Starting phenix.real_space_refine on Fri Jul 3 19:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.cif" model { file = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upd_26662/07_2026/7upd_26662.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.245 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10014 2.51 5 N 2574 2.21 5 O 3117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15801 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "D" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.96, per 1000 atoms: 0.19 Number of scatterers: 15801 At special positions: 0 Unit cell: (137.28, 132.66, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3117 8.00 N 2574 7.00 C 10014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.04 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 626.7 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 30 sheets defined 30.7% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.713A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.950A pdb=" N THR A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.681A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.514A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.641A pdb=" N THR B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 52A through 54 Processing helix chain 'B' and resid 83 through 87 removed outlier: 4.016A pdb=" N THR B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.642A pdb=" N THR C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 52A through 54 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.556A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.998A pdb=" N THR C 87 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 36 Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.690A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.716A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 137 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.653A pdb=" N LYS D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.962A pdb=" N THR D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.674A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.826A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.506A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 474 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.827A pdb=" N LEU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.854A pdb=" N LEU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.735A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 137 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.639A pdb=" N LYS G 146 " --> pdb=" O ASP G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.955A pdb=" N THR G 168 " --> pdb=" O ALA G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 182 through 187 removed outlier: 3.675A pdb=" N THR G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.830A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.514A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 474 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.621A pdb=" N THR H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.997A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.804A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.228A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY A 264 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 281 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE A 266 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 279 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 268 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.627A pdb=" N VAL G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.614A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY B 96 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY C 96 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.811A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.195A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.611A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.490A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.496A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.803A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL G 338 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS G 45 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N CYS G 340 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS G 47 " --> pdb=" O CYS G 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.232A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY G 264 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR G 281 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE G 266 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG G 279 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 268 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR G 275 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLY H 96 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.493A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5020 1.34 - 1.46: 3684 1.46 - 1.58: 7238 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16086 