Starting phenix.real_space_refine on Sat Jul 4 11:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyn_30501/07_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_30501/07_2026/7cyn_30501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyn_30501/07_2026/7cyn_30501.cif" } 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-dev-6108/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: 8.72, per 1000 atoms: 0.43 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=16, 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 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: 1.49 Conformation dependent library (CDL) restraints added in 800.0 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: 0.41 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: 3.41 Time building geometry restraints manager: 1.93 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: 858 34.44 - 51.66: 168 51.66 - 68.88: 20 68.88 - 86.10: 18 Dihedral angle restraints: 12510 sinusoidal: 5040 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 B 787 " pdb=" SG CYS B 787 " pdb=" SG CYS B 814 " pdb=" CB CYS B 814 " ideal model delta sinusoidal sigma weight residual 93.00 130.98 -37.98 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 12507 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: 2.03 - 2.60: 184 2.60 - 3.18: 17533 3.18 - 3.75: 32163 3.75 - 4.33: 43974 4.33 - 4.90: 70992 Nonbonded interactions: 164846 Sorted by model distance: nonbonded pdb=" SG CYS C 260 " pdb=" SG CYS C 368 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 260 " pdb=" SG CYS D 368 " model vdw 2.031 3.760 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 ... (remaining 164841 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: 0.800 Set stop_for_unknowns flag: 0.010 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: 0.060 Process input model: 22.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- 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 20934 Z= 0.115 Angle : 0.519 9.492 28424 Z= 0.289 Chirality : 0.039 0.141 3264 Planarity : 0.003 0.050 3548 Dihedral : 12.561 86.102 7634 Min Nonbonded Distance : 2.030 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 0.00122 / 0.07 ( 16) SS BOND : angle 0.39036 / 0.22 ( 32) 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 : 0.799 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: 0.1272 time to fit residues: 92.7424 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: 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** ** A 763 GLN ** 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 = 0.3422 r_free = 0.3422 target = 0.056275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044616 restraints weight = 147941.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045545 restraints weight = 115837.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046231 restraints weight = 95851.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046757 restraints weight = 82743.