Starting phenix.real_space_refine on Mon Oct 26 09:01:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyn_30501/10_2026/7cyn_30501.map" } resolution = 4.2 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= 0.003 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 110 5.16 5 C 13252 2.51 5 N 3424 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20432 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6319 Classifications: {'peptide': 786} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 750} Chain breaks: 2 Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "E" 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 chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, D, F Time building chain proxies: 8.56, per 1000 atoms: 0.42 Number of scatterers: 20432 At special positions: 0 Unit cell: (97.11, 130.725, 171.81, 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 110 16.00 O 3646 8.00 N 3424 7.00 C 13252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 601 " - " ASN C 251 " " NAG D 601 " - " ASN D 251 " " NAG E 1 " - " ASN C 272 " " NAG F 1 " - " ASN D 272 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 800.3 milliseconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 39.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.804A pdb=" N ALA A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.835A pdb=" N ASN A 276 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.040A pdb=" N LEU A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Proline residue: A 392 - end of helix removed outlier: 4.329A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.632A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 removed outlier: 4.034A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 692 through 698 removed outlier: 3.771A pdb=" N GLN A 696 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 838 through 864 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.805A pdb=" N ALA B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.835A pdb=" N ASN B 276 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 363 through 369 removed outlier: 4.041A pdb=" N LEU B 369 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Proline residue: B 392 - end of helix removed outlier: 4.329A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.632A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 removed outlier: 4.034A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 692 through 698 removed outlier: 3.770A pdb=" N GLN B 696 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 838 through 864 Processing helix chain 'C' and resid 46 through 89 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 134 removed outlier: 3.948A pdb=" N LEU C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Proline residue: C 127 - end of helix removed outlier: 3.542A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 157 through 199 Proline residue: C 163 - end of helix removed outlier: 4.660A pdb=" N VAL C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Proline residue: C 174 - end of helix Processing helix chain 'C' and resid 213 through 235 removed outlier: 3.885A pdb=" N VAL C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 233 " --> pdb=" O HIS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.955A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 306 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.534A pdb=" N GLU C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 339 through 359 Proline residue: C 345 - end of helix Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.486A pdb=" N SER C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 374 through 396 removed outlier: 3.586A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 422 removed outlier: 3.523A pdb=" N ALA C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 461 removed outlier: 3.690A pdb=" N TYR C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 488 Processing helix chain 'C' and resid 494 through 518 removed outlier: 3.525A pdb=" N LEU C 518 " --> pdb=" O MET C 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 89 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.949A pdb=" N LEU D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Proline residue: D 127 - end of helix removed outlier: 3.541A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 157 through 199 Proline residue: D 163 - end of helix removed outlier: 4.660A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Processing helix chain 'D' and resid 213 through 235 removed outlier: 3.886A pdb=" N VAL D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 233 " --> pdb=" O HIS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.955A pdb=" N THR D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 306 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 359 Proline residue: D 345 - end of helix Processing helix chain 'D' and resid 365 through 370 removed outlier: 4.487A pdb=" N SER D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 374 through 396 removed outlier: 3.585A pdb=" N LEU D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 422 removed outlier: 3.523A pdb=" N ALA D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 461 removed outlier: 3.691A pdb=" N TYR D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 488 Processing helix chain 'D' and resid 494 through 518 removed outlier: 3.524A pdb=" N LEU D 518 " --> pdb=" O MET D 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.626A pdb=" N ASN A 69 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 70 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 132 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 177 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 209 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 230 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 319 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 376 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 375 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 