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG G 503 " pdb=" O5 NAG G 503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 16081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20990 1.26 - 2.52: 666 2.52 - 3.79: 133 3.79 - 5.05: 28 5.05 - 6.31: 11 Bond angle restraints: 21828 Sorted by residual: angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.79 118.29 4.50 1.78e+00 3.16e-01 6.39e+00 angle pdb=" C PRO A 191 " pdb=" N CYS A 192 " pdb=" CA CYS A 192 " ideal model delta sigma weight residual 122.56 118.24 4.32 1.72e+00 3.38e-01 6.29e+00 angle pdb=" C ILE E 48 " pdb=" N TYR E 49 " pdb=" CA TYR E 49 " ideal model delta sigma weight residual 122.79 118.35 4.44 1.78e+00 3.16e-01 6.21e+00 angle pdb=" C PRO G 191 " pdb=" N CYS G 192 " pdb=" CA CYS G 192 " ideal model delta sigma weight residual 122.56 118.29 4.27 1.72e+00 3.38e-01 6.16e+00 angle pdb=" C ILE F 48 " pdb=" N TYR F 49 " pdb=" CA TYR F 49 " ideal model delta sigma weight residual 122.79 118.48 4.31 1.78e+00 3.16e-01 5.87e+00 ... (remaining 21823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8601 17.98 - 35.95: 749 35.95 - 53.93: 229 53.93 - 71.90: 59 71.90 - 89.88: 19 Dihedral angle restraints: 9657 sinusoidal: 3774 harmonic: 5883 Sorted by residual: dihedral pdb=" CB CYS G 104 " pdb=" SG CYS G 104 " pdb=" SG CYS G 114 " pdb=" CB CYS G 114 " ideal model delta sinusoidal sigma weight residual 93.00 5.80 87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 114 " pdb=" CB CYS A 114 " ideal model delta sinusoidal sigma weight residual -86.00 -0.92 -85.08 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS D 104 " pdb=" SG CYS D 104 " pdb=" SG CYS D 114 " pdb=" CB CYS D 114 " ideal model delta sinusoidal sigma weight residual -86.00 -6.37 -79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 9654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1507 0.032 - 0.065: 686 0.065 - 0.097: 217 0.097 - 0.130: 142 0.130 - 0.162: 22 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" C1 NAG G 502 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 502 " pdb=" O5 NAG G 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL G 312 " pdb=" N VAL G 312 " pdb=" C VAL G 312 " pdb=" CB VAL G 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2571 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 186 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C THR G 186 " 0.038 2.00e-02 2.50e+03 pdb=" O THR G 186 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE G 187 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 105 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" CD GLN B 105 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 105 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 105 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 31 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C THR B 31 " -0.028 2.00e-02 2.50e+03 pdb=" O THR B 31 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 32 " 0.010 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1735 2.76 - 3.29: 13976 3.29 - 3.83: 25669 3.83 - 4.36: 31371 4.36 - 4.90: 52973 Nonbonded interactions: 125724 Sorted by model distance: nonbonded pdb=" O TYR F 49 " pdb=" OH TYR F 91 " model vdw 2.222 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OH TYR L 91 " model vdw 2.227 3.040 nonbonded pdb=" O TYR E 49 " pdb=" OH TYR E 91 " model vdw 2.231 3.040 nonbonded pdb=" NH2 ARG E 54 " pdb=" OD1 ASP E 60 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS C 35 " pdb=" OE1 GLU C 95 " model vdw 2.401 3.120 ... (remaining 125719 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.520 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 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 0.031 16122 Z= 0.145 Angle : 0.574 6.310 21912 Z= 0.315 Chirality : 0.047 0.162 2574 Planarity : 0.004 0.038 2742 Dihedral : 15.862 89.880 5817 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 14.16 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1992 helix: 1.87 (0.25), residues: 435 sheet: 0.92 (0.20), residues: 642 loop : -0.28 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.019 0.001 TYR E 49 PHE 0.013 0.001 PHE G 301 TRP 0.008 0.001 TRP L 50 HIS 0.006 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (16086) covalent geometry : angle 0.56851 / 0.31 (21828) SS BOND : bond 0.00482 / 0.29 ( 24) SS BOND : angle 1.26345 / 0.83 ( 48) hydrogen bonds : bond 0.13966 / 9.04 ( 655) hydrogen bonds : angle 6.21734 / 4.68 ( 1755) link_NAG-ASN : bond 0.00225 / 0.15 ( 12) link_NAG-ASN : angle 1.45922 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.539 Fit side-chains REVERT: C 105 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8145 (mm110) outliers start: 21 outliers final: 18 residues processed: 268 average time/residue: 0.5501 time to fit residues: 163.4280 Evaluate side-chains 259 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN C 30 ASN G 465 GLN H 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099568 restraints weight = 17373.684| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.73 r_work: 0.3041 