Starting phenix.real_space_refine on Wed Mar 4 22:54:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512.map" model { file = "/net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1m_21512/03_2026/6w1m_21512_neut.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 50 5.16 5 C 11105 2.51 5 N 2710 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16885 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, I, L, O, R, J, M, P, S, K, N, Q, T Time building chain proxies: 3.67, per 1000 atoms: 0.22 Number of scatterers: 16885 At special positions: 0 Unit cell: (103.456, 106, 172.992, 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 50 16.00 O 3020 8.00 N 2710 7.00 C 11105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG H 1 " - " ASN A 148 " " NAG K 1 " - " ASN B 148 " " NAG N 1 " - " ASN C 148 " " NAG Q 1 " - " ASN D 148 " " NAG T 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 783.5 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 40.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.565A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.718A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.755A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 225 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.963A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 271 removed outlier: 4.283A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.824A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 398 through 415 removed outlier: 3.669A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 461 removed outlier: 3.613A pdb=" N MET A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.565A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.719A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.755A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 removed outlier: 3.963A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 271 removed outlier: 4.284A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.825A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 398 through 415 removed outlier: 3.669A pdb=" N LEU B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 461 removed outlier: 3.612A pdb=" N MET B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.565A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.719A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.754A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 225 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 3.963A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 271 removed outlier: 4.283A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.825A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 398 through 415 removed outlier: 3.669A pdb=" N LEU C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 461 removed outlier: 3.612A pdb=" N MET C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 20 removed outlier: 3.565A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.718A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 3.755A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D 225 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 removed outlier: 3.964A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 271 removed outlier: 4.283A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.825A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 398 through 415 removed outlier: 3.670A pdb=" N LEU D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 461 removed outlier: 3.612A pdb=" N MET D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.566A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.719A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 225 removed outlier: 3.754A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 225 " --> pdb=" O PHE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 240 removed outlier: 3.963A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 271 removed outlier: 4.283A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 258 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.825A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 323 Processing helix chain 'E' and resid 398 through 415 removed outlier: 3.669A pdb=" N LEU E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 461 removed outlier: 3.612A pdb=" N MET E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.929A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 131 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.929A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 131 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.929A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 