402 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 426 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 498 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 547 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 601 " --> pdb=" O GLU A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.530A pdb=" N ILE A 163 " --> pdb=" O SER A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 359 removed outlier: 6.642A pdb=" N ALA A 358 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 411 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 729 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.627A pdb=" N ASN B 69 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 70 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 132 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU B 177 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 209 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 230 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 319 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 376 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 375 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 402 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 426 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 498 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 547 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 601 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.530A pdb=" N ILE B 163 " --> pdb=" O SER B 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 359 removed outlier: 6.642A pdb=" N ALA B 358 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 411 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 729 684 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6425 1.34 - 1.46: 4580 1.46 - 1.58: 9737 1.58 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 20912 Sorted by residual: bond pdb=" C PRO D 208 " pdb=" N PRO D 209 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.34e+00 bond pdb=" C PRO C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.26e+00 bond pdb=" C VAL C 403 " pdb=" N PRO C 404 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.26e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 20907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 28049 1.90 - 3.80: 274 3.80 - 5.70: 45 5.70 - 7.59: 4 7.59 - 9.49: 2 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N ILE A 573 " pdb=" CA ILE A 573 " pdb=" C ILE A 573 " ideal model delta sigma weight residual 111.88 108.05 3.83 1.06e+00 8.90e-01 1.30e+01 angle pdb=" N ILE B 573 " pdb=" CA ILE B 573 " pdb=" C ILE B 573 " ideal model delta sigma weight residual 111.88 108.07 3.81 1.06e+00 8.90e-01 1.29e+01 angle pdb=" C VAL D 117 " pdb=" N THR D 118 " pdb=" CA THR D 118 " ideal model delta sigma weight residual 120.06 123.71 -3.65 1.19e+00 7.06e-01 9.42e+00 angle pdb=" C VAL C 117 " pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 120.06 123.71 -3.65 1.19e+00 7.06e-01 9.39e+00 angle pdb=" CA LEU B 786 " pdb=" CB LEU B 786 " pdb=" CG LEU B 786 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 11446 17.22 - 34.44: 860 34.44 - 51.66: 172 51.66 - 68.88: 20 68.88 - 86.10: 18 Dihedral angle restraints: 12516 sinusoidal: 5046 harmonic: 7470 Sorted by residual: dihedral pdb=" CB CYS B 789 " pdb=" SG CYS B 789 " pdb=" SG CYS B 833 " pdb=" CB CYS B 833 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS A 789 " pdb=" SG CYS A 789 " pdb=" SG CYS A 833 " pdb=" CB CYS A 833 " ideal model delta sinusoidal sigma weight residual -86.00 -161.68 75.68 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS D 260 " pdb=" SG CYS D 260 " pdb=" SG CYS D 368 " pdb=" CB CYS D 368 " ideal model delta sinusoidal sigma weight residual 93.00 143.76 -50.76 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 12513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1878 0.028 - 0.057: 974 0.057 - 0.085: 258 0.085 - 0.113: 124 0.113 - 0.141: 30 Chirality restraints: 3264 Sorted by residual: chirality pdb=" CA THR D 126 " pdb=" N THR D 126 " pdb=" C THR D 126 " pdb=" CB THR D 126 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 142 " pdb=" N ILE A 142 " pdb=" C ILE A 142 " pdb=" CB ILE A 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 251 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 3261 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 118 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO D 119 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 118 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO C 119 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 207 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 208 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " 0.026 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1515 2.74 - 3.28: 20870 3.28 - 3.82: 34244 3.82 - 4.36: 40363 4.36 - 4.90: 67848 Nonbonded interactions: 164840 Sorted by model distance: nonbonded pdb=" OD1 ASN A 733 " pdb=" ND2 ASN A 757 " model vdw 2.204 3.120 nonbonded pdb=" OD1 ASN B 733 " pdb=" ND2 ASN B 757 " model vdw 2.204 3.120 nonbonded pdb=" O ASN B 431 " pdb=" ND2 ASN B 503 " model vdw 2.218 3.120 nonbonded pdb=" O ASN A 431 " pdb=" ND2 ASN A 503 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR D 99 " pdb=" OE1 GLU D 156 " model vdw 2.227 3.040 ... (remaining 164835 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.820 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.660 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.002 0.050 20936 Z= 0.115 Angle : 0.519 9.492 28428 Z= 0.289 Chirality : 0.039 0.141 3264 Planarity : 0.003 0.050 3548 Dihedral : 12.561 86.102 7634 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -2.47 (0.16), residues: 2522 helix: -0.50 (0.17), residues: 870 sheet: -2.68 (0.33), residues: 260 loop : -2.24 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.014 0.001 TYR D 190 PHE 0.013 0.001 PHE C 346 TRP 0.006 0.000 TRP A 793 HIS 0.004 0.000 HIS C 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 (20912) covalent geometry : angle 0.51911 / 0.29 (28374) SS BOND : bond 0.00117 / 0.07 ( 18) SS BOND : angle 0.37525 / 0.21 ( 36) hydrogen bonds : bond 0.15422 / 10.21 ( 684) hydrogen bonds : angle 5.60707 / 3.83 ( 1902) link_BETA1-4 : bond 0.00301 / 0.21 ( 2) link_BETA1-4 : angle 0.72373 / 0.46 ( 6) link_NAG-ASN : bond 0.00234 / 0.14 ( 4) link_NAG-ASN : angle 0.99871 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8641 (tp) cc_final: 0.8438 (tp) REVERT: A 500 LEU cc_start: 0.9139 (mt) cc_final: 0.8745 (mt) REVERT: A 690 PHE cc_start: 0.6363 (t80) cc_final: 0.6023 (t80) REVERT: A 779 LEU cc_start: 0.7682 (mp) cc_final: 0.7308 (mp) REVERT: A 848 SER cc_start: 0.8940 (m) cc_final: 0.8662 (p) REVERT: B 302 LEU cc_start: 0.8745 (mt) cc_final: 0.8503 (mt) REVERT: B 779 LEU cc_start: 0.7996 (mp) cc_final: 0.7732 (mp) REVERT: C 128 VAL cc_start: 0.8460 (m) cc_final: 0.8191 (p) REVERT: C 170 MET cc_start: 0.5838 (tpt) cc_final: 0.5407 (tpt) REVERT: D 128 VAL cc_start: 0.8501 (m) cc_final: 0.8288 (p) REVERT: D 384 LEU cc_start: 0.8725 (mt) cc_final: 0.8409 (pp) outliers start: 2 outliers final: 0 residues processed: 453 average time/residue: 0.1228 time to fit residues: 89.7264 Evaluate side-chains 287 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 0.0870 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 overall best weight: 2.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 640 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044564 restraints weight = 147185.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.045468 restraints weight = 115305.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046178 restraints weight = 95586.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.046688 restraints weight = 82576.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047067 restraints weight = 74238.360| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20936 Z= 0.128 Angle : 0.618 9.711 28428 Z= 0.304 Chirality : 0.043 0.221 3264 Planarity : 0.004 0.056 3548 Dihedral : 3.812 22.581 2746 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -1.61 (0.17), residues: 2522 helix: 0.26 (0.17), residues: 894 sheet: -2.56 (0.32), residues: 272 loop : -1.68 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 376 TYR 0.012 0.001 TYR A 751 PHE 0.023 0.001 PHE C 346 TRP 0.022 0.001 TRP D 476 HIS 0.007 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (20912) covalent geometry : angle 0.61779 / 0.30 (28374) SS BOND : bond 0.00763 / 0.50 ( 18) SS BOND : angle 0.70150 / 0.41 ( 36) hydrogen bonds : bond 0.03687 / 2.53 ( 684) hydrogen bonds : angle 4.20769 / 2.87 ( 1902) link_BETA1-4 : bond 0.00456 / 0.31 ( 2) link_BETA1-4 : angle 0.83898 / 0.63 ( 6) link_NAG-ASN : bond 0.00323 / 0.19 ( 4) link_NAG-ASN : angle 0.94919 / 0.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.9440 (m-30) cc_final: 0.9141 (p0) REVERT: A 309 TRP cc_start: 0.8565 (m-10) cc_final: 0.7910 (m-10) REVERT: A 417 PHE cc_start: 0.9473 (m-80) cc_final: 0.9056 (m-80) REVERT: A 498 LEU cc_start: 0.9812 (tp) cc_final: 0.9565 (tp) REVERT: A 602 MET cc_start: 0.8918 (mpp) cc_final: 0.8661 (mpp) REVERT: A 603 MET cc_start: 0.9365 (tmm) cc_final: 0.9099 (tmm) REVERT: A 711 LEU cc_start: 0.9148 (tp) cc_final: 0.8899 (tt) REVERT: A 714 VAL cc_start: 0.8154 (m) cc_final: 0.7718 (m) REVERT: B 275 ASN cc_start: 0.9581 (m110) cc_final: 0.9358 (p0) REVERT: B 302 LEU cc_start: 0.9622 (mt) cc_final: 0.9333 (mt) REVERT: B 417 PHE cc_start: 0.9340 (m-80) cc_final: 0.8899 (m-80) REVERT: B 498 LEU cc_start: 0.9727 (tp) cc_final: 0.9518 (tp) REVERT: B 603 MET cc_start: 0.9354 (tmm) cc_final: 0.9066 (tmm) REVERT: B 761 MET cc_start: 0.7952 (tmm) cc_final: 0.7372 (tmm) REVERT: B 777 MET cc_start: 0.8867 (tpt) cc_final: 0.8665 (tpp) REVERT: B 779 LEU cc_start: 0.9081 (mp) cc_final: 0.8569 (mp) REVERT: C 72 MET cc_start: 0.9341 (ppp) cc_final: 0.8500 (tmm) REVERT: C 73 LEU cc_start: 0.9760 (tp) cc_final: 0.9490 (tp) REVERT: C 84 MET cc_start: 0.9589 (tmm) cc_final: 0.9373 (tmm) REVERT: C 108 ASP cc_start: 0.9359 (m-30) cc_final: 0.9032 (m-30) REVERT: C 138 MET cc_start: 0.9444 (tpt) cc_final: 0.9196 (tpp) REVERT: C 170 MET cc_start: 0.8194 (tpt) cc_final: 0.7963 (tpt) REVERT: C 220 PHE cc_start: 0.9461 (m-10) cc_final: 0.9257 (m-10) REVERT: C 306 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8605 (tt) REVERT: C 476 TRP cc_start: 0.9291 (t60) cc_final: 0.8811 (t60) REVERT: D 108 ASP cc_start: 0.9350 (m-30) cc_final: 0.8995 (m-30) REVERT: D 306 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8621 (tt) REVERT: D 384 LEU cc_start: 0.9053 (mt) cc_final: 0.8720 (pp) REVERT: D 476 TRP cc_start: 0.9252 (t60) cc_final: 0.8946 (t60) outliers start: 4 outliers final: 1 residues processed: 355 average time/residue: 0.1151 time to fit residues: 67.5939 Evaluate side-chains 260 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [235, 128, 199, 145, 55, 117, 112, 140, 143, 33, 6] chunk 235 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 199 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 140 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 33 optimal weight: 0.0470 chunk 6 optimal weight: 30.0000 overall best weight: 2.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.055124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043668 restraints weight = 150675.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044573 restraints weight = 117233.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.045241 restraints weight = 96777.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.045763 restraints weight = 83598.