Starting phenix.real_space_refine on Thu Feb 5 02:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9haa_51980/02_2026/9haa_51980.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 81 5.16 5 C 9231 2.51 5 N 2287 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14256 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2750 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2785 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 326} Chain breaks: 1 Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2785 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 13, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2719 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "E" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2747 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 322} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' ZN': 1, 'BUA': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 0.21 Number of scatterers: 14256 At special positions: 0 Unit cell: (104.65, 102.05, 131.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 81 16.00 O 2656 8.00 N 2287 7.00 C 9231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " BETA1-3 " NAG J 2 " - " BMA J 3 " " NAG K 2 " - " BMA K 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " BETA1-6 " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 401 " - " ASN D 113 " " NAG F 1 " - " ASN A 204 " " NAG G 1 " - " ASN A 113 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN B 80 " " NAG J 1 " - " ASN C 80 " " NAG K 1 " - " ASN C 149 " " NAG L 1 " - " ASN D 204 " " NAG M 1 " - " ASN E 149 " " NAG N 1 " - " ASN E 80 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 494.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 267 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS C 267 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS E 267 " 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 44.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 75 through 78 removed outlier: 3.530A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 176 through 181 removed outlier: 4.474A pdb=" N VAL A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.506A pdb=" N VAL A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.723A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 253 through 279 removed outlier: 3.851A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.609A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 351 removed outlier: 4.278A pdb=" N ASP A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 3.597A pdb=" N ASN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 removed outlier: 3.908A pdb=" N LYS B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.889A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.412A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 removed outlier: 3.603A pdb=" N LYS B 173 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.810A pdb=" N ILE B 181 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.611A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.593A pdb=" N ARG B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.575A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 582 removed outlier: 3.951A pdb=" N ALA B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Proline residue: B 567 - end of helix Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.580A pdb=" N VAL C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 139 through 145 removed outlier: 4.286A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Proline residue: C 144 - end of helix Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.624A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.538A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.927A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 584 removed outlier: 3.705A pdb=" N ASP C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Proline residue: C 567 - end of helix removed outlier: 4.552A pdb=" N VAL C 582 " --> pdb=" O TRP C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 26 removed outlier: 3.677A pdb=" N THR D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.512A pdb=" N SER D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 removed outlier: 4.123A pdb=" N ASP D 147 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 253 through 276 Processing helix chain 'D' and resid 286 through 315 removed outlier: 3.566A pdb=" N VAL D 294 " --> pdb=" O TRP D 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 350 removed outlier: 3.695A pdb=" N ARG D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.516A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.545A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.544A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.652A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.621A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.522A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.509A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 584 removed outlier: 3.928A pdb=" N ARG E 563 " --> pdb=" O ASP E 559 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Proline residue: E 567 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 4.638A pdb=" N LEU A 121 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU A 61 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 63 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 52 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP A 65 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS A 73 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN A 42 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 111 removed outlier: 6.981A pdb=" N SER A 138 