131 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.929A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 131 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.929A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 131 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4838 1.33 - 1.45: 3170 1.45 - 1.57: 9267 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17350 Sorted by residual: bond pdb=" C06 S87 B 508 " pdb=" O01 S87 B 508 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" C06 S87 E 508 " pdb=" O01 S87 E 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C06 S87 C 508 " pdb=" O01 S87 C 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C06 S87 D 508 " pdb=" O01 S87 D 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C06 S87 A 508 " pdb=" O01 S87 A 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.97e+01 ... (remaining 17345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.06: 23575 6.06 - 12.12: 130 12.12 - 18.17: 0 18.17 - 24.23: 0 24.23 - 30.29: 10 Bond angle restraints: 23715 Sorted by residual: angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 137.58 -30.29 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 137.54 -30.25 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sigma weight residual 107.29 137.50 -30.21 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C3 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 107.29 137.49 -30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C3 NAG Q 1 " pdb=" C4 NAG Q 1 " pdb=" O4 NAG Q 1 " ideal model delta sigma weight residual 107.29 137.47 -30.18 3.00e+00 1.11e-01 1.01e+02 ... (remaining 23710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10040 21.43 - 42.86: 475 42.86 - 64.29: 80 64.29 - 85.71: 30 85.71 - 107.14: 20 Dihedral angle restraints: 10645 sinusoidal: 4765 harmonic: 5880 Sorted by residual: dihedral pdb=" CA ILE A 41 " pdb=" C ILE A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE E 41 " pdb=" C ILE E 41 " pdb=" N ASP E 42 " pdb=" CA ASP E 42 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE B 41 " pdb=" C ILE B 41 " pdb=" N ASP B 42 " pdb=" CA ASP B 42 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 10642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.527: 2805 0.527 - 1.055: 0 1.055 - 1.582: 5 1.582 - 2.110: 0 2.110 - 2.637: 10 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C4 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O4 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C4 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" C5 NAG T 1 " pdb=" O4 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 ... (remaining 2817 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " 0.023 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP D 168 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.023 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP A 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " 0.023 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP C 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.008 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5062 2.83 - 3.35: 14287 3.35 - 3.86: 26623 3.86 - 4.38: 29766 4.38 - 4.90: 50961 Nonbonded interactions: 126699 Sorted by model distance: nonbonded pdb=" O4 NAG O 1 " pdb=" O3 NAG O 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG L 1 " pdb=" O3 NAG L 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG F 1 " pdb=" O3 NAG F 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG I 1 " pdb=" O3 NAG I 2 " model vdw 2.310 2.432 nonbonded pdb=" O4 NAG R 1 " pdb=" O3 NAG R 2 " model vdw 2.310 2.432 ... (remaining 126694 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'H' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'I' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'K' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'L' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'N' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'O' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'Q' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'R' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'T' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.900 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.168 17375 Z= 0.466 Angle : 1.419 33.846 23775 Z= 0.622 Chirality : 0.173 2.637 2820 Planarity : 0.006 0.044 2855 Dihedral : 14.389 107.142 6815 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.27 % Allowed : 8.99 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.48 (0.13), residues: 1950 helix: -4.49 (0.07), residues: 