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16122 Z= 0.112 Angle : 0.504 4.805 21912 Z= 0.277 Chirality : 0.045 0.178 2574 Planarity : 0.004 0.037 2742 Dihedral : 5.712 59.306 2192 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.55 % Allowed : 12.75 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.10 (0.19), residues: 1992 helix: 2.28 (0.26), residues: 441 sheet: 0.92 (0.20), residues: 645 loop : -0.14 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.019 0.001 TYR L 49 PHE 0.012 0.001 PHE G 301 TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16086) covalent geometry : angle 0.49879 / 0.28 (21828) SS BOND : bond 0.00487 / 0.29 ( 24) SS BOND : angle 1.09918 / 0.72 ( 48) hydrogen bonds : bond 0.04713 / 3.09 ( 655) hydrogen bonds : angle 5.14297 / 3.85 ( 1755) link_NAG-ASN : bond 0.00139 / 0.09 ( 12) link_NAG-ASN : angle 1.40416 / 0.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 0.625 Fit side-chains REVERT: A 240 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: A 390 VAL cc_start: 0.8794 (p) cc_final: 0.8540 (t) REVERT: B 3 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8157 (tp40) REVERT: C 3 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8142 (tp40) REVERT: D 258 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: F 103 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8261 (tmtp) REVERT: G 336 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8462 (mtp-110) REVERT: H 3 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8233 (tp40) REVERT: H 82 MET cc_start: 0.8490 (mtm) cc_final: 0.8250 (mtm) outliers start: 63 outliers final: 28 residues processed: 293 average time/residue: 0.5420 time to fit residues: 176.5481 Evaluate side-chains 282 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN C 30 ASN C 105 GLN D 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096213 restraints weight = 17542.440| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.73 r_work: 0.2988 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16122 Z= 0.151 Angle : 0.581 5.311 21912 Z= 0.321 Chirality : 0.048 0.183 2574 Planarity : 0.004 0.038 2742 Dihedral : 5.691 47.063 2187 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.67 % Allowed : 12.80 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 1992 helix: 2.28 (0.26), residues: 441 sheet: 0.77 (0.20), residues: 606 loop : -0.12 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 319 TYR 0.024 0.002 TYR L 49 PHE 0.013 0.001 PHE D 301 TRP 0.012 0.002 TRP F 50 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16086) covalent geometry : angle 0.57467 / 0.32 (21828) SS BOND : bond 0.00730 / 0.44 ( 24) SS BOND : angle 1.51005 / 1.04 ( 48) hydrogen bonds : bond 0.05532 / 3.65 ( 655) hydrogen bonds : angle 5.18647 / 3.87 ( 1755) link_NAG-ASN : bond 0.00173 / 0.11 ( 12) link_NAG-ASN : angle 1.58544 / 0.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 0.678 Fit side-chains REVERT: A 152 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: A 410 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 3 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: C 3 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8192 (tp40) REVERT: C 105 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8329 (mm110) REVERT: D 258 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: E 27 GLN cc_start: 0.8148 (mt0) cc_final: 0.7881 (mt0) REVERT: E 106 ILE cc_start: 0.8303 (mm) cc_final: 0.8069 (tp) REVERT: F 103 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8286 (tmtp) REVERT: G 139 LYS cc_start: 0.8454 (mptp) cc_final: 0.8245 (mmtm) REVERT: G 152 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: G 336 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8478 (mtp180) REVERT: G 468 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6101 (mp10) REVERT: H 3 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: L 55 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7693 (tp30) outliers start: 65 outliers final: 26 residues processed: 286 average time/residue: 0.5418 time to fit residues: 171.9299 Evaluate side-chains 277 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN B 105 GLN C 30 ASN D 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097238 restraints weight = 17387.667| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.73 r_work: 0.3004 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16122 Z= 0.126 Angle : 0.537 5.715 21912 Z= 0.296 Chirality : 0.046 0.179 2574 Planarity : 0.004 0.036 2742 Dihedral : 5.238 46.206 2183 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.33 % Allowed : 13.42 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.99 (0.19), residues: 1992 helix: 2.40 (0.26), residues: 438 sheet: 0.74 (0.20), residues: 606 loop : -0.18 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.021 0.001 TYR L 49 PHE 0.012 0.001 PHE D 301 TRP 0.010 0.001 TRP F 50 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (16086) covalent geometry : angle 0.53030 / 0.29 (21828) SS BOND : bond 0.00598 / 0.36 ( 24) SS BOND : angle 1.33725 / 0.92 ( 48) hydrogen bonds : bond 0.04910 / 3.24 ( 655) hydrogen bonds : angle 5.02130 / 3.74 ( 1755) link_NAG-ASN : bond 0.00140 / 0.09 ( 12) link_NAG-ASN : angle 1.54717 / 0.