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 109 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 136 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA A 111 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG A 134 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU A 61 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 63 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 52 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP A 65 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS A 73 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN A 42 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.722A pdb=" N GLY A 197 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.453A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 60 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 47 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N TYR B 62 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 45 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN B 64 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP B 43 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TYR B 66 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 41 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ARG B 68 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N GLY B 39 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.764A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 60 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 47 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N TYR B 62 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 45 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN B 64 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP B 43 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TYR B 66 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 41 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ARG B 68 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N GLY B 39 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.708A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.558A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.743A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.795A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 200 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.092A pdb=" N THR D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU D 61 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR D 63 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE D 52 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP D 65 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 73 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN D 42 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 106 through 111 removed outlier: 6.894A pdb=" N SER D 138 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER D 109 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR D 136 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA D 111 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ARG D 134 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU D 61 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR D 63 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE D 52 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP D 65 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 73 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN D 42 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 103 removed outlier: 4.572A pdb=" N SER D 161 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 213 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER D 206 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR D 212 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN D 204 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 214 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR D 202 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR D 216 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 200 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS D 218 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN D 198 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N HIS D 220 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.369A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.800A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.919A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.56 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: 4299 1.34 - 1.46: 2965 1.46 - 1.58: 7204 1.58 - 1.70: 0 1.70 - 1.81: 141 Bond restraints: 14609 Sorted by residual: bond pdb=" CB PRO E 6 " pdb=" CG PRO E 6 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO C 6 " pdb=" CG PRO C 6 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.45e+00 bond pdb=" CB PRO B 6 " pdb=" CG PRO B 6 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 bond pdb=" CG LEU A 135 " pdb=" CD1 LEU A 135 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CA THR A 115 " pdb=" C THR A 115 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.13e+00 ... (remaining 14604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19363 1.57 - 3.14: 397 3.14 - 4.71: 83 4.71 - 6.28: 13 6.28 - 7.85: 4 Bond angle restraints: 19860 Sorted by residual: angle pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " pdb=" C5 NAG K 1 " ideal model delta sigma weight residual 113.21 121.06 -7.85 3.00e+00 1.11e-01 6.85e+00 angle pdb=" C4 BMA K 3 " pdb=" C3 BMA K 3 " pdb=" O3 BMA K 3 " ideal model delta sigma weight residual 113.17 120.05 -6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" N ILE D 332 " pdb=" CA ILE D 332 " pdb=" C ILE D 332 " ideal model delta sigma