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046138 restraints weight = 74556.813| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20936 Z= 0.115 Angle : 0.571 8.290 28428 Z= 0.282 Chirality : 0.042 0.214 3264 Planarity : 0.004 0.053 3548 Dihedral : 3.870 22.184 2746 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -1.13 (0.17), residues: 2522 helix: 0.70 (0.18), residues: 896 sheet: -2.16 (0.36), residues: 236 loop : -1.50 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 784 TYR 0.012 0.001 TYR A 751 PHE 0.018 0.001 PHE C 346 TRP 0.010 0.001 TRP C 176 HIS 0.006 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20912) covalent geometry : angle 0.57044 / 0.28 (28374) SS BOND : bond 0.00283 / 0.18 ( 18) SS BOND : angle 0.70498 / 0.40 ( 36) hydrogen bonds : bond 0.03195 / 2.20 ( 684) hydrogen bonds : angle 4.00674 / 2.74 ( 1902) link_BETA1-4 : bond 0.00091 / 0.06 ( 2) link_BETA1-4 : angle 0.97863 / 0.65 ( 6) link_NAG-ASN : bond 0.00255 / 0.15 ( 4) link_NAG-ASN : angle 1.05329 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.9503 (m-30) cc_final: 0.9206 (p0) REVERT: A 417 PHE cc_start: 0.9462 (m-80) cc_final: 0.9106 (m-80) REVERT: A 602 MET cc_start: 0.8920 (mpp) cc_final: 0.8613 (mpp) REVERT: A 711 LEU cc_start: 0.9173 (tp) cc_final: 0.8915 (tt) REVERT: A 714 VAL cc_start: 0.8365 (m) cc_final: 0.7932 (m) REVERT: A 761 MET cc_start: 0.7988 (tmm) cc_final: 0.7767 (tmm) REVERT: A 785 PHE cc_start: 0.8543 (m-80) cc_final: 0.8300 (m-80) REVERT: B 302 LEU cc_start: 0.9652 (mt) cc_final: 0.9342 (mt) REVERT: B 309 TRP cc_start: 0.8636 (m-10) cc_final: 0.8057 (m-10) REVERT: B 402 LEU cc_start: 0.9520 (tp) cc_final: 0.9267 (tp) REVERT: B 417 PHE cc_start: 0.9395 (m-80) cc_final: 0.8988 (m-80) REVERT: B 498 LEU cc_start: 0.9733 (tp) cc_final: 0.9434 (tp) REVERT: B 603 MET cc_start: 0.9310 (tmm) cc_final: 0.9069 (tmm) REVERT: B 690 PHE cc_start: 0.8846 (t80) cc_final: 0.8546 (t80) REVERT: B 761 MET cc_start: 0.8268 (tmm) cc_final: 0.7653 (tmm) REVERT: B 779 LEU cc_start: 0.9226 (mp) cc_final: 0.8759 (mp) REVERT: B 785 PHE cc_start: 0.8586 (m-80) cc_final: 0.8302 (m-80) REVERT: C 72 MET cc_start: 0.9390 (ppp) cc_final: 0.9060 (ppp) REVERT: C 84 MET cc_start: 0.9558 (tmm) cc_final: 0.9315 (tmm) REVERT: C 108 ASP cc_start: 0.9359 (m-30) cc_final: 0.8984 (m-30) REVERT: C 139 MET cc_start: 0.9575 (mmm) cc_final: 0.9232 (mmm) REVERT: C 170 MET cc_start: 0.8077 (tpt) cc_final: 0.7824 (tpt) REVERT: C 179 MET cc_start: 0.9507 (ptm) cc_final: 0.9237 (ptm) REVERT: C 306 LEU cc_start: 0.8893 (tt) cc_final: 0.8534 (tp) REVERT: C 476 TRP cc_start: 0.9301 (t60) cc_final: 0.8675 (t60) REVERT: D 72 MET cc_start: 0.9274 (ppp) cc_final: 0.9046 (ppp) REVERT: D 138 MET cc_start: 0.9474 (tpp) cc_final: 0.9032 (tpt) REVERT: D 139 MET cc_start: 0.9696 (mmm) cc_final: 0.9340 (mmm) REVERT: D 186 MET cc_start: 0.9168 (mmp) cc_final: 0.8934 (mmp) REVERT: D 306 LEU cc_start: 0.8749 (tt) cc_final: 0.8307 (tt) REVERT: D 384 LEU cc_start: 0.9009 (mt) cc_final: 0.8709 (pp) REVERT: D 476 TRP cc_start: 0.9347 (t60) cc_final: 0.8794 (t60) REVERT: D 483 PHE cc_start: 0.9696 (t80) cc_final: 0.9407 (t80) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.1140 time to fit residues: 61.0602 Evaluate side-chains 235 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [73, 41, 108, 141, 247, 96, 72, 165, 125, 172, 85] chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 141 optimal weight: 0.0370 chunk 247 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 85 optimal weight: 0.0070 overall best weight: 2.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043025 restraints weight = 152015.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043919 restraints weight = 117379.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044574 restraints weight = 96982.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045071 restraints weight = 83670.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.045352 restraints weight = 74662.728| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20936 Z= 0.119 Angle : 0.580 7.754 28428 Z= 0.284 Chirality : 0.042 0.245 3264 Planarity : 0.004 0.054 3548 Dihedral : 3.899 22.707 2746 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.87 (0.17), residues: 2522 helix: 0.91 (0.18), residues: 894 sheet: -2.37 (0.33), residues: 272 loop : -1.22 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 736 TYR 0.013 0.001 TYR A 751 PHE 0.017 0.001 PHE C 297 TRP 0.022 0.001 TRP A 635 HIS 0.006 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (20912) covalent geometry : angle 0.57938 / 0.28 (28374) SS BOND : bond 0.00205 / 0.11 ( 18) SS BOND : angle 0.66269 / 0.38 ( 36) hydrogen bonds : bond 0.03081 / 2.13 ( 684) hydrogen bonds : angle 3.93909 / 2.69 ( 1902) link_BETA1-4 : bond 0.00069 / 0.05 ( 2) link_BETA1-4 : angle 1.01124 / 0.69 ( 6) link_NAG-ASN : bond 0.00240 / 0.14 ( 4) link_NAG-ASN : angle 1.09201 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.9532 (m-30) cc_final: 0.9257 (p0) REVERT: A 417 PHE cc_start: 0.9436 (m-80) cc_final: 0.9100 (m-80) REVERT: A 602 MET cc_start: 0.8836 (mpp) cc_final: 0.8561 (mpp) REVERT: B 302 LEU cc_start: 0.9682 (mt) cc_final: 0.9348 (mt) REVERT: B 402 LEU cc_start: 0.9565 (tp) cc_final: 0.9322 (tp) REVERT: B 417 PHE cc_start: 0.9429 (m-80) cc_final: 0.8988 (m-80) REVERT: B 498 LEU cc_start: 0.9736 (tp) cc_final: 0.9421 (tp) REVERT: B 635 TRP cc_start: 0.8824 (m-90) cc_final: 0.8067 (m-90) REVERT: B 690 PHE cc_start: 0.8671 (t80) cc_final: 0.8432 (t80) REVERT: B 761 MET cc_start: 0.8326 (tmm) cc_final: 0.7752 (tmm) REVERT: B 777 MET cc_start: 0.8852 (tpt) cc_final: 0.8504 (tpp) REVERT: B 779 LEU cc_start: 0.9101 (mp) cc_final: 0.8814 (mp) REVERT: B 785 PHE cc_start: 0.8594 (m-80) cc_final: 0.8278 (m-80) REVERT: C 72 MET cc_start: 0.9368 (ppp) cc_final: 0.9040 (ppp) REVERT: C 84 MET cc_start: 0.9556 (tmm) cc_final: 0.9303 (tmm) REVERT: C 139 MET cc_start: 0.9622 (mmm) cc_final: 0.9401 (mmm) REVERT: C 306 LEU cc_start: 0.8702 (tt) cc_final: 0.8382 (tp) REVERT: C 476 TRP cc_start: 0.9364 (t60) cc_final: 0.8744 (t60) REVERT: D 72 MET cc_start: 0.9319 (ppp) cc_final: 0.9031 (ppp) REVERT: D 120 ILE cc_start: 0.8849 (mp) cc_final: 0.8640 (mp) REVERT: D 138 MET cc_start: 0.9477 (tpp) cc_final: 0.8997 (tpt) REVERT: D 139 MET cc_start: 0.9543 (mmm) cc_final: 0.9330 (mmm) REVERT: D 306 LEU cc_start: 0.8672 (tt) cc_final: 0.8310 (tp) REVERT: D 384 LEU cc_start: 0.9030 (mt) cc_final: 0.8712 (pp) REVERT: D 476 TRP cc_start: 0.9352 (t60) cc_final: 0.8831 (t60) REVERT: D 483 PHE cc_start: 0.9693 (t80) cc_final: 0.9405 (t80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1119 time to fit residues: 57.8186 Evaluate side-chains 218 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [154, 96, 100, 66, 103, 196, 67, 20, 213, 136, 230] chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 337 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 820 HIS B 167 ASN B 181 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.049252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038930 restraints weight = 167899.