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.667 Fit side-chains REVERT: A 152 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: B 3 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (tp40) REVERT: C 3 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (tp40) REVERT: D 258 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: F 103 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8283 (tmtp) REVERT: G 139 LYS cc_start: 0.8442 (mptp) cc_final: 0.8230 (mmtm) REVERT: G 152 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: G 336 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8436 (mtp180) REVERT: H 3 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8251 (tp40) outliers start: 59 outliers final: 24 residues processed: 275 average time/residue: 0.5392 time to fit residues: 164.3402 Evaluate side-chains 266 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 465 GLN B 105 GLN C 30 ASN C 105 GLN D 102 HIS G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096343 restraints weight = 17301.587| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.71 r_work: 0.2993 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16122 Z= 0.138 Angle : 0.565 5.700 21912 Z= 0.310 Chirality : 0.047 0.184 2574 Planarity : 0.004 0.037 2742 Dihedral : 5.148 47.144 2178 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.89 % Allowed : 13.14 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.97 (0.19), residues: 1992 helix: 2.39 (0.26), residues: 441 sheet: 0.69 (0.20), residues: 606 loop : -0.18 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.001 PHE D 301 TRP 0.011 0.002 TRP F 50 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16086) covalent geometry : angle 0.55751 / 0.31 (21828) SS BOND : bond 0.00670 / 0.40 ( 24) SS BOND : angle 1.51359 / 1.02 ( 48) hydrogen bonds : bond 0.05215 / 3.44 ( 655) hydrogen bonds : angle 5.04587 / 3.76 ( 1755) link_NAG-ASN : bond 0.00158 / 0.10 ( 12) link_NAG-ASN : angle 1.59114 / 0.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 0.564 Fit side-chains REVERT: A 71 CYS cc_start: 0.3995 (OUTLIER) cc_final: 0.3706 (t) REVERT: A 152 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: B 3 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8171 (tp40) REVERT: C 3 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8157 (tp40) REVERT: C 105 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8371 (mm110) REVERT: D 71 CYS cc_start: 0.3905 (OUTLIER) cc_final: 0.3698 (t) REVERT: D 258 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: D 336 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8517 (mtp-110) REVERT: D 350 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8339 (t0) REVERT: G 139 LYS cc_start: 0.8436 (mptp) cc_final: 0.8225 (mmtm) REVERT: G 152 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: G 336 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (mtp180) REVERT: G 468 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6129 (mp10) REVERT: H 3 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8256 (tp40) outliers start: 69 outliers final: 29 residues processed: 281 average time/residue: 0.5181 time to fit residues: 161.7829 Evaluate side-chains 273 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 465 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097363 restraints weight = 17341.485| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.71 r_work: 0.3009 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16122 Z= 0.117 Angle : 0.527 5.822 21912 Z= 0.289 Chirality : 0.046 0.182 2574 Planarity : 0.004 0.041 2742 Dihedral : 4.992 46.852 2178 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.99 % Allowed : 14.21 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.98 (0.19), residues: 1992 helix: 2.47 (0.26), residues: 438 sheet: 0.70 (0.20), residues: 606 loop : -0.20 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.022 0.001 TYR L 49 PHE 0.012 0.001 PHE D 301 TRP 0.010 0.001 TRP F 50 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16086) covalent geometry : angle 0.52078 / 0.29 (21828) SS BOND : bond 0.00539 / 0.32 ( 24) SS BOND : angle 1.35963 / 0.93 ( 48) hydrogen bonds : bond 0.04697 / 3.10 ( 655) hydrogen bonds : angle 4.92490 / 3.66 ( 1755) link_NAG-ASN : bond 0.00109 / 0.07 ( 12) link_NAG-ASN : angle 1.56428 / 0.