750 sheet: -2.09 (0.22), residues: 395 loop : -3.40 (0.17), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 315 TYR 0.025 0.002 TYR D 67 PHE 0.021 0.003 PHE B 72 TRP 0.056 0.003 TRP D 168 HIS 0.005 0.002 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.01030 (17350) covalent geometry : angle 1.26762 (23715) hydrogen bonds : bond 0.31474 ( 635) hydrogen bonds : angle 9.74294 ( 1875) Misc. bond : bond 0.00034 ( 5) link_BETA1-4 : bond 0.04099 ( 15) link_BETA1-4 : angle 14.69448 ( 45) link_NAG-ASN : bond 0.00764 ( 5) link_NAG-ASN : angle 2.12988 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 300 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8563 (mmpt) cc_final: 0.8290 (ptmm) REVERT: A 268 ILE cc_start: 0.9102 (tp) cc_final: 0.8901 (tt) REVERT: A 311 GLN cc_start: 0.6625 (pm20) cc_final: 0.6244 (pm20) REVERT: A 313 LEU cc_start: 0.6972 (pt) cc_final: 0.6564 (pt) REVERT: A 411 HIS cc_start: 0.9036 (t70) cc_final: 0.8802 (t70) REVERT: B 267 ILE cc_start: 0.8711 (mt) cc_final: 0.8470 (pt) REVERT: B 311 GLN cc_start: 0.6626 (pm20) cc_final: 0.6384 (pm20) REVERT: B 313 LEU cc_start: 0.7246 (pt) cc_final: 0.6678 (pt) REVERT: B 314 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7768 (pt0) REVERT: B 411 HIS cc_start: 0.8991 (t70) cc_final: 0.8770 (t70) REVERT: B 417 ASP cc_start: 0.8604 (p0) cc_final: 0.8221 (t0) REVERT: C 264 VAL cc_start: 0.8230 (t) cc_final: 0.8024 (t) REVERT: C 267 ILE cc_start: 0.8772 (mt) cc_final: 0.8518 (pt) REVERT: C 311 GLN cc_start: 0.6439 (pm20) cc_final: 0.6168 (pm20) REVERT: C 314 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7693 (mm-40) REVERT: C 411 HIS cc_start: 0.8864 (t70) cc_final: 0.8508 (t-90) REVERT: C 417 ASP cc_start: 0.8690 (p0) cc_final: 0.8314 (t0) REVERT: D 311 GLN cc_start: 0.6258 (pm20) cc_final: 0.5885 (pm20) REVERT: D 314 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7654 (pt0) REVERT: D 411 HIS cc_start: 0.8832 (t70) cc_final: 0.8478 (t-90) REVERT: D 417 ASP cc_start: 0.8570 (p0) cc_final: 0.8227 (t0) REVERT: E 311 GLN cc_start: 0.6483 (pm20) cc_final: 0.5951 (pm20) REVERT: E 313 LEU cc_start: 0.7263 (pt) cc_final: 0.6810 (pt) REVERT: E 411 HIS cc_start: 0.8951 (t70) cc_final: 0.8713 (t70) REVERT: E 417 ASP cc_start: 0.8689 (p0) cc_final: 0.8329 (t0) REVERT: E 434 ASP cc_start: 0.8261 (t70) cc_final: 0.8014 (t0) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.1592 time to fit residues: 66.6919 Evaluate side-chains 195 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 205 ASN B 82 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 205 ASN C 82 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 205 ASN D 82 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 82 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.070697 restraints weight = 29286.473| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.87 r_work: 0.2692 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17375 Z= 0.191 Angle : 0.884 20.806 23775 Z= 0.400 Chirality : 0.053 0.413 2820 Planarity : 0.005 0.052 2855 Dihedral : 11.641 68.569 2950 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 11.06 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.48 (0.16), residues: 1950 helix: -1.74 (0.16), residues: 745 sheet: -2.09 (0.20), residues: 450 loop : -2.87 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 315 TYR 0.019 0.002 TYR D 448 PHE 0.012 0.001 PHE A 412 TRP 0.023 0.002 TRP B 168 HIS 0.005 0.001 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00426 (17350) covalent geometry : angle 0.80003 (23715) hydrogen bonds : bond 0.06634 ( 635) hydrogen bonds : angle 5.72657 ( 1875) Misc. bond : bond 0.00007 ( 5) link_BETA1-4 : bond 0.02301 ( 15) link_BETA1-4 : angle 8.35022 ( 45) link_NAG-ASN : bond 0.00492 ( 5) link_NAG-ASN : angle 4.15038 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 311 GLN cc_start: 0.6464 (pm20) cc_final: 0.6202 (pm20) REVERT: A 313 LEU cc_start: 0.7007 (pt) cc_final: 0.6639 (pt) REVERT: B 180 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8686 (pp) REVERT: B 417 ASP cc_start: 0.8492 (p0) cc_final: 0.8186 (t0) REVERT: C 180 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 411 HIS cc_start: 0.8868 (t70) cc_final: 0.8629 (t-90) REVERT: C 417 ASP cc_start: 0.8418 (p0) cc_final: 0.8099 (p0) REVERT: C 443 LEU cc_start: 0.8544 (mt) cc_final: 0.8180 (tt) REVERT: D 180 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8746 (pp) REVERT: D 311 GLN cc_start: 0.6147 (pm20) cc_final: 0.5882 (pm20) REVERT: D 411 HIS cc_start: 0.8793 (t70) cc_final: 0.8564 (t70) REVERT: E 310 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7998 (mtpp) REVERT: E 311 GLN cc_start: 0.6375 (pm20) cc_final: 0.5832 (pm20) REVERT: E 314 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: E 434 ASP cc_start: 0.8200 (t70) cc_final: 0.7957 (t0) REVERT: E 459 TRP cc_start: 0.6261 (t60) cc_final: 0.6023 (t60) outliers start: 66 outliers final: 24 residues processed: 265 average time/residue: 0.1139 time to fit residues: 46.7884 Evaluate side-chains 180 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 138 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 191 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 205 ASN B 101 ASN C 101 ASN C 205 ASN D 101 ASN D 183 ASN D 184 GLN E 101 ASN E 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071270 restraints weight = 29477.898| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.89 r_work: 0.2702 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17375 Z= 0.141 Angle : 0.747 19.013 23775 Z= 0.340 Chirality : 0.050 0.430 2820 Planarity : 0.004 0.033 2855 Dihedral : 10.081 59.707 2950 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.14 % Allowed : 12.04 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.57 (0.17), residues: 1950 helix: -0.51 (0.18), residues: 745 sheet: -2.05 (0.21), residues: 445 loop : -2.61 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 424 TYR 0.016 0.001 TYR A 448 PHE 0.009 0.001 PHE C 412 TRP 0.019 0.001 TRP E 320 HIS 0.011 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00302 (17350) covalent geometry : angle 0.67673 (23715) hydrogen bonds : bond 0.05421 ( 635) hydrogen bonds : angle 5.10539 ( 1875) Misc. bond : bond 0.00033 ( 5) link_BETA1-4 : bond 0.02139 ( 15) link_BETA1-4 : angle 7.17169 ( 45) link_NAG-ASN : bond 0.00138 ( 5) link_NAG-ASN : angle 2.34476 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8855 (pp) REVERT: A 311 GLN cc_start: 0.6569 (pm20) cc_final: 0.6365 (pm20) REVERT: B 9 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7986 (pm20) REVERT: B 103 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8560 (m-10) REVERT: B 180 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 417 ASP cc_start: 0.8514 (p0) cc_final: 0.8259 (t0) REVERT: C 180 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8538 (pp) REVERT: C 328 ARG cc_start: 0.6764 (mmp80) cc_final: 0.5453 (mmp80) REVERT: C 411 HIS cc_start: 0.8837 (t70) cc_final: 0.8634 (t70) REVERT: C 443 LEU cc_start: 0.8454 (mt) cc_final: 0.8160 (tt) REVERT: D 180 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8731 (pp) REVERT: E 310 LYS cc_start: 0.8228 (mtpp) cc_final: 0.8021 (mtpp) REVERT: E 311 GLN cc_start: 0.6406 (pm20) cc_final: 0.6100 (pm20) outliers start: 76 outliers final: 28 residues processed: 240 average time/residue: 0.1119 time to fit residues: 42.1767 Evaluate side-chains 185 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 171 optimal weight: 0.0020 chunk 191 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN E 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.072386 restraints weight = 29460.664| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.90 r_work: 0.2725 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17375 Z= 0.121 Angle : 0.702 17.835 23775 Z= 0.317 Chirality : 0.049 0.406 2820 Planarity : 0.004 0.035 2855 Dihedral : 8.445 54.836 2950 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.83 % Allowed : 13.57 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.18), residues: 1950 helix: 0.37 (0.19), residues: 745 sheet: -1.87 (0.21), residues: 440 loop : -2.39 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 315 TYR 0.011 0.001 TYR C 64 PHE 0.009 0.001 PHE C 412 TRP 0.014 0.001 TRP E 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00246 (17350) covalent geometry : angle 0.63748 (23715) hydrogen bonds : bond 0.04518 ( 635) hydrogen bonds : angle 4.75423 ( 1875) Misc. bond : bond 0.00038 ( 5) link_BETA1-4 : bond 0.02246 ( 15) link_BETA1-4 : angle 6.71372 ( 45) link_NAG-ASN : bond 0.00024 ( 5) link_NAG-ASN : angle 1.94684 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.651 Fit side-chains REVERT: A 180 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 311 GLN cc_start: 0.6798 (pm20) cc_final: 0.6401 (pm20) REVERT: B 103 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8537 (m-10) REVERT: B 180 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8588 (pp) REVERT: C 180 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8529 (pp) REVERT: C 443 LEU cc_start: 0.8491 (mt) cc_final: 0.8214 (tt) REVERT: D 180 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8680 (pp) REVERT: E 20 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8905 (mp) REVERT: E 310 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7998 (mtpp) REVERT: E 311 GLN cc_start: 0.6436 (pm20) cc_final: 0.6103 (pm20) outliers start: 52 outliers final: 20 residues processed: 213 average time/residue: 0.1201 time to fit residues: 39.8658 Evaluate side-chains 177 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 411 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 187 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 HIS E 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.068392 restraints weight = 29509.257| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.88 r_work: 0.2638 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17375 Z= 0.214 Angle : 0.750 18.346 23775 Z= 0.345 Chirality : 0.050 0.426 2820 Planarity : 0.004 0.041 2855 Dihedral : 8.064 56.556 2950 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.65 % Allowed : 14.01 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.18), residues: 1950 helix: 0.91 (0.20), residues: 750 sheet: -1.80 (0.21), residues: 445 loop : -2.28 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 315 TYR 0.013 0.001 TYR C 126 PHE 0.018 0.002 PHE B 153 TRP 0.027 0.001 TRP D 320 HIS 0.013 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00508 (17350) covalent geometry : angle 0.68904 (23715) hydrogen bonds : bond 0.04943 ( 635) hydrogen bonds : angle 4.70699 ( 1875) Misc. bond : bond 0.00020 ( 5) link_BETA1-4 : bond 0.02066 ( 15) link_BETA1-4 : angle 6.74090 ( 45) link_NAG-ASN : bond 0.00437 ( 5) link_NAG-ASN : angle 2.05201 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 0.690 Fit side-chains REVERT: A 311 GLN cc_start: 0.6784 (pm20) cc_final: 0.6556 (pm20) REVERT: A 320 TRP cc_start: 0.7111 (m100) cc_final: 0.6870 (m-10) REVERT: B 103 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: B 180 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8770 (pp) REVERT: C 180 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8615 (pp) REVERT: C 443 LEU cc_start: 0.8430 (mt) cc_final: 0.8158 (tt) REVERT: D 180 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8741 (pp) REVERT: D 311 GLN cc_start: 0.6249 (pm20) cc_final: 0.6010 (pm20) REVERT: E 310 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8078 (mtpp) REVERT: E 311 GLN cc_start: 0.6570 (pm20) cc_final: 0.6272 (pm20) outliers start: 67 outliers final: 50 residues processed: 209 average time/residue: 0.1238 time to fit residues: 40.1976 Evaluate side-chains 204 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 411 HIS Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 29 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 183 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.071011 restraints weight = 29401.652| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.90 r_work: 0.2694 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17375 Z= 0.119 Angle : 0.677 17.635 23775 Z= 0.309 Chirality : 0.047 0.388 2820 Planarity : 0.004 0.032 2855 Dihedral : 7.365 54.407 2950 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.40 % Allowed : 15.86 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.19), residues: 1950 helix: 1.40 (0.20), residues: 750 sheet: -1.71 (0.21), residues: 460 loop : -2.11 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 315 TYR 0.012 0.001 TYR C 64 PHE 0.008 0.001 PHE E 303 TRP 0.030 0.001 TRP D 320 HIS 0.013 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00251 (17350) covalent geometry : angle 0.61652 (23715) hydrogen bonds : bond 0.04028 ( 635) hydrogen bonds : angle 4.49691 ( 1875) Misc. bond : bond 0.00031 ( 5) link_BETA1-4 : bond 0.02282 ( 15) link_BETA1-4 : angle 6.42471 ( 45) link_NAG-ASN : bond 0.00030 ( 5) link_NAG-ASN : angle 1.55802 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.662 Fit side-chains REVERT: A 180 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 320 TRP cc_start: 0.7108 (m100) cc_final: 0.6855 (m-10) REVERT: A 459 TRP cc_start: 0.6333 (t60) cc_final: 0.5901 (m-10) REVERT: B 103 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: B 180 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8646 (pp) REVERT: C 180 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8587 (pp) REVERT: C 443 LEU cc_start: 0.8424 (mt) cc_final: 0.8151 (tt) REVERT: D 180 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8707 (pp) REVERT: D 311 GLN cc_start: 0.6126 (pm20) cc_final: 0.5903 (pm20) REVERT: D 322 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8318 (mmm160) REVERT: E 310 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7989 (mtpp) REVERT: E 311 