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039761 restraints weight = 127244.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040381 restraints weight = 103452.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.040775 restraints weight = 88363.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041148 restraints weight = 79112.976| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 20936 Z= 0.246 Angle : 0.781 9.911 28428 Z= 0.381 Chirality : 0.044 0.228 3264 Planarity : 0.005 0.051 3548 Dihedral : 4.581 24.217 2746 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2522 helix: 0.77 (0.17), residues: 906 sheet: -2.50 (0.31), residues: 272 loop : -1.07 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 723 TYR 0.018 0.002 TYR C 349 PHE 0.020 0.002 PHE B 794 TRP 0.016 0.002 TRP C 476 HIS 0.010 0.002 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (20912) covalent geometry : angle 0.77837 / 0.38 (28374) SS BOND : bond 0.00831 / 0.32 ( 18) SS BOND : angle 1.70183 / 1.01 ( 36) hydrogen bonds : bond 0.03639 / 2.48 ( 684) hydrogen bonds : angle 4.37666 / 3.01 ( 1902) link_BETA1-4 : bond 0.00812 / 0.56 ( 2) link_BETA1-4 : angle 1.75539 / 1.38 ( 6) link_NAG-ASN : bond 0.00903 / 0.56 ( 4) link_NAG-ASN : angle 1.76619 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.9666 (tp) cc_final: 0.9463 (tp) REVERT: A 417 PHE cc_start: 0.9537 (m-80) cc_final: 0.9236 (m-80) REVERT: A 602 MET cc_start: 0.8916 (mpp) cc_final: 0.8635 (mpp) REVERT: A 635 TRP cc_start: 0.9189 (m-90) cc_final: 0.8821 (m-90) REVERT: A 777 MET cc_start: 0.8949 (tpt) cc_final: 0.8628 (tpt) REVERT: A 785 PHE cc_start: 0.8994 (m-80) cc_final: 0.8661 (m-80) REVERT: B 111 MET cc_start: 0.6469 (mmm) cc_final: 0.6124 (mmm) REVERT: B 402 LEU cc_start: 0.9644 (tp) cc_final: 0.9414 (tp) REVERT: B 417 PHE cc_start: 0.9502 (m-80) cc_final: 0.9174 (m-80) REVERT: B 498 LEU cc_start: 0.9729 (tp) cc_final: 0.9490 (tp) REVERT: B 761 MET cc_start: 0.8587 (tmm) cc_final: 0.8209 (tmm) REVERT: B 777 MET cc_start: 0.8954 (tpt) cc_final: 0.8626 (tpt) REVERT: B 779 LEU cc_start: 0.9267 (mp) cc_final: 0.8813 (mp) REVERT: B 785 PHE cc_start: 0.8793 (m-80) cc_final: 0.8292 (m-10) REVERT: B 847 ILE cc_start: 0.9435 (tt) cc_final: 0.9216 (pt) REVERT: C 73 LEU cc_start: 0.9804 (tp) cc_final: 0.9573 (tp) REVERT: C 139 MET cc_start: 0.9640 (mmm) cc_final: 0.9404 (mmm) REVERT: C 186 MET cc_start: 0.9043 (mmp) cc_final: 0.8828 (mmp) REVERT: C 220 PHE cc_start: 0.9458 (m-10) cc_final: 0.9240 (m-10) REVERT: C 476 TRP cc_start: 0.9519 (t60) cc_final: 0.9047 (t60) REVERT: C 514 MET cc_start: 0.8804 (mmt) cc_final: 0.8407 (mmm) REVERT: D 72 MET cc_start: 0.9371 (ppp) cc_final: 0.9020 (ppp) REVERT: D 138 MET cc_start: 0.9518 (tpp) cc_final: 0.9065 (tpp) REVERT: D 139 MET cc_start: 0.9516 (mmm) cc_final: 0.9227 (mmm) REVERT: D 186 MET cc_start: 0.9257 (mmp) cc_final: 0.9008 (mmp) REVERT: D 220 PHE cc_start: 0.9557 (m-10) cc_final: 0.9290 (m-10) REVERT: D 301 LEU cc_start: 0.9702 (mm) cc_final: 0.9500 (tt) REVERT: D 476 TRP cc_start: 0.9373 (t60) cc_final: 0.8599 (t60) outliers start: 2 outliers final: 1 residues processed: 260 average time/residue: 0.1183 time to fit residues: 51.2653 Evaluate side-chains 188 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [54, 46, 133, 43, 134, 108, 121, 139, 114, 110, 106] chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 108 optimal weight: 0.0870 chunk 121 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 181 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040928 restraints weight = 170436.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041826 restraints weight = 125260.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.042486 restraints weight = 99308.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042994 restraints weight = 83674.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043346 restraints weight = 73122.045| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20936 Z= 0.177 Angle : 0.663 7.918 28428 Z= 0.326 Chirality : 0.044 0.306 3264 Planarity : 0.004 0.045 3548 Dihedral : 4.491 25.792 2746 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.04 % Allowed : 1.14 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.63 (0.17), residues: 2522 helix: 0.95 (0.18), residues: 914 sheet: -2.54 (0.31), residues: 270 loop : -0.89 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 784 TYR 0.027 0.001 TYR D 146 PHE 0.028 0.001 PHE C 483 TRP 0.021 0.002 TRP B 796 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (20912) covalent geometry : angle 0.65641 / 0.32 (28374) SS BOND : bond 0.00827 / 0.53 ( 18) SS BOND : angle 1.86157 / 1.07 ( 36) hydrogen bonds : bond 0.03360 / 2.32 ( 684) hydrogen bonds : angle 4.30013 / 2.95 ( 1902) link_BETA1-4 : bond 0.00823 / 0.58 ( 2) link_BETA1-4 : angle 1.87355 / 1.39 ( 6) link_NAG-ASN : bond 0.00476 / 0.30 ( 4) link_NAG-ASN : angle 3.06543 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6813 (mmm) cc_final: 0.6364 (mmm) REVERT: A 417 PHE cc_start: 0.9486 (m-80) cc_final: 0.9194 (m-80) REVERT: A 498 LEU cc_start: 0.9788 (tp) cc_final: 0.9482 (tp) REVERT: A 602 MET cc_start: 0.8828 (mpp) cc_final: 0.8495 (mpp) REVERT: A 635 TRP cc_start: 0.9139 (m-90) cc_final: 0.8642 (m-90) REVERT: A 777 MET cc_start: 0.9066 (tpt) cc_final: 0.8724 (tpp) REVERT: B 111 MET cc_start: 0.6548 (mmm) cc_final: 