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047178 restraints weight = 74126.822| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20934 Z= 0.126 Angle : 0.621 8.211 28424 Z= 0.305 Chirality : 0.043 0.225 3264 Planarity : 0.004 0.056 3548 Dihedral : 3.843 22.666 2746 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.18 % Allowed : 3.07 % Favored : 96.75 % 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: -1.59 (0.17), residues: 2522 helix: 0.25 (0.17), residues: 906 sheet: -2.59 (0.32), residues: 274 loop : -1.65 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 376 TYR 0.011 0.001 TYR A 751 PHE 0.023 0.002 PHE C 346 TRP 0.015 0.001 TRP D 476 HIS 0.007 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20912) covalent geometry : angle 0.62111 / 0.30 (28374) SS BOND : bond 0.00269 / 0.15 ( 16) SS BOND : angle 0.66855 / 0.38 ( 32) hydrogen bonds : bond 0.03551 / 2.44 ( 684) hydrogen bonds : angle 4.19829 / 2.86 ( 1902) link_BETA1-4 : bond 0.00283 / 0.19 ( 2) link_BETA1-4 : angle 0.85627 / 0.64 ( 6) link_NAG-ASN : bond 0.00275 / 0.16 ( 4) link_NAG-ASN : angle 1.01122 / 0.56 ( 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 358 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 354 time to evaluate : 0.745 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: A 243 ASP cc_start: 0.9445 (m-30) cc_final: 0.9145 (p0) REVERT: A 309 TRP cc_start: 0.8576 (m-10) cc_final: 0.7916 (m-10) REVERT: A 417 PHE cc_start: 0.9486 (m-80) cc_final: 0.9067 (m-80) REVERT: A 498 LEU cc_start: 0.9812 (tp) cc_final: 0.9569 (tp) REVERT: A 602 MET cc_start: 0.8894 (mpp) cc_final: 0.8628 (mpp) REVERT: A 603 MET cc_start: 0.9382 (tmm) cc_final: 0.9097 (tmm) REVERT: A 714 VAL cc_start: 0.8155 (m) cc_final: 0.7722 (m) REVERT: A 779 LEU cc_start: 0.9143 (mp) cc_final: 0.8549 (mp) REVERT: B 275 ASN cc_start: 0.9582 (m110) cc_final: 0.9360 (p0) REVERT: B 302 LEU cc_start: 0.9625 (mt) cc_final: 0.9333 (mt) REVERT: B 309 TRP cc_start: 0.8744 (m-10) cc_final: 0.8158 (m-10) REVERT: B 402 LEU cc_start: 0.9495 (tp) cc_final: 0.9241 (tp) REVERT: B 417 PHE cc_start: 0.9352 (m-80) cc_final: 0.8923 (m-80) REVERT: B 498 LEU cc_start: 0.9729 (tp) cc_final: 0.9516 (tp) REVERT: B 603 MET cc_start: 0.9389 (tmm) cc_final: 0.9086 (tmm) REVERT: B 761 MET cc_start: 0.7956 (tmm) cc_final: 0.7299 (tmm) REVERT: B 779 LEU cc_start: 0.9110 (mp) cc_final: 0.8470 (mp) REVERT: B 785 PHE cc_start: 0.8142 (m-80) cc_final: 0.7892 (m-80) REVERT: C 72 MET cc_start: 0.9338 (ppp) cc_final: 0.8502 (tmm) REVERT: C 73 LEU cc_start: 0.9759 (tp) cc_final: 0.9495 (tp) REVERT: C 84 MET cc_start: 0.9591 (tmm) cc_final: 0.9372 (tmm) REVERT: C 108 ASP cc_start: 0.9357 (m-30) cc_final: 0.9033 (m-30) REVERT: C 220 PHE cc_start: 0.9471 (m-10) cc_final: 0.9265 (m-10) REVERT: C 306 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 476 TRP cc_start: 0.9290 (t60) cc_final: 0.8822 (t60) REVERT: D 108 ASP cc_start: 0.9348 (m-30) cc_final: 0.8992 (m-30) REVERT: D 181 ASN cc_start: 0.9599 (t0) cc_final: 0.9192 (m-40) REVERT: D 306 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8622 (tt) REVERT: D 384 LEU cc_start: 0.9054 (mt) cc_final: 0.8724 (pp) REVERT: D 476 TRP cc_start: 0.9231 (t60) cc_final: 0.8967 (t60) outliers start: 4 outliers final: 1 residues processed: 356 average time/residue: 0.1274 time to fit residues: 74.6467 Evaluate side-chains 259 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 181 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS ** 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** A 800 HIS A 820 HIS B 138 GLN 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 398 ASN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS 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** B 820 HIS C 85 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** 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 221 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041273 restraints weight = 176637.