weight residual 111.67 109.50 2.17 9.50e-01 1.11e+00 5.20e+00 angle pdb=" N PHE D 148 " pdb=" CA PHE D 148 " pdb=" C PHE D 148 " ideal model delta sigma weight residual 109.81 114.83 -5.02 2.21e+00 2.05e-01 5.16e+00 angle pdb=" N ASP A 100 " pdb=" CA ASP A 100 " pdb=" C ASP A 100 " ideal model delta sigma weight residual 112.97 110.57 2.40 1.06e+00 8.90e-01 5.12e+00 ... (remaining 19855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 8519 22.19 - 44.38: 422 44.38 - 66.58: 69 66.58 - 88.77: 20 88.77 - 110.96: 7 Dihedral angle restraints: 9037 sinusoidal: 4029 harmonic: 5008 Sorted by residual: dihedral pdb=" CA CYS E 150 " pdb=" C CYS E 150 " pdb=" N THR E 151 " pdb=" CA THR E 151 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PHE B 200 " pdb=" C PHE B 200 " pdb=" N ALA B 201 " pdb=" CA ALA B 201 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA VAL D 66 " pdb=" C VAL D 66 " pdb=" N PHE D 67 " pdb=" CA PHE D 67 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 9034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1705 0.040 - 0.080: 468 0.080 - 0.119: 146 0.119 - 0.159: 25 0.159 - 0.199: 4 Chirality restraints: 2348 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.26e+00 chirality pdb=" C3 BMA M 3 " pdb=" C2 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" O3 BMA M 3 " both_signs ideal model delta sigma weight residual False 2.41 2.21 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" O3 BMA K 3 " both_signs ideal model delta sigma weight residual False 2.41 2.22 0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2345 not shown) Planarity restraints: 2423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 316 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 317 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 275 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO C 276 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 80 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.11e+00 pdb=" CG ASN E 80 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 80 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 80 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 2420 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1975 2.75 - 3.29: 13927 3.29 - 3.83: 22879 3.83 - 4.36: 28115 4.36 - 4.90: 49752 Nonbonded interactions: 116648 Sorted by model distance: nonbonded pdb=" N GLU C 179 " pdb=" OE1 GLU C 179 " model vdw 2.217 3.120 nonbonded pdb=" N GLU A 185 " pdb=" OE1 GLU A 185 " model vdw 2.220 3.120 nonbonded pdb=" NH2 ARG C 68 " pdb=" OD2 ASP C 121 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR D 101 " pdb=" OH TYR D 171 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 101 " pdb=" OH TYR A 171 " model vdw 2.258 3.040 ... (remaining 116643 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 11 through 316 or resid 320 through 352)) selection = (chain 'D' and resid 11 through 352) } ncs_group { reference = (chain 'B' and (resid 6 through 308 or resid 552 through 584)) selection = (chain 'C' and (resid 6 through 308 or resid 552 through 584)) selection = (chain 'E' and resid 6 through 584) } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } 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: 7.260 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 0.080 14652 Z= 0.144 Angle : 0.654 11.758 19975 Z= 0.325 Chirality : 0.042 0.199 2348 Planarity : 0.005 0.062 2413 Dihedral : 13.763 110.960 5802 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1678 helix: 0.03 (0.21), residues: 599 sheet: 0.06 (0.25), residues: 386 loop : -0.37 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 560 TYR 0.015 0.001 TYR C 277 PHE 0.026 0.001 PHE A 148 TRP 0.012 0.001 TRP E 168 HIS 0.008 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00328 (14609) covalent geometry : angle 0.59568 (19860) SS BOND : bond 0.00266 ( 5) SS BOND : angle 0.96559 ( 10) hydrogen bonds : bond 0.21777 ( 718) hydrogen bonds : angle 8.24647 ( 2316) metal coordination : bond 0.00068 ( 3) link_ALPHA1-3 : bond 0.01148 ( 6) link_ALPHA1-3 : angle 3.70910 ( 18) link_ALPHA1-6 : bond 0.01216 ( 3) link_ALPHA1-6 : angle 1.40592 ( 9) link_BETA1-3 : bond 0.00752 ( 2) link_BETA1-3 : angle 3.73355 ( 6) link_BETA1-4 : bond 0.00868 ( 13) link_BETA1-4 : angle 4.61378 ( 39) link_BETA1-6 : bond 0.00358 ( 1) link_BETA1-6 : angle 1.27784 ( 3) link_NAG-ASN : bond 0.00511 ( 10) link_NAG-ASN : angle 3.15987 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8132 (mtm110) REVERT: A 222 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7544 (tptt) REVERT: B 17 ASP cc_start: 0.7792 (m-30) cc_final: 0.7367 (m-30) REVERT: B 52 GLU cc_start: 0.8388 (mp0) cc_final: 0.8082 (mp0) REVERT: B 64 GLN cc_start: 0.8729 (mt0) cc_final: 0.8471 (mt0) REVERT: B 307 PHE cc_start: 0.7255 (m-80) cc_final: 0.7008 (m-80) REVERT: C 17 ASP cc_start: 0.7904 (m-30) cc_final: 0.7541 (m-30) REVERT: C 153 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 265 ASN cc_start: 0.7559 (t0) cc_final: 0.6492 (m110) REVERT: C 560 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7601 (mtm-85) REVERT: C 569 THR cc_start: 0.7105 (m) cc_final: 0.6575 (p) REVERT: D 39 ARG cc_start: 0.8294 (ptp-110) cc_final: 0.7414 (ptt90) REVERT: D 42 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8093 (mm-40) REVERT: D 44 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7671 (mtm-85) REVERT: D 122 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7731 (mtp-110) REVERT: D 126 ASP cc_start: 0.7942 (m-30) cc_final: 0.7628 (m-30) REVERT: D 241 ILE cc_start: 0.8481 (mm) cc_final: 0.8237 (mt) REVERT: E 54 ASN cc_start: 0.7964 (m110) cc_final: 0.7645 (m110) REVERT: E 245 ASP cc_start: 