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.657 Fit side-chains REVERT: A 71 CYS cc_start: 0.3585 (OUTLIER) cc_final: 0.3307 (t) REVERT: A 152 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 390 VAL cc_start: 0.8792 (p) cc_final: 0.8536 (t) REVERT: B 3 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (tp40) REVERT: C 3 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: C 105 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8366 (mm110) REVERT: D 71 CYS cc_start: 0.3539 (OUTLIER) cc_final: 0.3273 (t) REVERT: D 258 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: D 336 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8519 (mtp180) REVERT: D 350 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8339 (t0) REVERT: G 139 LYS cc_start: 0.8440 (mptp) cc_final: 0.8227 (mmtm) REVERT: G 152 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: G 336 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8441 (mtp180) REVERT: H 3 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8240 (tp40) outliers start: 53 outliers final: 28 residues processed: 269 average time/residue: 0.5462 time to fit residues: 162.7264 Evaluate side-chains 274 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095410 restraints weight = 17254.175| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.71 r_work: 0.2978 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16122 Z= 0.161 Angle : 0.601 6.307 21912 Z= 0.329 Chirality : 0.048 0.189 2574 Planarity : 0.004 0.043 2742 Dihedral : 5.202 48.293 2178 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.05 % Allowed : 14.04 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 1992 helix: 2.34 (0.26), residues: 441 sheet: 0.65 (0.20), residues: 621 loop : -0.25 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 319 TYR 0.024 0.002 TYR L 49 PHE 0.013 0.001 PHE A 301 TRP 0.013 0.002 TRP F 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16086) covalent geometry : angle 0.59363 / 0.33 (21828) SS BOND : bond 0.00814 / 0.49 ( 24) SS BOND : angle 1.67920 / 1.13 ( 48) hydrogen bonds : bond 0.05562 / 3.67 ( 655) hydrogen bonds : angle 5.09763 / 3.80 ( 1755) link_NAG-ASN : bond 0.00211 / 0.13 ( 12) link_NAG-ASN : angle 1.65645 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.727 Fit side-chains REVERT: A 152 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: B 3 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: C 3 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8155 (tp40) REVERT: C 105 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8411 (mm110) REVERT: D 258 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: D 336 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8523 (mtp180) REVERT: D 350 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8353 (t0) REVERT: G 139 LYS cc_start: 0.8450 (mptp) cc_final: 0.8238 (mmtm) REVERT: G 152 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: G 468 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6136 (mp10) REVERT: H 3 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8261 (tp40) outliers start: 54 outliers final: 31 residues processed: 275 average time/residue: 0.5427 time to fit residues: 165.4508 Evaluate side-chains 278 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096916 restraints weight = 17426.645| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.72 r_work: 0.3000 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16122 Z= 0.120 Angle : 0.537 6.088 21912 Z= 0.293 Chirality : 0.046 0.183 2574 Planarity : 0.004 0.039 2742 Dihedral : 4.985 47.848 2178 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 1992 helix: 2.46 (0.26), residues: 438 sheet: 0.65 (0.20), residues: 606 loop : -0.20 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.022 0.001 TYR L 49 PHE 0.012 0.001 PHE D 301 TRP 0.010 0.001 TRP F 50 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (16086) covalent geometry : angle 0.52924 / 0.29 (21828) SS BOND : bond 0.00558 / 0.33 ( 24) SS BOND : angle 1.43262 / 0.91 ( 48) hydrogen bonds : bond 0.04781 / 3.15 ( 655) hydrogen bonds : angle 4.93245 / 3.67 ( 1755) link_NAG-ASN : bond 0.00105 / 0.07 ( 12) link_NAG-ASN : angle 1.62759 / 1.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.637 Fit side-chains REVERT: A 138 MET cc_start: 0.8139 (mmm) cc_final: 0.7902 (mmp) REVERT: A 152 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: B 3 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: C 3 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: C 105 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8413 (mm110) REVERT: D 258 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: D 336 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8517 (mtp180) REVERT: D 350 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (t0) REVERT: G 139 LYS cc_start: 0.8429 (mptp) cc_final: 0.8215 (mmtm) REVERT: G 152 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: H 3 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8242 (tp40) outliers start: 46 outliers final: 30 residues processed: 261 average time/residue: 0.5707 time to fit residues: 164.9379 Evaluate side-chains 274 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093330 restraints weight = 17236.458| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.70 r_work: 0.2944 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16122 Z= 0.228 Angle : 0.711 7.699 21912 Z= 0.390 Chirality : 0.052 0.226 2574 Planarity : 0.005 0.062 2742 Dihedral : 5.461 50.684 2178 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.76 % Allowed : 14.55 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.72 (0.18), residues: 1992 helix: 1.97 (0.25), residues: 456 sheet: 0.56 (0.20), residues: 591 loop : -0.26 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 319 TYR 0.026 0.002 TYR L 49 PHE 0.016 0.002 PHE A 301 TRP 0.016 0.003 TRP F 50 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (16086) covalent geometry : angle 0.70348 / 0.39 (21828) SS BOND : bond 0.01131 / 0.69 ( 24) SS BOND : angle 1.82242 / 1.22 ( 48) hydrogen bonds : bond 0.06663 / 4.40 ( 655) hydrogen bonds : angle 5.35474 / 4.01 ( 1755) link_NAG-ASN : bond 0.00381 / 0.22 ( 12) link_NAG-ASN : angle 1.85349 / 1.