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042105 restraints weight = 128659.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.042776 restraints weight = 102747.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043198 restraints weight = 86254.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043643 restraints weight = 76106.646| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 20934 Z= 0.310 Angle : 0.900 11.822 28424 Z= 0.440 Chirality : 0.047 0.252 3264 Planarity : 0.005 0.050 3548 Dihedral : 4.988 23.196 2746 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % 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: -1.26 (0.17), residues: 2522 helix: 0.40 (0.17), residues: 912 sheet: -2.58 (0.31), residues: 274 loop : -1.31 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.021 0.003 TYR B 741 PHE 0.029 0.003 PHE C 224 TRP 0.019 0.002 TRP C 176 HIS 0.013 0.002 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.31 (20912) covalent geometry : angle 0.89646 / 0.44 (28374) SS BOND : bond 0.00845 / 0.47 ( 16) SS BOND : angle 1.91551 / 1.12 ( 32) hydrogen bonds : bond 0.04169 / 2.84 ( 684) hydrogen bonds : angle 4.69077 / 3.22 ( 1902) link_BETA1-4 : bond 0.02193 / 1.47 ( 2) link_BETA1-4 : angle 2.62273 / 2.06 ( 6) link_NAG-ASN : bond 0.01311 / 0.83 ( 4) link_NAG-ASN : angle 2.05016 / 1.27 ( 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 263 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 0.792 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 339 LEU cc_start: 0.9474 (mm) cc_final: 0.9273 (mt) REVERT: A 402 LEU cc_start: 0.9645 (tp) cc_final: 0.9442 (tp) REVERT: A 417 PHE cc_start: 0.9449 (m-80) cc_final: 0.9150 (m-80) REVERT: A 602 MET cc_start: 0.8834 (mpp) cc_final: 0.8535 (mpp) REVERT: A 761 MET cc_start: 0.8897 (tmm) cc_final: 0.8678 (tmm) REVERT: A 779 LEU cc_start: 0.9378 (mp) cc_final: 0.9065 (mp) REVERT: B 111 MET cc_start: 0.7284 (mmm) cc_final: 0.7079 (mmm) REVERT: B 402 LEU cc_start: 0.9606 (tp) cc_final: 0.9398 (tp) REVERT: B 417 PHE cc_start: 0.9504 (m-80) cc_final: 0.9236 (m-80) REVERT: B 603 MET cc_start: 0.9255 (tmm) cc_final: 0.9023 (tmm) REVERT: B 690 PHE cc_start: 0.8858 (t80) cc_final: 0.8581 (t80) REVERT: B 761 MET cc_start: 0.8774 (tmm) cc_final: 0.8514 (tmm) REVERT: B 785 PHE cc_start: 0.8988 (m-80) cc_final: 0.8374 (m-80) REVERT: B 847 ILE cc_start: 0.9428 (tt) cc_final: 0.9222 (pt) REVERT: C 72 MET cc_start: 0.9424 (ppp) cc_final: 0.9052 (ppp) REVERT: C 84 MET cc_start: 0.9526 (tmm) cc_final: 0.9305 (tmm) REVERT: C 102 MET cc_start: 0.8409 (mpp) cc_final: 0.8182 (mpp) REVERT: C 138 MET cc_start: 0.9598 (tpp) cc_final: 0.9049 (tpt) REVERT: C 139 MET cc_start: 0.9642 (mmm) cc_final: 0.9277 (mmm) REVERT: C 179 MET cc_start: 0.9575 (ptm) cc_final: 0.9310 (ptt) REVERT: C 186 MET cc_start: 0.9080 (mmp) cc_final: 0.8872 (mmp) REVERT: C 514 MET cc_start: 0.8778 (mmt) cc_final: 0.8378 (mmm) REVERT: D 72 MET cc_start: 0.9376 (ppp) cc_final: 0.8960 (ppp) REVERT: D 138 MET cc_start: 0.9570 (tpt) cc_final: 0.9206 (tpp) REVERT: D 139 MET cc_start: 0.9766 (mmm) cc_final: 0.9395 (mmm) REVERT: D 186 MET cc_start: 0.9258 (mmp) cc_final: 0.9001 (mmp) REVERT: D 220 PHE cc_start: 0.9545 (m-10) cc_final: 0.9278 (m-10) REVERT: D 483 PHE cc_start: 0.9625 (t80) cc_final: 0.9361 (t80) outliers start: 4 outliers final: 3 residues processed: 263 average time/residue: 0.1321 time to fit residues: 56.5711 Evaluate side-chains 182 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 247 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 chunk 172 optimal weight: 40.0000 chunk 85 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 138 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 475 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.049650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039165 restraints weight = 164040.