0.8171 (p0) cc_final: 0.7836 (p0) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.1386 time to fit residues: 65.7479 Evaluate side-chains 308 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS C 54 ASN C 243 ASN D 175 ASN D 194 HIS E 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132106 restraints weight = 15933.438| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.54 r_work: 0.3258 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14652 Z= 0.182 Angle : 0.714 10.975 19975 Z= 0.350 Chirality : 0.049 0.279 2348 Planarity : 0.005 0.052 2413 Dihedral : 10.688 110.099 2609 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.32 % Allowed : 6.40 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1678 helix: 0.83 (0.21), residues: 601 sheet: 0.03 (0.24), residues: 398 loop : -0.35 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 189 TYR 0.024 0.002 TYR E 299 PHE 0.022 0.002 PHE D 17 TRP 0.012 0.001 TRP E 168 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00419 (14609) covalent geometry : angle 0.67398 (19860) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.26350 ( 10) hydrogen bonds : bond 0.04936 ( 718) hydrogen bonds : angle 5.07802 ( 2316) metal coordination : bond 0.00163 ( 3) link_ALPHA1-3 : bond 0.00622 ( 6) link_ALPHA1-3 : angle 3.20784 ( 18) link_ALPHA1-6 : bond 0.00859 ( 3) link_ALPHA1-6 : angle 1.62586 ( 9) link_BETA1-3 : bond 0.00863 ( 2) link_BETA1-3 : angle 3.72190 ( 6) link_BETA1-4 : bond 0.00647 ( 13) link_BETA1-4 : angle 4.03391 ( 39) link_BETA1-6 : bond 0.00279 ( 1) link_BETA1-6 : angle 1.17197 ( 3) link_NAG-ASN : bond 0.00369 ( 10) link_NAG-ASN : angle 2.65756 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8301 (mtm110) cc_final: 0.8044 (mtm110) REVERT: A 125 ASP cc_start: 0.7606 (t70) cc_final: 0.7234 (p0) REVERT: B 52 GLU cc_start: 0.8466 (mp0) cc_final: 0.8154 (mp0) REVERT: B 64 GLN cc_start: 0.8648 (mt0) cc_final: 0.8351 (mt0) REVERT: C 153 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 265 ASN cc_start: 0.7501 (t0) cc_final: 0.6623 (m110) REVERT: C 298 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 560 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7861 (mtm-85) REVERT: C 569 THR cc_start: 0.7513 (m) cc_final: 0.6959 (p) REVERT: D 39 ARG cc_start: 0.8200 (ptp-110) cc_final: 0.7344 (ptt90) REVERT: D 42 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8221 (mm-40) REVERT: D 44 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7719 (mtm-85) REVERT: D 122 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7699 (mtp-110) REVERT: D 126 ASP cc_start: 0.7900 (m-30) cc_final: 0.7531 (m-30) REVERT: D 194 HIS cc_start: 0.7584 (m-70) cc_final: 0.7342 (m90) REVERT: D 230 ILE cc_start: 0.8559 (tt) cc_final: 0.8216 (tt) REVERT: D 241 ILE cc_start: 0.8221 (mm) cc_final: 0.7974 (mt) REVERT: E 54 ASN cc_start: 0.7724 (m110) cc_final: 0.7367 (m110) outliers start: 20 outliers final: 16 residues processed: 323 average time/residue: 0.1433 time to fit residues: 64.8378 Evaluate side-chains 304 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 162 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN C 243 ASN D 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132659 restraints weight = 15895.080| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.23 r_work: 0.3327 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14652 Z= 0.113 Angle : 0.620 10.177 19975 Z= 0.298 Chirality : 0.045 0.286 2348 Planarity : 0.004 0.059 2413 Dihedral : 9.799 110.546 2609 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.52 % Allowed : 9.30 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1678 helix: 1.22 (0.21), residues: 604 sheet: 0.21 (0.23), residues: 412 loop : -0.25 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 560 TYR 0.027 0.001 TYR E 299 PHE 0.017 0.001 PHE A 260 TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00242 (14609) covalent geometry : angle 0.58081 (19860) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.71591 ( 10) hydrogen bonds : bond 0.03924 ( 718) hydrogen bonds : angle 4.48242 ( 2316) metal coordination : bond 0.00190 ( 3) link_ALPHA1-3 : bond 0.00614 ( 6) link_ALPHA1-3 : angle 3.16666 ( 18) link_ALPHA1-6 : bond 0.00977 ( 3) link_ALPHA1-6 : angle 1.61826 ( 9) link_BETA1-3 : bond 0.00683 ( 2) link_BETA1-3 : angle 3.03547 ( 6) link_BETA1-4 : bond 0.00688 ( 13) link_BETA1-4 : angle 3.63058 ( 39) link_BETA1-6 : bond 0.00311 ( 1) link_BETA1-6 : angle 1.03931 ( 3) link_NAG-ASN : bond 0.00374 ( 10) link_NAG-ASN : angle 2.48408 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 222 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6757 (tptt) REVERT: A 251 ARG cc_start: 0.7428 (ptt180) cc_final: 0.6389 (ptm160) REVERT: A 329 MET cc_start: 0.5339 (mmt) cc_final: 0.3991 (ptt) REVERT: B 48 ASP cc_start: 0.8219 (t0) cc_final: 0.7368 (m-30) REVERT: B 64 GLN cc_start: 0.8769 (mt0) cc_final: 0.8452 (mt0) REVERT: C 17 ASP cc_start: 0.7814 (m-30) cc_final: 0.7403 (m-30) REVERT: C 68 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8231 (ttm170) REVERT: C 103 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8340 (ttmm) REVERT: C 265 ASN cc_start: 0.7358 (t0) cc_final: 0.6479 (m110) REVERT: C 569 THR cc_start: 0.7316 (m) cc_final: 0.6675 (p) REVERT: D 39 ARG cc_start: 0.8225 (ptp-110) cc_final: 0.7283 (ptt90) REVERT: D 42 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8269 (mm-40) REVERT: D 44 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7607 (mpp-170) REVERT: D 122 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7702 (mtp-110) REVERT: D 126 ASP cc_start: 0.8059 (m-30) cc_final: 0.7729 (m-30) REVERT: D 194 HIS cc_start: 0.7611 (m-70) cc_final: 