0.6171 (mmm) REVERT: B 417 PHE cc_start: 0.9474 (m-80) cc_final: 0.9175 (m-80) REVERT: B 498 LEU cc_start: 0.9729 (tp) cc_final: 0.9514 (tp) REVERT: B 571 LEU cc_start: 0.9809 (tp) cc_final: 0.9525 (tt) REVERT: B 761 MET cc_start: 0.8780 (tmm) cc_final: 0.8400 (tmm) REVERT: B 777 MET cc_start: 0.9006 (tpt) cc_final: 0.8640 (tpp) REVERT: B 779 LEU cc_start: 0.9295 (mp) cc_final: 0.8969 (mp) REVERT: B 785 PHE cc_start: 0.8782 (m-80) cc_final: 0.8491 (m-80) REVERT: C 73 LEU cc_start: 0.9819 (tp) cc_final: 0.9600 (tp) REVERT: C 84 MET cc_start: 0.9463 (tmm) cc_final: 0.9262 (tmm) REVERT: C 125 TYR cc_start: 0.8183 (m-80) cc_final: 0.7973 (m-10) REVERT: C 220 PHE cc_start: 0.9532 (m-10) cc_final: 0.9305 (m-10) REVERT: C 306 LEU cc_start: 0.9324 (mm) cc_final: 0.8755 (tt) REVERT: C 476 TRP cc_start: 0.9452 (t60) cc_final: 0.8870 (t60) REVERT: C 483 PHE cc_start: 0.9688 (t80) cc_final: 0.9482 (t80) REVERT: D 72 MET cc_start: 0.9318 (ppp) cc_final: 0.9016 (ppp) REVERT: D 138 MET cc_start: 0.9605 (tpp) cc_final: 0.9130 (tpp) REVERT: D 139 MET cc_start: 0.9569 (mmm) cc_final: 0.9280 (mmm) REVERT: D 186 MET cc_start: 0.9285 (mmp) cc_final: 0.9048 (mmp) REVERT: D 220 PHE cc_start: 0.9601 (m-10) cc_final: 0.9343 (m-10) REVERT: D 293 MET cc_start: 0.9660 (tmm) cc_final: 0.9455 (tpp) REVERT: D 300 MET cc_start: 0.9550 (tpt) cc_final: 0.9329 (tpp) REVERT: D 306 LEU cc_start: 0.9259 (mm) cc_final: 0.8656 (tt) REVERT: D 476 TRP cc_start: 0.9403 (t60) cc_final: 0.8891 (t60) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.1119 time to fit residues: 48.8458 Evaluate side-chains 186 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [173, 189, 148, 181, 130, 164, 195, 115, 206, 51, 40] chunk 173 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.049834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039802 restraints weight = 172670.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040714 restraints weight = 125247.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041364 restraints weight = 98586.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041874 restraints weight = 82800.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042252 restraints weight = 72158.650| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20936 Z= 0.169 Angle : 0.653 10.112 28428 Z= 0.319 Chirality : 0.043 0.244 3264 Planarity : 0.004 0.042 3548 Dihedral : 4.443 24.245 2746 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.55 (0.17), residues: 2522 helix: 1.08 (0.18), residues: 908 sheet: -2.41 (0.33), residues: 244 loop : -0.95 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 519 TYR 0.013 0.001 TYR D 248 PHE 0.020 0.001 PHE C 483 TRP 0.022 0.002 TRP B 796 HIS 0.006 0.001 HIS B 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (20912) covalent geometry : angle 0.64929 / 0.32 (28374) SS BOND : bond 0.00380 / 0.20 ( 18) SS BOND : angle 1.56974 / 0.90 ( 36) hydrogen bonds : bond 0.03269 / 2.24 ( 684) hydrogen bonds : angle 4.29506 / 2.95 ( 1902) link_BETA1-4 : bond 0.00156 / 0.11 ( 2) link_BETA1-4 : angle 1.44773 / 1.09 ( 6) link_NAG-ASN : bond 0.00131 / 0.08 ( 4) link_NAG-ASN : angle 2.07312 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6618 (mmm) cc_final: 0.6273 (mmm) REVERT: A 417 PHE cc_start: 0.9484 (m-80) cc_final: 0.9165 (m-80) REVERT: A 498 LEU cc_start: 0.9787 (tp) cc_final: 0.9477 (tp) REVERT: A 549 PHE cc_start: 0.8969 (t80) cc_final: 0.8311 (t80) REVERT: A 602 MET cc_start: 0.8804 (mpp) cc_final: 0.8480 (mpp) REVERT: A 635 TRP cc_start: 0.9147 (m-90) cc_final: 0.8900 (m-90) REVERT: A 777 MET cc_start: 0.9111 (tpt) cc_final: 0.8799 (tpp) REVERT: A 785 PHE cc_start: 0.8896 (m-80) cc_final: 0.8583 (m-80) REVERT: B 417 PHE cc_start: 0.9463 (m-80) cc_final: 0.9109 (m-80) REVERT: B 498 LEU cc_start: 0.9731 (tp) cc_final: 0.9466 (tp) REVERT: B 571 LEU cc_start: 0.9798 (tp) cc_final: 0.9531 (tt) REVERT: B 761 MET cc_start: 0.8839 (tmm) cc_final: 0.8623 (tmm) REVERT: B 777 MET cc_start: 0.8965 (tpt) cc_final: 0.8611 (tpp) REVERT: B 785 PHE cc_start: 0.8857 (m-80) cc_final: 0.8578 (m-80) REVERT: C 73 LEU cc_start: 0.9819 (tp) cc_final: 0.9585 (tp) REVERT: C 84 MET cc_start: 0.9450 (tmm) cc_final: 0.9212 (tmm) REVERT: C 139 MET cc_start: 0.9640 (mmm) cc_final: 0.9388 (mmm) REVERT: C 220 PHE cc_start: 0.9506 (m-10) cc_final: 0.9283 (m-10) REVERT: C 306 LEU cc_start: 0.9315 (mm) cc_final: 0.8753 (tt) REVERT: C 476 TRP cc_start: 0.9508 (t60) cc_final: 0.8930 (t60) REVERT: C 483 PHE cc_start: 0.9728 (t80) cc_final: 0.9408 (t80) REVERT: D 72 MET cc_start: 0.9387 (ppp) cc_final: 0.9090 (ppp) REVERT: D 138 MET cc_start: 0.9628 (tpp) cc_final: 0.9230 (tpp) REVERT: D 139 MET cc_start: 0.9514 (mmm) cc_final: 0.9235 (mmm) REVERT: D 186 MET cc_start: 0.9280 (mmp) cc_final: 0.9053 (mmp) REVERT: D 220 PHE cc_start: 0.9609 (m-10) cc_final: 0.9363 (m-10) REVERT: D 293 MET cc_start: 0.9658 (tmm) cc_final: 0.9441 (tpp) REVERT: D 306 LEU cc_start: 0.9289 (mm) cc_final: 0.8680 (tt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1092 time to fit residues: 46.2152 Evaluate side-chains 185 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [203, 107, 162, 79, 65, 212, 36, 213, 181, 125, 54] chunk 203 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037412 restraints weight = 169516.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038305 restraints weight = 122838.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038948 restraints weight = 97176.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.039471 restraints weight = 81971.