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040034 restraints weight = 122489.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040716 restraints weight = 98641.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041234 restraints weight = 83233.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.041546 restraints weight = 73071.743| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20934 Z= 0.127 Angle : 0.623 8.052 28424 Z= 0.307 Chirality : 0.043 0.224 3264 Planarity : 0.004 0.048 3548 Dihedral : 4.411 23.512 2746 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -0.81 (0.17), residues: 2522 helix: 0.94 (0.18), residues: 894 sheet: -2.53 (0.32), residues: 270 loop : -1.12 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 736 TYR 0.016 0.001 TYR D 349 PHE 0.026 0.001 PHE C 346 TRP 0.018 0.001 TRP A 796 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (20912) covalent geometry : angle 0.61910 / 0.31 (28374) SS BOND : bond 0.00350 / 0.20 ( 16) SS BOND : angle 1.14539 / 0.65 ( 32) hydrogen bonds : bond 0.03318 / 2.26 ( 684) hydrogen bonds : angle 4.22069 / 2.87 ( 1902) link_BETA1-4 : bond 0.00350 / 0.24 ( 2) link_BETA1-4 : angle 1.77761 / 1.42 ( 6) link_NAG-ASN : bond 0.00307 / 0.19 ( 4) link_NAG-ASN : angle 2.59704 / 2.00 ( 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 270 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 PHE cc_start: 0.9526 (m-80) cc_final: 0.9186 (m-80) REVERT: A 498 LEU cc_start: 0.9817 (tp) cc_final: 0.9562 (tp) REVERT: A 602 MET cc_start: 0.8851 (mpp) cc_final: 0.8572 (mpp) REVERT: A 779 LEU cc_start: 0.9245 (mp) cc_final: 0.8960 (mp) REVERT: B 111 MET cc_start: 0.7480 (mmm) cc_final: 0.7219 (mmm) REVERT: B 417 PHE cc_start: 0.9511 (m-80) cc_final: 0.9186 (m-80) REVERT: B 498 LEU cc_start: 0.9768 (tp) cc_final: 0.9480 (tp) REVERT: B 602 MET cc_start: 0.9192 (mpp) cc_final: 0.8937 (mpp) REVERT: B 603 MET cc_start: 0.9257 (tmm) cc_final: 0.8985 (tmm) REVERT: B 690 PHE cc_start: 0.8855 (t80) cc_final: 0.8578 (t80) REVERT: B 761 MET cc_start: 0.8866 (tmm) cc_final: 0.8616 (tmm) REVERT: B 777 MET cc_start: 0.9132 (tpt) cc_final: 0.8746 (tpt) REVERT: B 785 PHE cc_start: 0.8677 (m-80) cc_final: 0.8339 (m-80) REVERT: C 73 LEU cc_start: 0.9822 (tp) cc_final: 0.9620 (tp) REVERT: C 84 MET cc_start: 0.9495 (tmm) cc_final: 0.9216 (tmm) REVERT: C 102 MET cc_start: 0.8354 (mpp) cc_final: 0.8063 (mmm) REVERT: C 138 MET cc_start: 0.9639 (tpp) cc_final: 0.9143 (tpt) REVERT: C 139 MET cc_start: 0.9597 (mmm) cc_final: 0.9319 (mmm) REVERT: C 186 MET cc_start: 0.9016 (mmp) cc_final: 0.8816 (mmp) REVERT: C 220 PHE cc_start: 0.9477 (m-10) cc_final: 0.9215 (m-10) REVERT: C 306 LEU cc_start: 0.9333 (mm) cc_final: 0.8762 (tt) REVERT: C 450 LYS cc_start: 0.9681 (mmtt) cc_final: 0.9389 (mmtm) REVERT: C 476 TRP cc_start: 0.9459 (t60) cc_final: 0.8761 (t60) REVERT: D 72 MET cc_start: 0.9355 (ppp) cc_final: 0.9056 (ppp) REVERT: D 138 MET cc_start: 0.9547 (tpt) cc_final: 0.9254 (tpt) REVERT: D 139 MET cc_start: 