0.7357 (m90) REVERT: D 241 ILE cc_start: 0.7995 (mm) cc_final: 0.7749 (mt) REVERT: E 51 SER cc_start: 0.8768 (p) cc_final: 0.8400 (p) REVERT: E 52 GLU cc_start: 0.7953 (mp0) cc_final: 0.7728 (mp0) REVERT: E 54 ASN cc_start: 0.7419 (m110) cc_final: 0.6990 (m110) REVERT: E 131 THR cc_start: 0.9000 (m) cc_final: 0.8796 (m) outliers start: 23 outliers final: 17 residues processed: 319 average time/residue: 0.1400 time to fit residues: 63.1227 Evaluate side-chains 308 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 106 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134084 restraints weight = 15772.579| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.21 r_work: 0.3248 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14652 Z= 0.116 Angle : 0.602 9.852 19975 Z= 0.290 Chirality : 0.045 0.282 2348 Planarity : 0.004 0.064 2413 Dihedral : 9.538 110.216 2609 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.98 % Allowed : 9.89 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1678 helix: 1.37 (0.21), residues: 606 sheet: 0.28 (0.23), residues: 423 loop : -0.18 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 560 TYR 0.031 0.002 TYR B 581 PHE 0.014 0.001 PHE A 17 TRP 0.008 0.001 TRP C 67 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00261 (14609) covalent geometry : angle 0.56539 (19860) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.79038 ( 10) hydrogen bonds : bond 0.03550 ( 718) hydrogen bonds : angle 4.32414 ( 2316) metal coordination : bond 0.00147 ( 3) link_ALPHA1-3 : bond 0.00601 ( 6) link_ALPHA1-3 : angle 3.07867 ( 18) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 1.64166 ( 9) link_BETA1-3 : bond 0.00668 ( 2) link_BETA1-3 : angle 2.83596 ( 6) link_BETA1-4 : bond 0.00651 ( 13) link_BETA1-4 : angle 3.46248 ( 39) link_BETA1-6 : bond 0.00299 ( 1) link_BETA1-6 : angle 1.11367 ( 3) link_NAG-ASN : bond 0.00332 ( 10) link_NAG-ASN : angle 2.32043 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 222 LYS cc_start: 0.7508 (ttpt) cc_final: 0.6706 (tttt) REVERT: A 238 MET cc_start: 0.8300 (mmm) cc_final: 0.8081 (mmm) REVERT: A 251 ARG cc_start: 0.7443 (ptt180) cc_final: 0.6382 (ptm160) REVERT: A 329 MET cc_start: 0.5412 (mmt) cc_final: 0.4070 (ptt) REVERT: B 48 ASP cc_start: 0.8236 (t0) cc_final: 0.7369 (m-30) REVERT: B 64 GLN cc_start: 0.8780 (mt0) cc_final: 0.8466 (mt0) REVERT: C 17 ASP cc_start: 0.7801 (m-30) cc_final: 0.7396 (m-30) REVERT: C 68 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8271 (ttm170) REVERT: C 86 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7524 (ptp-170) REVERT: C 103 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8376 (ttmm) REVERT: C 265 ASN cc_start: 0.7395 (t0) cc_final: 0.6476 (m110) REVERT: C 569 THR cc_start: 0.7332 (m) cc_final: 0.6694 (p) REVERT: D 39 ARG cc_start: 0.8251 (ptp-110) cc_final: 0.7322 (ptt90) REVERT: D 42 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8276 (mm-40) REVERT: D 44 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7638 (mpp-170) REVERT: D 122 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7719 (mtp-110) REVERT: D 126 ASP cc_start: 0.8038 (m-30) cc_final: 0.7717 (m-30) REVERT: D 241 ILE cc_start: 0.7988 (mm) cc_final: 0.7750 (mt) REVERT: E 51 SER cc_start: 0.8708 (p) cc_final: 0.8372 (p) REVERT: E 54 ASN cc_start: 0.7405 (m110) cc_final: 0.7019 (m110) REVERT: E 90 GLN cc_start: 0.8093 (mt0) cc_final: 0.7866 (mp10) outliers start: 30 outliers final: 24 residues processed: 305 average time/residue: 0.1378 time to fit residues: 59.9025 Evaluate side-chains 306 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118797 restraints weight = 16473.275| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.63 r_work: 0.3209 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14652 Z= 0.258 Angle : 0.695 11.350 19975 Z= 0.343 Chirality : 0.049 0.290 2348 Planarity : 0.005 0.067 2413 Dihedral : 9.875 111.749 2609 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.77 % Allowed : 11.54 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1678 helix: 1.14 (0.21), residues: 604 sheet: 0.04 (0.23), residues: 401 loop : -0.50 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 560 TYR 0.024 0.002 TYR C 299 PHE 0.020 0.002 PHE D 306 TRP 0.012 0.002 TRP E 168 HIS 0.007 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00613 (14609) covalent geometry : angle 0.66184 (19860) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.46858 ( 10) hydrogen bonds : bond 0.04318 ( 718) hydrogen bonds : angle 4.64280 ( 2316) metal coordination : bond 0.00094 ( 3) link_ALPHA1-3 : bond 0.00626 ( 6) link_ALPHA1-3 : angle 2.99069 ( 18) link_ALPHA1-6 : bond 0.00935 ( 3) link_ALPHA1-6 : angle 1.65275 ( 9) link_BETA1-3 : bond 0.00796 ( 2) link_BETA1-3 : angle 2.91360 ( 6) link_BETA1-4 : bond 0.00555 ( 13) link_BETA1-4 : angle 3.64633 ( 39) link_BETA1-6 : bond 0.00129 ( 1) link_BETA1-6 : angle 1.40963 ( 3) link_NAG-ASN : bond 0.00356 ( 10) link_NAG-ASN : angle 2.29306 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8744 (mtpt) REVERT: A 124 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7276 (mp0) REVERT: A 125 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7372 (p0) REVERT: A 192 GLN cc_start: 0.7832 (pt0) cc_final: 0.7628 (pt0) REVERT: A 222 LYS cc_start: 0.7695 (ttpt) cc_final: 0.6968 (tttt) REVERT: B 17 ASP cc_start: 0.7954 (m-30) cc_final: 0.7738 (m-30) REVERT: C 17 ASP cc_start: 0.7927 (m-30) cc_final: 0.7524 (m-30) REVERT: C 86 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7673 (ptp-170) REVERT: C 103 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8535 (ttmm) REVERT: C 265 ASN cc_start: 0.7713 (t0) cc_final: 0.6699 (m110) REVERT: C 569 THR cc_start: 0.7621 (m) cc_final: 0.6896 (p) REVERT: D 39 ARG cc_start: 0.8272 (ptp-110) cc_final: 0.7536 (ptt90) REVERT: D 42 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8119 (mm-40) REVERT: D 44 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7868 (mtm-85) REVERT: D 122 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7799 (mtp-110) REVERT: D 126 ASP cc_start: 0.8026 (m-30) cc_final: 0.7666 (m-30) REVERT: D 241 ILE cc_start: 0.8238 (mm) cc_final: 0.8016 (mt) REVERT: D 248 TRP cc_start: 0.8539 (m-90) cc_final: 0.8067 (m-90) REVERT: E 51 SER cc_start: 0.8818 (p) cc_final: 0.8604 (p) REVERT: E 54 ASN cc_start: 0.7870 (m110) cc_final: 0.7541 (m110) outliers start: 42 outliers final: 36 residues processed: 314 average time/residue: 0.1394 time to fit residues: 62.2103 Evaluate side-chains 323 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.161261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129525 restraints weight = 15932.781| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.17 r_work: 0.3288 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14652 Z= 0.119 Angle : 0.600 10.571 19975 Z= 0.291 Chirality : 0.045 0.282 2348 Planarity : 0.004 0.068 2413 Dihedral : 9.400 112.237 2609 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.85 % Allowed : 12.99 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1678 helix: 1.41 (0.21), residues: 607 sheet: 0.12 (0.23), residues: 415 loop : -0.37 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 560 TYR 0.024 0.001 TYR E 299 PHE 0.016 0.001 PHE A 17 TRP 0.008 0.001 TRP B 168 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00270 (14609) covalent geometry : angle 0.56526 (19860) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.79431 ( 10) hydrogen bonds : bond 0.03447 ( 718) hydrogen bonds : angle 4.31278 ( 2316) metal coordination : bond 0.00512 ( 3) link_ALPHA1-3 : bond 0.00585 ( 6) link_ALPHA1-3 : angle 3.03472 ( 18) link_ALPHA1-6 : bond 0.00998 ( 3) link_ALPHA1-6 : angle 1.63427 ( 9) link_BETA1-3 : bond 0.00698 ( 2) link_BETA1-3 : angle 2.61932 ( 6) link_BETA1-4 : bond 0.00637 ( 13) link_BETA1-4 : angle 3.37965 ( 39) link_BETA1-6 : bond 0.00289 ( 1) link_BETA1-6 : angle 1.04974 ( 3) link_NAG-ASN : bond 0.00318 ( 10) link_NAG-ASN : angle 2.30788 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7116 (mp0) REVERT: A 125 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7300 (p0) REVERT: A 222 LYS cc_start: 0.7530 (ttpt) cc_final: 0.6746 (tttt) REVERT: A 251 ARG cc_start: 0.7510 (ptt180) cc_final: 0.6444 (ptm160) REVERT: A 329 MET cc_start: 0.5341 (mmt) cc_final: 0.4111 (ptt) REVERT: B 17 ASP cc_start: 0.7986 (m-30) cc_final: 0.7751 (m-30) REVERT: B 48 ASP cc_start: 0.8233 (t0) cc_final: 0.7345 (m-30) REVERT: C 17 ASP cc_start: 0.7881 (m-30) cc_final: 0.7441 (m-30) REVERT: C 86 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7529 (ptp-170) REVERT: C 103 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8447 (ttmm) REVERT: C 265 ASN cc_start: 0.7435 (t0) cc_final: 0.6506 (m110) REVERT: D 39 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.7473 (ptt90) REVERT: D 42 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8240 (mm-40) REVERT: D 44 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7651 (mpp-170) REVERT: D 78 ARG cc_start: 0.8611 (ttp-170) cc_final: 0.8194 (mtm180) REVERT: D 122 ARG cc_start: 0.8436 (mtt180) cc_final: 0.7736 (mtp-110) REVERT: D 126 ASP cc_start: 0.8047 (m-30) cc_final: 0.7693 (m-30) REVERT: D 241 ILE cc_start: 0.7980 (mm) cc_final: 0.7754 (mt) REVERT: E 54 ASN cc_start: 0.7501 (m110) cc_final: 0.7144 (m110) outliers start: 28 outliers final: 23 residues processed: 306 average time/residue: 0.1369 time to fit residues: 59.1473 Evaluate side-chains 310 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 124 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.162013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125414 restraints weight = 16133.798| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.63 r_work: 0.3283 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14652 Z= 0.109 Angle : 0.583 9.834 19975 Z= 0.282 Chirality : 0.044 0.262 2348 Planarity : 0.004 0.070 2413 Dihedral : 9.091 110.791 2609 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.04 % Allowed : 12.99 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1678 helix: 1.60 (0.21), residues: 607 sheet: 0.24 (0.24), residues: 415 loop : -0.28 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 78 TYR 0.023 0.001 TYR E 299 PHE 0.015 0.001 PHE B 306 TRP 0.011 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00244 (14609) covalent geometry : angle 0.54975 (19860) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.74868 ( 10) hydrogen bonds : bond 0.03190 ( 718) hydrogen bonds : angle 4.17575 ( 2316) metal coordination : bond 0.00356 ( 3) link_ALPHA1-3 : bond 0.00594 ( 6) link_ALPHA1-3 : angle 2.96227 ( 18) link_ALPHA1-6 : bond 0.01045 ( 3) link_ALPHA1-6 : angle 1.62559 ( 9) link_BETA1-3 : bond 0.00663 ( 2) link_BETA1-3 : angle 2.55572 ( 6) link_BETA1-4 : bond 0.00660 ( 13) link_BETA1-4 : angle 3.19695 ( 39) link_BETA1-6 : bond 0.00315 ( 1) link_BETA1-6 : angle 1.11348 ( 3) link_NAG-ASN : bond 0.00338 ( 10) link_NAG-ASN : angle 2.22256 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 LYS cc_start: 0.7548 (ttpt) cc_final: 0.6850 (tttt) REVERT: A 251 ARG cc_start: 0.7590 (ptt180) cc_final: 0.6619 (ptm160) REVERT: A 329 MET cc_start: 0.5605 (mmt) cc_final: 0.4347 (ptt) REVERT: B 17 ASP cc_start: 0.7951 (m-30) cc_final: 0.7736 (m-30) REVERT: B 48 ASP cc_start: 0.8039 (t0) cc_final: 0.7308 (m-30) REVERT: C 17 ASP cc_start: 0.7834 (m-30) cc_final: 