GLN cc_start: 0.6453 (pm20) cc_final: 0.6151 (pm20) outliers start: 44 outliers final: 28 residues processed: 207 average time/residue: 0.1346 time to fit residues: 42.7761 Evaluate side-chains 187 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 411 HIS Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.0050 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 148 optimal weight: 0.0170 overall best weight: 0.8034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071051 restraints weight = 29436.017| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.88 r_work: 0.2694 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17375 Z= 0.121 Angle : 0.672 17.522 23775 Z= 0.307 Chirality : 0.047 0.389 2820 Planarity : 0.004 0.039 2855 Dihedral : 6.955 54.668 2950 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.94 % Allowed : 15.91 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.19), residues: 1950 helix: 1.73 (0.20), residues: 750 sheet: -1.64 (0.22), residues: 460 loop : -1.99 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 315 TYR 0.011 0.001 TYR B 64 PHE 0.007 0.001 PHE C 303 TRP 0.017 0.001 TRP E 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00261 (17350) covalent geometry : angle 0.61366 (23715) hydrogen bonds : bond 0.03883 ( 635) hydrogen bonds : angle 4.35616 ( 1875) Misc. bond : bond 0.00028 ( 5) link_BETA1-4 : bond 0.02249 ( 15) link_BETA1-4 : angle 6.29076 ( 45) link_NAG-ASN : bond 0.00099 ( 5) link_NAG-ASN : angle 1.44242 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 0.722 Fit side-chains REVERT: A 180 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 320 TRP cc_start: 0.7080 (m100) cc_final: 0.6829 (m-10) REVERT: B 180 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 180 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8622 (pp) REVERT: C 328 ARG cc_start: 0.6270 (mmp80) cc_final: 0.6068 (mmp80) REVERT: C 443 LEU cc_start: 0.8436 (mt) cc_final: 0.8168 (tt) REVERT: D 180 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8704 (pp) REVERT: E 311 GLN cc_start: 0.6487 (pm20) cc_final: 0.6177 (pm20) outliers start: 54 outliers final: 35 residues processed: 204 average time/residue: 0.1407 time to fit residues: 44.0557 Evaluate side-chains 192 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 411 HIS Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 56 optimal weight: 0.0050 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070663 restraints weight = 29522.299| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.88 r_work: 0.2688 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17375 Z= 0.130 Angle : 0.681 17.502 23775 Z= 0.310 Chirality : 0.047 0.391 2820 Planarity : 0.004 0.039 2855 Dihedral : 6.718 54.725 2950 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.56 % Allowed : 16.68 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1950 helix: 1.89 (0.20), residues: 750 sheet: -1.58 (0.22), residues: 460 loop : -1.91 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 315 TYR 0.011 0.001 TYR C 64 PHE 0.016 0.001 PHE B 142 TRP 0.024 0.001 TRP D 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00289 (17350) covalent geometry : angle 0.62375 (23715) hydrogen bonds : bond 0.03829 ( 635) hydrogen bonds : angle 4.28455 ( 1875) Misc. bond : bond 0.00024 ( 5) link_BETA1-4 : bond 0.02250 ( 15) link_BETA1-4 : angle 6.24797 ( 45) link_NAG-ASN : bond 0.00104 ( 5) link_NAG-ASN : angle 1.37676 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.673 Fit side-chains REVERT: A 180 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8787 (pp) REVERT: A 459 TRP cc_start: 0.6291 (t60) cc_final: 0.5892 (m-10) REVERT: B 180 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8657 (pp) REVERT: C 180 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8622 (pp) REVERT: C 443 LEU cc_start: 0.8420 (mt) cc_final: 0.8154 (tt) REVERT: D 180 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8670 (pp) REVERT: E 311 GLN cc_start: 0.6479 (pm20) cc_final: 0.6170 (pm20) outliers start: 47 outliers final: 37 residues processed: 190 average time/residue: 0.1294 time to fit residues: 38.0894 Evaluate side-chains 190 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 411 HIS Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 0.0770 chunk 121 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.067949 restraints weight = 29499.156| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.88 r_work: 0.2648 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17375 Z= 0.178 Angle : 0.717 17.885 23775 Z= 0.329 Chirality : 0.049 0.404 2820 Planarity : 0.004 0.058 2855 Dihedral : 6.842 55.858 2950 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.78 % Allowed : 16.