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.797 Fit side-chains REVERT: A 152 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: B 3 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8183 (tp40) REVERT: C 3 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8189 (tp40) REVERT: D 258 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: D 350 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8382 (t0) REVERT: D 410 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8711 (mp) REVERT: E 27 GLN cc_start: 0.8183 (mt0) cc_final: 0.7924 (mt0) REVERT: E 103 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8259 (tttp) REVERT: G 152 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: G 468 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6164 (mp10) REVERT: H 3 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8268 (tp40) outliers start: 49 outliers final: 26 residues processed: 276 average time/residue: 0.5797 time to fit residues: 177.1298 Evaluate side-chains 277 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 465 GLN B 105 GLN C 30 ASN C 105 GLN D 465 GLN G 465 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094604 restraints weight = 17236.180| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.70 r_work: 0.2963 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16122 Z= 0.173 Angle : 0.639 6.934 21912 Z= 0.349 Chirality : 0.049 0.190 2574 Planarity : 0.005 0.057 2742 Dihedral : 5.243 49.552 2176 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.43 % Allowed : 14.89 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.73 (0.18), residues: 1992 helix: 2.21 (0.26), residues: 438 sheet: 0.48 (0.20), residues: 621 loop : -0.29 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 279 TYR 0.022 0.002 TYR F 49 PHE 0.014 0.002 PHE A 301 TRP 0.014 0.002 TRP E 50 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (16086) covalent geometry : angle 0.63128 / 0.35 (21828) SS BOND : bond 0.00876 / 0.53 ( 24) SS BOND : angle 1.71172 / 1.18 ( 48) hydrogen bonds : bond 0.05858 / 3.87 ( 655) hydrogen bonds : angle 5.20183 / 3.88 ( 1755) link_NAG-ASN : bond 0.00240 / 0.14 ( 12) link_NAG-ASN : angle 1.81760 / 1.10 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.663 Fit side-chains REVERT: A 152 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B 3 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8191 (tp40) REVERT: C 3 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8168 (tp40) REVERT: C 105 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8358 (mm110) REVERT: D 258 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: D 350 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8362 (t0) REVERT: D 410 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 103 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8241 (tttp) REVERT: G 139 LYS cc_start: 0.8480 (mptp) cc_final: 0.8275 (mmtm) REVERT: G 152 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: G 468 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6179 (mp10) REVERT: H 3 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8259 (tp40) outliers start: 43 outliers final: 28 residues processed: 270 average time/residue: 0.5560 time to fit residues: 166.1359 Evaluate side-chains 279 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 144 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN B 105 GLN C 30 ASN D 465 GLN G 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099681 restraints weight = 17526.454| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.71 r_work: 0.3046 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16122 Z= 0.095 Angle : 0.487 6.103 21912 Z= 0.265 Chirality : 0.044 0.173 2574 Planarity : 0.004 0.036 2742 Dihedral : 4.699 46.379 2176 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.92 % Allowed : 15.34 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.99 (0.19), residues: 1992 helix: 2.54 (0.26), residues: 438 sheet: 0.68 (0.20), residues: 600 loop : -0.21 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.018 0.001 TYR F 49 PHE 0.010 0.001 PHE G 212 TRP 0.006 0.001 TRP C 36 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 (16086) covalent geometry : angle 0.48013 / 0.26 (21828) SS BOND : bond 0.00311 / 0.19 ( 24) SS BOND : angle 1.29409 / 0.94 ( 48) hydrogen bonds : bond 0.03749 / 2.47 ( 655) hydrogen bonds : angle 4.70164 / 3.48 ( 1755) link_NAG-ASN : bond 0.00111 / 0.07 ( 12) link_NAG-ASN : angle 1.58793 / 0.97 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.32 seconds wall clock time: 111 minutes 30.25 seconds (6690.25 seconds total)