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039850 restraints weight = 71672.525| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20936 Z= 0.166 Angle : 0.650 8.273 28428 Z= 0.320 Chirality : 0.043 0.250 3264 Planarity : 0.004 0.041 3548 Dihedral : 4.495 24.905 2746 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2522 helix: 1.17 (0.18), residues: 898 sheet: -2.62 (0.31), residues: 272 loop : -0.86 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.015 0.001 TYR C 248 PHE 0.029 0.001 PHE B 767 TRP 0.025 0.002 TRP B 796 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (20912) covalent geometry : angle 0.64788 / 0.32 (28374) SS BOND : bond 0.00400 / 0.21 ( 18) SS BOND : angle 1.27025 / 0.74 ( 36) hydrogen bonds : bond 0.03207 / 2.20 ( 684) hydrogen bonds : angle 4.29239 / 2.96 ( 1902) link_BETA1-4 : bond 0.00254 / 0.18 ( 2) link_BETA1-4 : angle 1.19883 / 0.86 ( 6) link_NAG-ASN : bond 0.00187 / 0.12 ( 4) link_NAG-ASN : angle 2.06604 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6465 (mmm) cc_final: 0.6183 (mmm) REVERT: A 402 LEU cc_start: 0.9669 (tp) cc_final: 0.9469 (tp) REVERT: A 417 PHE cc_start: 0.9547 (m-80) cc_final: 0.9214 (m-80) REVERT: A 498 LEU cc_start: 0.9799 (tp) cc_final: 0.9517 (tp) REVERT: A 549 PHE cc_start: 0.9033 (t80) cc_final: 0.8384 (t80) REVERT: A 602 MET cc_start: 0.8860 (mpp) cc_final: 0.8548 (mpp) REVERT: A 635 TRP cc_start: 0.9180 (m-90) cc_final: 0.8911 (m-90) REVERT: A 761 MET cc_start: 0.8806 (tmm) cc_final: 0.8339 (tmm) REVERT: A 777 MET cc_start: 0.9184 (tpt) cc_final: 0.8864 (tpp) REVERT: B 417 PHE cc_start: 0.9562 (m-80) cc_final: 0.9270 (m-80) REVERT: B 498 LEU cc_start: 0.9770 (tp) cc_final: 0.9495 (tp) REVERT: B 571 LEU cc_start: 0.9771 (tp) cc_final: 0.9471 (tt) REVERT: B 602 MET cc_start: 0.8948 (mpp) cc_final: 0.8731 (mpp) REVERT: B 777 MET cc_start: 0.9094 (tpt) cc_final: 0.8754 (tpp) REVERT: B 856 MET cc_start: 0.9552 (tmm) cc_final: 0.9093 (ppp) REVERT: B 857 MET cc_start: 0.8512 (tpt) cc_final: 0.8137 (tpp) REVERT: C 73 LEU cc_start: 0.9809 (tp) cc_final: 0.9586 (tp) REVERT: C 139 MET cc_start: 0.9611 (mmm) cc_final: 0.9332 (mmm) REVERT: C 220 PHE cc_start: 0.9504 (m-10) cc_final: 0.9270 (m-10) REVERT: C 306 LEU cc_start: 0.9318 (mm) cc_final: 0.8779 (tt) REVERT: C 476 TRP cc_start: 0.9476 (t60) cc_final: 0.8890 (t60) REVERT: C 483 PHE cc_start: 0.9755 (t80) cc_final: 0.9412 (t80) REVERT: D 72 MET cc_start: 0.9393 (ppp) cc_final: 0.9096 (ppp) REVERT: D 138 MET cc_start: 0.9675 (tpp) cc_final: 0.9264 (tpp) REVERT: D 139 MET cc_start: 0.9540 (mmm) cc_final: 0.9265 (mmm) REVERT: D 186 MET cc_start: 0.9291 (mmp) cc_final: 0.9055 (mmp) REVERT: D 220 PHE cc_start: 0.9609 (m-10) cc_final: 0.9361 (m-10) REVERT: D 293 MET cc_start: 0.9652 (tmm) cc_final: 0.9422 (tpp) REVERT: D 300 MET cc_start: 0.9635 (tpt) cc_final: 0.9418 (tpp) REVERT: D 306 LEU cc_start: 0.9299 (mm) cc_final: 0.8648 (tt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1122 time to fit residues: 47.0459 Evaluate side-chains 186 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [94, 3, 232, 39, 43, 237, 216, 55, 30, 16, 212] chunk 94 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 237 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN A 757 ASN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 757 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039550 restraints weight = 171610.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040479 restraints weight = 121998.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041168 restraints weight = 95497.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041688 restraints weight = 79255.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042078 restraints weight = 68752.270| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20936 Z= 0.126 Angle : 0.638 10.387 28428 Z= 0.312 Chirality : 0.043 0.260 3264 Planarity : 0.004 0.042 3548 Dihedral : 4.440 24.435 2746 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.09 % Allowed : 0.57 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2522 helix: 1.23 (0.18), residues: 884 sheet: -2.59 (0.31), residues: 272 loop : -0.82 (0.18), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.019 0.001 TYR D 474 PHE 0.031 0.001 PHE B 767 TRP 0.020 0.001 TRP B 796 HIS 0.008 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20912) covalent geometry : angle 0.63557 / 0.31 (28374) SS BOND : bond 0.00349 / 0.20 ( 18) SS BOND : angle 1.46627 / 0.88 ( 36) hydrogen bonds : bond 0.03232 / 2.20 ( 684) hydrogen bonds : angle 4.30822 / 2.97 ( 1902) link_BETA1-4 : bond 0.00175 / 0.12 ( 2) link_BETA1-4 : angle 1.02095 / 0.70 ( 6) link_NAG-ASN : bond 0.00202 / 0.12 ( 4) link_NAG-ASN : angle 1.85188 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6275 (mmm) cc_final: 0.5984 (mmm) REVERT: A 402 LEU cc_start: 0.9616 (tp) cc_final: 0.9410 (tp) REVERT: A 417 PHE cc_start: 0.9527 (m-80) cc_final: 0.9203 (m-80) REVERT: A 498 LEU cc_start: 0.9779 (tp) cc_final: 0.9486 (tp) REVERT: A 549 PHE cc_start: 0.8963 (t80) cc_final: 0.8311 (t80) REVERT: A 602 MET cc_start: 0.8785 (mpp) cc_final: 0.8479 (mpp) REVERT: A 635 TRP cc_start: 0.9098 (m-90) cc_final: 0.8822 (m-90) REVERT: A 761 MET cc_start: 0.8852 (tmm) cc_final: 0.8584 (tmm) REVERT: A 777 MET cc_start: 0.9139 (tpt) cc_final: 0.8817 (tpp) REVERT: A 856 MET cc_start: 0.8160 (ttt) cc_final: 0.7919 (ppp) REVERT: B 417 PHE cc_start: 0.9478 (m-80) cc_final: 0.9202 (m-80) REVERT: B 427 ASP cc_start: 0.8742 (t0) cc_final: 0.8427 (t0) REVERT: B 498 LEU cc_start: 0.9762 (tp) cc_final: 0.9505 (tp) REVERT: B 571 LEU cc_start: 0.9761 (tp) cc_final: 0.9440 (tt) REVERT: B 777 MET cc_start: 0.9081 (tpt) cc_final: 0.8772 (tpp) REVERT: B 785 PHE cc_start: 0.8855 (m-80) cc_final: 0.8489 (m-80) REVERT: B 856 MET cc_start: 0.9560 (tmm) cc_final: 0.9098 (ppp) REVERT: B 857 MET cc_start: 0.8500 (tpt) cc_final: 0.8155 (tpp) REVERT: C 73 LEU cc_start: 0.9819 (tp) cc_final: 0.9606 (tp) REVERT: C 84 MET cc_start: 0.9429 (tmm) cc_final: 0.9226 (tmm) REVERT: C 138 MET cc_start: 0.9529 (tpt) cc_final: 0.9324 (tpp) REVERT: C 139 MET cc_start: 0.9664 (mmm) cc_final: 0.9383 (mmm) REVERT: C 306 LEU cc_start: 0.9301 (mm) cc_final: 0.8699 (tt) REVERT: C 476 TRP cc_start: 0.9465 (t60) cc_final: 0.8815 (t60) REVERT: C 483 PHE cc_start: 0.9722 (t80) cc_final: 0.9363 (t80) REVERT: D 72 MET cc_start: 0.9406 (ppp) cc_final: 0.9177 (ppp) REVERT: D 138 MET cc_start: 0.9633 (tpp) cc_final: 0.9198 (tpp) REVERT: D 139 MET cc_start: 0.9527 (mmm) cc_final: 0.9259 (mmm) REVERT: D 186 MET cc_start: 0.9222 (mmp) cc_final: 0.9001 (mmp) REVERT: D 220 PHE cc_start: 0.9633 (m-10) cc_final: 0.9425 (m-10) REVERT: D 293 MET cc_start: 0.9634 (tmm) cc_final: 0.9372 (tpp) REVERT: D 300 MET cc_start: 0.9618 (tpt) cc_final: 0.9411 (tpp) REVERT: D 306 LEU cc_start: 0.9277 (mm) cc_final: 0.8626 (tt) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.1045 time to fit residues: 45.7555 Evaluate side-chains 188 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [98, 251, 112, 155, 243, 107, 145, 127, 24, 200, 51] chunk 98 optimal weight: 0.7980 chunk 251 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 51 optimal weight: 0.0030 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** 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 = 0.3226 r_free = 0.3226 target = 0.048131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037946 restraints weight = 167077.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038863 restraints weight = 119654.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.039533 restraints weight = 94393.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040035 restraints weight = 78900.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040400 restraints weight = 69001.622| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20936 Z= 0.127 Angle : 0.643 11.860 28428 Z= 0.312 Chirality : 0.043 0.255 3264 Planarity : 0.004 0.043 3548 Dihedral : 4.402 28.563 2746 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.43 (0.17), residues: 2522 helix: 1.24 (0.18), residues: 876 sheet: -2.54 (0.31), residues: 272 loop : -0.79 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 519 TYR 0.014 0.001 TYR C 474 PHE 0.030 0.001 PHE B 767 TRP 0.020 0.001 TRP B 796 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20912) covalent geometry : angle 0.64054 / 0.31 (28374) SS BOND : bond 0.00429 / 0.26 ( 18) SS BOND : angle 1.28887 / 0.76 ( 36) hydrogen bonds : bond 0.03231 / 2.20 ( 684) hydrogen bonds : angle 4.27959 / 2.94 ( 1902) link_BETA1-4 : bond 0.00198 / 0.14 ( 2) link_BETA1-4 : angle 1.00827 / 0.67 ( 6) link_NAG-ASN : bond 0.00150 / 0.09 ( 4) link_NAG-ASN : angle 1.82749 / 1.14 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6113 (mmm) cc_final: 0.5888 (mmm) REVERT: A 402 LEU cc_start: 0.9644 (tp) cc_final: 0.9434 (tp) REVERT: A 417 PHE cc_start: 0.9565 (m-80) cc_final: 0.9233 (m-80) REVERT: A 498 LEU cc_start: 0.9793 (tp) cc_final: 0.9514 (tp) REVERT: A 549 PHE cc_start: 0.8998 (t80) cc_final: 0.8342 (t80) REVERT: A 602 MET cc_start: 0.8807 (mpp) cc_final: 0.8525 (mpp) REVERT: A 635 TRP cc_start: 0.9076 (m-90) cc_final: 0.8769 (m-90) REVERT: A 777 MET cc_start: 0.9166 (tpt) cc_final: 0.8893 (tpt) REVERT: A 856 MET cc_start: 0.8101 (ttt) cc_final: 0.7890 (ppp) REVERT: A 857 MET cc_start: 0.8300 (tpt) cc_final: 0.8098 (tpp) REVERT: B 417 PHE cc_start: 0.9564 (m-80) cc_final: 0.9268 (m-80) REVERT: B 427 ASP cc_start: 0.8849 (t0) cc_final: 0.8505 (t0) REVERT: B 498 LEU cc_start: 0.9773 (tp) cc_final: 0.9511 (tp) REVERT: B 571 LEU cc_start: 0.9766 (tp) cc_final: 0.9557 (tt) REVERT: B 777 MET cc_start: 0.9108 (tpt) cc_final: 0.8836 (tpt) REVERT: B 856 MET cc_start: 0.9581 (tmm) cc_final: 0.9174 (ppp) REVERT: B 857 MET cc_start: 0.8417 (tpt) cc_final: 0.8134 (tpp) REVERT: C 73 LEU cc_start: 0.9820 (tp) cc_final: 0.9611 (tp) REVERT: C 139 MET cc_start: 0.9648 (mmm) cc_final: 0.9376 (mmm) REVERT: C 306 LEU cc_start: 0.9307 (mm) cc_final: 0.8675 (tt) REVERT: C 476 TRP cc_start: 0.9420 (t60) cc_final: 0.8717 (t60) REVERT: C 483 PHE cc_start: 0.9726 (t80) cc_final: 0.9374 (t80) REVERT: D 72 MET cc_start: 0.9402 (ppp) cc_final: 0.9192 (ppp) REVERT: D 138 MET cc_start: 0.9628 (tpp) cc_final: 0.9218 (tpp) REVERT: D 139 MET cc_start: 0.9564 (mmm) cc_final: 0.9317 (mmm) REVERT: D 186 MET cc_start: 0.9193 (mmp) cc_final: 0.8971 (mmp) REVERT: D 220 PHE cc_start: 0.9616 (m-10) cc_final: 0.9409 (m-10) REVERT: D 293 MET cc_start: 0.9629 (tmm) cc_final: 0.9383 (tpp) REVERT: D 300 MET cc_start: 0.9628 (tpt) cc_final: 0.9420 (tpp) REVERT: D 306 LEU cc_start: 0.9259 (mm) cc_final: 0.8606 (tt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1095 time to fit residues: 46.7436 Evaluate side-chains 192 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [96, 212, 14, 3, 177, 38, 247, 220, 112, 199, 71] chunk 96 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 247 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** 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 = 0.3220 r_free = 0.3220 target = 0.049263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039374 restraints weight = 172595.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040275 restraints weight = 122077.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040923 restraints weight = 95824.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041333 restraints weight = 79995.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041761 restraints weight = 70313.163| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20936 Z= 0.139 Angle : 0.648 9.667 28428 Z= 0.315 Chirality : 0.043 0.227 3264 Planarity : 0.004 0.047 3548 Dihedral : 4.412 29.027 2746 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2522 helix: 1.17 (0.18), residues: 886 sheet: -2.53 (0.32), residues: 272 loop : -0.79 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 723 TYR 0.014 0.001 TYR C 474 PHE 0.027 0.001 PHE B 767 TRP 0.027 0.002 TRP B 796 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (20912) covalent geometry : angle 0.64547 / 0.31 (28374) SS BOND : bond 0.00416 / 0.23 ( 18) SS BOND : angle 1.20377 / 0.70 ( 36) hydrogen bonds : bond 0.03184 / 2.18 ( 684) hydrogen bonds : angle 4.32101 / 2.96 ( 1902) link_BETA1-4 : bond 0.00028 / 0.02 ( 2) link_BETA1-4 : angle 1.06288 / 0.72 ( 6) link_NAG-ASN : bond 0.00223 / 0.13 ( 4) link_NAG-ASN : angle 1.91848 / 1.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.38 seconds wall clock time: 48 minutes 44.42 seconds (2924.42 seconds total)