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.20), residues: 1950 helix: 1.98 (0.20), residues: 750 sheet: -1.57 (0.22), residues: 465 loop : -1.87 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 315 TYR 0.011 0.001 TYR C 126 PHE 0.013 0.001 PHE B 153 TRP 0.027 0.001 TRP D 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00419 (17350) covalent geometry : angle 0.66148 (23715) hydrogen bonds : bond 0.04236 ( 635) hydrogen bonds : angle 4.35297 ( 1875) Misc. bond : bond 0.00013 ( 5) link_BETA1-4 : bond 0.02156 ( 15) link_BETA1-4 : angle 6.35136 ( 45) link_NAG-ASN : bond 0.00293 ( 5) link_NAG-ASN : angle 1.57567 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.676 Fit side-chains REVERT: A 180 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 320 TRP cc_start: 0.7268 (m100) cc_final: 0.6638 (m-10) REVERT: A 459 TRP cc_start: 0.6366 (t60) cc_final: 0.5869 (m-10) REVERT: B 180 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8720 (pp) REVERT: C 180 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8672 (pp) REVERT: C 443 LEU cc_start: 0.8427 (mt) cc_final: 0.8163 (tt) REVERT: D 180 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8710 (pp) REVERT: E 311 GLN cc_start: 0.6553 (pm20) cc_final: 0.6121 (pm20) outliers start: 51 outliers final: 35 residues processed: 189 average time/residue: 0.1295 time to fit residues: 37.4512 Evaluate side-chains 186 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 411 HIS Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.069695 restraints weight = 29487.526| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.88 r_work: 0.2688 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17375 Z= 0.124 Angle : 0.689 17.308 23775 Z= 0.315 Chirality : 0.047 0.391 2820 Planarity : 0.004 0.056 2855 Dihedral : 6.562 54.219 2950 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.85 % Allowed : 17.66 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.20), residues: 1950 helix: 2.12 (0.20), residues: 750 sheet: -1.50 (0.22), residues: 460 loop : -1.81 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 328 TYR 0.012 0.001 TYR C 64 PHE 0.010 0.001 PHE B 142 TRP 0.027 0.001 TRP D 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00273 (17350) covalent geometry : angle 0.63497 (23715) hydrogen bonds : bond 0.03689 ( 635) hydrogen bonds : angle 4.26210 ( 1875) Misc. bond : bond 0.00024 ( 5) link_BETA1-4 : bond 0.02276 ( 15) link_BETA1-4 : angle 6.17401 ( 45) link_NAG-ASN : bond 0.00018 ( 5) link_NAG-ASN : angle 1.24687 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.700 Fit side-chains REVERT: A 180 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 320 TRP cc_start: 0.7211 (m100) cc_final: 0.6648 (m-10) REVERT: A 459 TRP cc_start: 0.6398 (t60) cc_final: 0.5895 (m-10) REVERT: B 180 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8677 (pp) REVERT: C 180 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8662 (pp) REVERT: C 443 LEU cc_start: 0.8435 (mt) cc_final: 0.8186 (tt) REVERT: D 180 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8672 (pp) REVERT: E 311 GLN cc_start: 0.6461 (pm20) cc_final: 0.6206 (pm20) outliers start: 34 outliers final: 28 residues processed: 182 average time/residue: 0.1331 time to fit residues: 37.3788 Evaluate side-chains 184 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069913 restraints weight = 29619.355| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.89 r_work: 0.2691 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17375 Z= 0.124 Angle : 0.688 17.225 23775 Z= 0.314 Chirality : 0.047 0.392 2820 Planarity : 0.004 0.050 2855 Dihedral : 6.489 54.554 2950 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.18 % Allowed : 17.33 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.20), residues: 1950 helix: 2.25 (0.20), residues: 750 sheet: -1.45 (0.22), residues: 460 loop : -1.74 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 315 TYR 0.011 0.001 TYR C 64 PHE 0.020 0.001 PHE B 233 TRP 0.029 0.001 TRP D 320 HIS 0.012 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00273 (17350) covalent geometry : angle 0.63491 (23715) hydrogen bonds : bond 0.03617 ( 635) hydrogen bonds : angle 4.18296 ( 1875) Misc. bond : bond 0.00020 ( 5) link_BETA1-4 : bond 0.02258 ( 15) link_BETA1-4 : angle 6.11187 ( 45) link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 1.21439 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4041.48 seconds wall clock time: 69 minutes 58.55 seconds (4198.55 seconds total)