0.7427 (m-30) REVERT: C 103 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8492 (ttmm) REVERT: C 265 ASN cc_start: 0.7637 (t0) cc_final: 0.6713 (m110) REVERT: C 569 THR cc_start: 0.7587 (t) cc_final: 0.7039 (p) REVERT: D 39 ARG cc_start: 0.8294 (ptp-110) cc_final: 0.7676 (ptt90) REVERT: D 42 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8097 (mm-40) REVERT: D 44 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7763 (mpp-170) REVERT: D 78 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.8097 (mtm180) REVERT: D 122 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7753 (mtp-110) REVERT: D 126 ASP cc_start: 0.7941 (m-30) cc_final: 0.7656 (m-30) REVERT: D 215 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8006 (mmp) REVERT: D 241 ILE cc_start: 0.8133 (mm) cc_final: 0.7915 (mt) REVERT: E 54 ASN cc_start: 0.7691 (m110) cc_final: 0.7491 (m110) REVERT: E 90 GLN cc_start: 0.8218 (mt0) cc_final: 0.7894 (mp10) outliers start: 31 outliers final: 25 residues processed: 307 average time/residue: 0.1353 time to fit residues: 59.2067 Evaluate side-chains 309 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127382 restraints weight = 16112.204| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.64 r_work: 0.3251 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14652 Z= 0.113 Angle : 0.581 9.724 19975 Z= 0.282 Chirality : 0.044 0.264 2348 Planarity : 0.004 0.072 2413 Dihedral : 8.902 111.291 2609 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.18 % Allowed : 13.46 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1678 helix: 1.67 (0.21), residues: 607 sheet: 0.34 (0.24), residues: 414 loop : -0.30 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 560 TYR 0.023 0.001 TYR E 299 PHE 0.014 0.001 PHE A 17 TRP 0.008 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00256 (14609) covalent geometry : angle 0.54983 (19860) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.74743 ( 10) hydrogen bonds : bond 0.03140 ( 718) hydrogen bonds : angle 4.12994 ( 2316) metal coordination : bond 0.00338 ( 3) link_ALPHA1-3 : bond 0.00627 ( 6) link_ALPHA1-3 : angle 2.91908 ( 18) link_ALPHA1-6 : bond 0.01070 ( 3) link_ALPHA1-6 : angle 1.62518 ( 9) link_BETA1-3 : bond 0.00662 ( 2) link_BETA1-3 : angle 2.49763 ( 6) link_BETA1-4 : bond 0.00644 ( 13) link_BETA1-4 : angle 3.11183 ( 39) link_BETA1-6 : bond 0.00299 ( 1) link_BETA1-6 : angle 1.12139 ( 3) link_NAG-ASN : bond 0.00323 ( 10) link_NAG-ASN : angle 2.18749 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.8041 (ptt180) REVERT: A 222 LYS cc_start: 0.7474 (ttpt) cc_final: 0.6798 (tttt) REVERT: A 251 ARG cc_start: 0.7597 (ptt180) cc_final: 0.6621 (ptm160) REVERT: A 329 MET cc_start: 0.5628 (mmt) cc_final: 0.4370 (ptt) REVERT: B 17 ASP cc_start: 0.7979 (m-30) cc_final: 0.7773 (m-30) REVERT: B 48 ASP cc_start: 0.8044 (t0) cc_final: 0.7307 (m-30) REVERT: C 17 ASP cc_start: 0.7847 (m-30) cc_final: 0.7445 (m-30) REVERT: C 86 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7519 (ptp-170) REVERT: C 103 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8528 (ttmm) REVERT: C 265 ASN cc_start: 0.7618 (t0) cc_final: 0.6677 (m110) REVERT: D 39 ARG cc_start: 0.8310 (ptp-110) cc_final: 0.7631 (ptt90) REVERT: D 42 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8176 (mm-40) REVERT: D 44 ARG cc_start: 0.8170 (mtm180) cc_final: 0.7755 (mpp-170) REVERT: D 78 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.8128 (mtm180) REVERT: D 122 ARG cc_start: 0.8311 (mtt180) cc_final: 0.7743 (mtp-110) REVERT: D 126 ASP cc_start: 0.7927 (m-30) cc_final: 0.7632 (m-30) REVERT: D 215 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8023 (mmp) REVERT: D 241 ILE cc_start: 0.8091 (mm) cc_final: 0.7885 (mt) REVERT: D 248 TRP cc_start: 0.8468 (m-90) cc_final: 0.8105 (m-90) outliers start: 33 outliers final: 25 residues processed: 307 average time/residue: 0.1325 time to fit residues: 57.9551 Evaluate side-chains 315 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127650 restraints weight = 16186.686| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.66 r_work: 0.3253 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14652 Z= 0.111 Angle : 0.578 9.546 19975 Z= 0.280 Chirality : 0.044 0.263 2348 Planarity : 0.004 0.073 2413 Dihedral : 8.749 111.039 2609 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.98 % Allowed : 13.85 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1678 helix: 1.75 (0.21), residues: 606 sheet: 0.39 (0.24), residues: 414 loop : -0.28 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 78 TYR 0.023 0.001 TYR E 299 PHE 0.017 0.001 PHE B 306 TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00249 (14609) covalent geometry : angle 0.54797 (19860) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.72751 ( 10) hydrogen bonds : bond 0.03073 ( 718) hydrogen bonds : angle 4.08553 ( 2316) metal coordination : bond 0.00325 ( 3) link_ALPHA1-3 : bond 0.00605 ( 6) link_ALPHA1-3 : angle 2.89178 ( 18) link_ALPHA1-6 : bond 0.01073 ( 3) link_ALPHA1-6 : angle 1.59161 ( 9) link_BETA1-3 : bond 0.00645 ( 2) link_BETA1-3 : angle 2.43347 ( 6) link_BETA1-4 : bond 0.00651 ( 13) link_BETA1-4 : angle 3.03788 ( 39) link_BETA1-6 : bond 0.00303 ( 1) link_BETA1-6 : angle 1.11392 ( 3) link_NAG-ASN : bond 0.00328 ( 10) link_NAG-ASN : angle 2.17362 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8105 (t0) cc_final: 0.7319 (p0) REVERT: A 222 LYS cc_start: 0.7413 (ttpt) cc_final: 0.6689 (tttt) REVERT: A 251 ARG cc_start: 0.7595 (ptt180) cc_final: 0.6611 (ptm160) REVERT: A 329 MET cc_start: 0.5563 (mmt) cc_final: 0.4324 (ptt) REVERT: C 17 ASP cc_start: 0.7836 (m-30) cc_final: 0.7431 (m-30) REVERT: C 70 LYS cc_start: 0.8335 (mmpt) cc_final: 0.8036 (mmpt) REVERT: C 86 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7513 (ptp-170) REVERT: C 103 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8524 (ttmm) REVERT: C 265 ASN cc_start: 0.7615 (t0) cc_final: 0.6666 (m110) REVERT: D 39 ARG cc_start: 0.8316 (ptp-110) cc_final: 0.7639 (ptt90) REVERT: D 42 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8179 (mm-40) REVERT: D 44 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7766 (mpp-170) REVERT: D 78 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8147 (mtm180) REVERT: D 122 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7737 (mtm110) REVERT: D 126 ASP cc_start: 0.7930 (m-30) cc_final: 0.7643 (m-30) REVERT: D 215 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8012 (mmp) REVERT: D 248 TRP cc_start: 0.8448 (m-90) cc_final: 0.8082 (m-90) REVERT: E 90 GLN cc_start: 0.8207 (mt0) cc_final: 0.7903 (mp10) outliers start: 30 outliers final: 27 residues processed: 304 average time/residue: 0.1255 time to fit residues: 54.0299 Evaluate side-chains 312 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 159 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129100 restraints weight = 16133.206| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.64 r_work: 0.3273 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14652 Z= 0.103 Angle : 0.571 9.653 19975 Z= 0.276 Chirality : 0.044 0.264 2348 Planarity : 0.004 0.075 2413 Dihedral : 8.547 111.081 2609 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.11 % Allowed : 14.05 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1678 helix: 1.87 (0.21), residues: 603 sheet: 0.47 (0.24), residues: 416 loop : -0.25 (0.26), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 560 TYR 0.022 0.001 TYR E 299 PHE 0.016 0.001 PHE C 306 TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00227 (14609) covalent geometry : angle 0.54131 (19860) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.59608 ( 10) hydrogen bonds : bond 0.02947 ( 718) hydrogen bonds : angle 4.01609 ( 2316) metal coordination : bond 0.00366 ( 3) link_ALPHA1-3 : bond 0.00611 ( 6) link_ALPHA1-3 : angle 2.86123 ( 18) link_ALPHA1-6 : bond 0.01094 ( 3) link_ALPHA1-6 : angle 1.56575 ( 9) link_BETA1-3 : bond 0.00631 ( 2) link_BETA1-3 : angle 2.34180 ( 6) link_BETA1-4 : bond 0.00670 ( 13) link_BETA1-4 : angle 2.94050 ( 39) link_BETA1-6 : bond 0.00323 ( 1) link_BETA1-6 : angle 1.08716 ( 3) link_NAG-ASN : bond 0.00322 ( 10) link_NAG-ASN : angle 2.16067 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8099 (t0) cc_final: 0.7308 (p0) REVERT: A 222 LYS cc_start: 0.7403 (ttpt) cc_final: 0.7134 (pttt) REVERT: A 329 MET cc_start: 0.5589 (mmt) cc_final: 0.4349 (ptt) REVERT: B 161 THR cc_start: 0.8454 (t) cc_final: 0.8207 (m) REVERT: C 17 ASP cc_start: 0.7825 (m-30) cc_final: 0.7397 (m-30) REVERT: C 70 LYS cc_start: 0.8279 (mmpt) cc_final: 0.8025 (mmpt) REVERT: C 86 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7508 (ptp-170) REVERT: C 103 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8539 (ttmm) REVERT: C 265 ASN cc_start: 0.7592 (t0) cc_final: 0.6659 (m110) REVERT: C 569 THR cc_start: 0.7556 (t) cc_final: 0.7029 (p) REVERT: D 39 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.7663 (ptt90) REVERT: D 42 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8195 (mm-40) REVERT: D 44 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7763 (mpp-170) REVERT: D 78 ARG cc_start: 0.8490 (ttp-170) cc_final: 0.8119 (mtm180) REVERT: D 122 ARG cc_start: 0.8311 (mtt180) cc_final: 0.7737 (mtm110) REVERT: D 126 ASP cc_start: 0.7930 (m-30) cc_final: 0.7627 (m-30) REVERT: D 215 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8027 (mmp) REVERT: D 230 ILE cc_start: 0.8424 (tt) cc_final: 0.8133 (tt) REVERT: D 248 TRP cc_start: 0.8464 (m-90) cc_final: 0.8094 (m-90) REVERT: E 90 GLN cc_start: 0.8207 (mt0) cc_final: 0.7906 (mp10) REVERT: E 297 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7387 (tt) outliers start: 32 outliers final: 24 residues processed: 300 average time/residue: 0.1278 time to fit residues: 54.9556 Evaluate side-chains 299 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130330 restraints weight = 16020.396| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.52 r_work: 0.3237 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14652 Z= 0.122 Angle : 0.583 9.330 19975 Z= 0.282 Chirality : 0.044 0.261 2348 Planarity : 0.004 0.075 2413 Dihedral : 8.532 110.784 2609 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.18 % Allowed : 14.71 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1678 helix: 1.80 (0.21), residues: 604 sheet: 0.46 (0.24), residues: 416 loop : -0.27 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 78 TYR 0.023 0.001 TYR C 299 PHE 0.017 0.001 PHE B 306 TRP 0.008 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00281 (14609) covalent geometry : angle 0.55446 (19860) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.79853 ( 10) hydrogen bonds : bond 0.03071 ( 718) hydrogen bonds : angle 4.06926 ( 2316) metal coordination : bond 0.00231 ( 3) link_ALPHA1-3 : bond 0.00604 ( 6) link_ALPHA1-3 : angle 2.81411 ( 18) link_ALPHA1-6 : bond 0.01072 ( 3) link_ALPHA1-6 : angle 1.55867 ( 9) link_BETA1-3 : bond 0.00636 ( 2) link_BETA1-3 : angle 2.34534 ( 6) link_BETA1-4 : bond 0.00634 ( 13) link_BETA1-4 : angle 2.94274 ( 39) link_BETA1-6 : bond 0.00291 ( 1) link_BETA1-6 : angle 1.14956 ( 3) link_NAG-ASN : bond 0.00312 ( 10) link_NAG-ASN : angle 2.12276 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.62 seconds wall clock time: 63 minutes 17.05 seconds (3797.05 seconds total)