_start: 0.8447 (tp) cc_final: 0.7777 (mt) REVERT: H 75 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8011 (mmtp) REVERT: L 74 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6972 (mtmt) outliers start: 29 outliers final: 13 residues processed: 135 average time/residue: 1.3908 time to fit residues: 203.0559 Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 153 SER 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 103 ASP Chi-restraints excluded: chain G residue 350 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 87 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 = 0.3421 r_free = 0.3421 target = 0.109758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.085367 restraints weight = 17033.168| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.17 r_work: 0.2910 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12392 Z= 0.135 Angle : 0.548 8.955 16861 Z= 0.280 Chirality : 0.046 0.242 2056 Planarity : 0.004 0.040 2104 Dihedral : 5.216 54.125 1949 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.81 % Allowed : 12.75 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1540 helix: 1.92 (0.26), residues: 426 sheet: 0.48 (0.26), residues: 400 loop : -0.88 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS D 102 PHE 0.014 0.001 PHE A 330 TYR 0.024 0.001 TYR L 49 ARG 0.004 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 12) link_NAG-ASN : angle 2.03728 ( 36) link_BETA1-4 : bond 0.01097 ( 2) link_BETA1-4 : angle 5.01570 ( 6) hydrogen bonds : bond 0.04323 ( 481) hydrogen bonds : angle 4.67649 ( 1356) SS BOND : bond 0.00414 ( 20) SS BOND : angle 2.09810 ( 40) covalent geometry : bond 0.00332 (12358) covalent geometry : angle 0.52322 (16779) *********************** 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 143 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9089 (mtp) REVERT: A 114 CYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7572 (m) REVERT: A 258 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: D 197 LEU cc_start: 0.8399 (tp) cc_final: 0.7638 (mt) REVERT: H 75 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7940 (mmtp) outliers start: 25 outliers final: 12 residues processed: 134 average time/residue: 1.3743 time to fit residues: 199.5133 Evaluate side-chains 122 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 258 GLU 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 G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR 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 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 29 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.111135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088098 restraints weight = 17298.362| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.00 r_work: 0.2959 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12392 Z= 0.142 Angle : 0.549 8.489 16861 Z= 0.281 Chirality : 0.046 0.235 2056 Planarity : 0.004 0.043 2104 Dihedral : 5.148 54.082 1949 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.32 % Allowed : 13.04 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1540 helix: 1.77 (0.26), residues: 441 sheet: 0.48 (0.26), residues: 400 loop : -0.84 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS L 27D PHE 0.014 0.001 PHE A 330 TYR 0.024 0.001 TYR L 49 ARG 0.004 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 2.04587 ( 36) link_BETA1-4 : bond 0.01090 ( 2) link_BETA1-4 : angle 5.01822 ( 6) hydrogen bonds : bond 0.04367 ( 481) hydrogen bonds : angle 4.65209 ( 1356) SS BOND : bond 0.00308 ( 20) SS BOND : angle 1.90600 ( 40) covalent geometry : bond 0.00350 (12358) covalent geometry : angle 0.52561 (16779) *********************** 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 137 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.295 Fit side-chains REVERT: A 61 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9053 (mtp) REVERT: A 114 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7551 (m) REVERT: A 258 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 471 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7235 (ttmt) REVERT: D 197 LEU cc_start: 0.8401 (tp) cc_final: 0.7670 (mt) REVERT: H 75 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8012 (mmtp) REVERT: L 74 LYS cc_start: 0.7253 (mtmt) cc_final: 0.7030 (mtmt) outliers start: 32 outliers final: 16 residues processed: 126 average time/residue: 1.3828 time to fit residues: 188.6616 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 : 1.454 ------------------------------------------------------------------------------- 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 258 GLU 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 G residue 217 ASN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR 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 101 ASP 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 65 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.104854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.080800 restraints weight = 17265.129| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.14 r_work: 0.2848 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12392 Z= 0.259 Angle : 0.655 9.951 16861 Z= 0.333 Chirality : 0.051 0.273 2056 Planarity : 0.005 0.046 2104 Dihedral : 5.519 53.904 1949 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 13.55 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1540 helix: 1.36 (0.25), residues: 459 sheet: 0.42 (0.26), residues: 400 loop : -0.97 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.003 0.001 HIS D 29 PHE 0.017 0.002 PHE A 330 TYR 0.026 0.002 TYR L 49 ARG 0.004 0.001 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 2.35138 ( 36) link_BETA1-4 : bond 0.01235 ( 2) link_BETA1-4 : angle 5.22642 ( 6) hydrogen bonds : bond 0.05789 ( 481) hydrogen bonds : angle 4.90461 ( 1356) SS BOND : bond 0.00481 ( 20) SS BOND : angle 2.29359 ( 40) covalent geometry : bond 0.00666 (12358) covalent geometry : angle 0.62961 (16779) *********************** 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: 29 poor density : 111 time to evaluate : 1.558 Fit side-chains REVERT: A 114 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7624 (m) REVERT: A 258 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: A 471 LYS cc_start: 0.7433 (mtpt) cc_final: 0.7177 (ttmt) REVERT: D 197 LEU cc_start: 0.8498 (tp) cc_final: 0.7710 (mt) REVERT: L 74 LYS cc_start: 0.7234 (mtmt) cc_final: 0.6974 (mtmt) outliers start: 29 outliers final: 16 residues processed: 128 average time/residue: 1.4115 time to fit residues: 195.1413 Evaluate side-chains 126 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 312 VAL 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 A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain G residue 217 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.111434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088600 restraints weight = 17278.866| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.06 r_work: 0.2963 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12392 Z= 0.116 Angle : 0.526 8.660 16861 Z= 0.270 Chirality : 0.046 0.235 2056 Planarity : 0.004 0.039 2104 Dihedral : 5.099 54.364 1949 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.10 % Allowed : 13.91 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1540 helix: 1.80 (0.26), residues: 441 sheet: 0.49 (0.26), residues: 400 loop : -0.98 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS G 372 PHE 0.010 0.001 PHE A 330 TYR 0.021 0.001 TYR L 49 ARG 0.004 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 1.97985 ( 36) link_BETA1-4 : bond 0.01067 ( 2) link_BETA1-4 : angle 5.08162 ( 6) hydrogen bonds : bond 0.03980 ( 481) hydrogen bonds : angle 4.60688 ( 1356) SS BOND : bond 0.00316 ( 20) SS BOND : angle 1.74457 ( 40) covalent geometry : bond 0.00276 (12358) covalent geometry : angle 0.50283 (16779) *********************** 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 146 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.428 Fit side-chains REVERT: A 114 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (m) REVERT: A 258 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: A 471 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7229 (ttmt) REVERT: D 197 LEU cc_start: 0.8370 (tp) cc_final: 0.7680 (mt) REVERT: H 16 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: L 74 LYS cc_start: 0.7218 (mtmt) cc_final: 0.6976 (mtmt) outliers start: 29 outliers final: 16 residues processed: 137 average time/residue: 1.4026 time to fit residues: 207.7060 Evaluate side-chains 128 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 258 GLU 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 G residue 159 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 373 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088806 restraints weight = 17299.559| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.99 r_work: 0.2995 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12392 Z= 0.109 Angle : 0.522 8.561 16861 Z= 0.267 Chirality : 0.045 0.219 2056 Planarity : 0.004 0.037 2104 Dihedral : 4.999 54.153 1949 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 14.71 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1540 helix: 1.91 (0.26), residues: 441 sheet: 0.51 (0.26), residues: 400 loop : -0.96 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.000 HIS G 102 PHE 0.013 0.001 PHE A 330 TYR 0.022 0.001 TYR L 49 ARG 0.005 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 12) link_NAG-ASN : angle 1.93875 ( 36) link_BETA1-4 : bond 0.01034 ( 2) link_BETA1-4 : angle 5.04845 ( 6) hydrogen bonds : bond 0.03843 ( 481) hydrogen bonds : angle 4.53206 ( 1356) SS BOND : bond 0.00264 ( 20) SS BOND : angle 1.66104 ( 40) covalent geometry : bond 0.00257 (12358) covalent geometry : angle 0.50046 (16779) *********************** 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 136 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.472 Fit side-chains REVERT: A 114 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7548 (m) REVERT: A 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: D 197 LEU cc_start: 0.8439 (tp) cc_final: 0.7668 (mt) REVERT: L 74 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6974 (mtmt) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 1.3503 time to fit residues: 190.4713 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 : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 258 GLU 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 G residue 159 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 373 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.110930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088091 restraints weight = 17170.664| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.07 r_work: 0.2953 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12392 Z= 0.140 Angle : 0.551 8.409 16861 Z= 0.282 Chirality : 0.046 0.213 2056 Planarity : 0.004 0.039 2104 Dihedral : 5.047 54.021 1949 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.52 % Allowed : 14.93 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1540 helix: 1.73 (0.25), residues: 459 sheet: 0.49 (0.26), residues: 400 loop : -0.90 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS D 102 PHE 0.015 0.001 PHE A 330 TYR 0.023 0.001 TYR L 49 ARG 0.005 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.00542 ( 36) link_BETA1-4 : bond 0.01071 ( 2) link_BETA1-4 : angle 5.04388 ( 6) hydrogen bonds : bond 0.04251 ( 481) hydrogen bonds : angle 4.55562 ( 1356) SS BOND : bond 0.00298 ( 20) SS BOND : angle 2.03530 ( 40) covalent geometry : bond 0.00344 (12358) covalent geometry : angle 0.52691 (16779) ********************** 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 128 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.583 Fit side-chains REVERT: A 114 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7600 (m) REVERT: A 258 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 416 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (p) REVERT: D 197 LEU cc_start: 0.8429 (tp) cc_final: 0.7693 (mt) REVERT: D 335 LYS cc_start: 0.8782 (tppt) cc_final: 0.8538 (ttmt) REVERT: L 74 LYS cc_start: 0.7200 (mtmt) cc_final: 0.6953 (mtmt) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 1.4722 time to fit residues: 198.4775 Evaluate side-chains 122 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 258 GLU 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 G residue 159 VAL Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 373 VAL 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 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 145 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088385 restraints weight = 17247.852| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.05 r_work: 0.2959 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12392 Z= 0.131 Angle : 0.545 8.745 16861 Z= 0.278 Chirality : 0.046 0.202 2056 Planarity : 0.004 0.039 2104 Dihedral : 5.015 54.102 1949 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.59 % Allowed : 14.86 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1540 helix: 1.74 (0.25), residues: 459 sheet: 0.51 (0.26), residues: 400 loop : -0.89 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS D 102 PHE 0.016 0.001 PHE A 330 TYR 0.022 0.001 TYR L 49 ARG 0.006 0.000 ARG D 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 1.96912 ( 36) link_BETA1-4 : bond 0.01065 ( 2) link_BETA1-4 : angle 5.03105 ( 6) hydrogen bonds : bond 0.04145 ( 481) hydrogen bonds : angle 4.53403 ( 1356) SS BOND : bond 0.00350 ( 20) SS BOND : angle 1.78999 ( 40) covalent geometry : bond 0.00322 (12358) covalent geometry : angle 0.52289 (16779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8745.03 seconds wall clock time: 154 minutes 35.15 seconds (9275.15 seconds total)