0.9743 (mmm) cc_final: 0.9419 (mmm) REVERT: D 186 MET cc_start: 0.9309 (mmp) cc_final: 0.9062 (mmp) REVERT: D 220 PHE cc_start: 0.9514 (m-10) cc_final: 0.9234 (m-10) REVERT: D 293 MET cc_start: 0.9638 (tmm) cc_final: 0.9416 (tpp) REVERT: D 306 LEU cc_start: 0.9300 (mm) cc_final: 0.8687 (tt) REVERT: D 476 TRP cc_start: 0.9397 (t60) cc_final: 0.8977 (t60) REVERT: D 483 PHE cc_start: 0.9632 (t80) cc_final: 0.9381 (t80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1209 time to fit residues: 54.2442 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** 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 182 ASN B 298 HIS B 337 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 83 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036529 restraints weight = 176461.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037420 restraints weight = 127065.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038061 restraints weight = 100256.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.038563 restraints weight = 84217.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.038845 restraints weight = 73696.298| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 20934 Z= 0.251 Angle : 0.754 10.629 28424 Z= 0.367 Chirality : 0.045 0.192 3264 Planarity : 0.005 0.045 3548 Dihedral : 4.799 24.267 2746 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.62 % 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: -0.78 (0.17), residues: 2522 helix: 0.85 (0.17), residues: 912 sheet: -2.60 (0.31), residues: 272 loop : -1.00 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 717 TYR 0.018 0.002 TYR B 807 PHE 0.015 0.002 PHE B 417 TRP 0.047 0.003 TRP A 635 HIS 0.008 0.002 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 (20912) covalent geometry : angle 0.75185 / 0.37 (28374) SS BOND : bond 0.01025 / 0.38 ( 16) SS BOND : angle 1.52289 / 0.86 ( 32) hydrogen bonds : bond 0.03625 / 2.47 ( 684) hydrogen bonds : angle 4.51544 / 3.10 ( 1902) link_BETA1-4 : bond 0.00271 / 0.18 ( 2) link_BETA1-4 : angle 1.59507 / 1.22 ( 6) link_NAG-ASN : bond 0.00695 / 0.43 ( 4) link_NAG-ASN : angle 1.98995 / 1.30 ( 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 235 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.847 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 111 MET cc_start: 0.6320 (mmm) cc_final: 0.5976 (mmm) REVERT: A 402 LEU cc_start: 0.9683 (tp) cc_final: 0.9460 (tp) REVERT: A 417 PHE cc_start: 0.9537 (m-80) cc_final: 0.9253 (m-80) REVERT: A 498 LEU cc_start: 0.9760 (tp) cc_final: 0.9475 (tp) REVERT: A 602 MET cc_start: 0.8879 (mpp) cc_final: 0.8563 (mpp) REVERT: A 635 TRP cc_start: 0.9254 (m-90) cc_final: 0.9030 (m-90) REVERT: A 777 MET cc_start: 0.9131 (tpt) cc_final: 0.8857 (tpp) REVERT: A 779 LEU cc_start: 0.9345 (mp) cc_final: 0.9137 (mp) REVERT: B 417 PHE cc_start: 0.9534 (m-80) cc_final: 0.9246 (m-80) REVERT: B 498 LEU cc_start: 0.9718 (tp) cc_final: 0.9472 (tp) REVERT: B 571 LEU cc_start: 0.9819 (tp) cc_final: 0.9504 (tt) REVERT: B 635 TRP cc_start: 0.9166 (m-90) cc_final: 0.8926 (m-90) REVERT: B 761 MET cc_start: 0.8886 (tmm) cc_final: 0.8603 (tmm) REVERT: B 777 MET cc_start: 0.9162 (tpt) cc_final: 0.8784 (tpt) REVERT: B 785 PHE cc_start: 0.8909 (m-80) cc_final: 0.8451 (m-80) REVERT: C 73 LEU cc_start: 0.9824 (tp) cc_final: 0.9617 (tp) REVERT: C 138 MET cc_start: 0.9719 (tpp) cc_final: 0.9342 (tpp) REVERT: C 139 MET cc_start: 0.9481 (mmm) cc_final: 0.9252 (mmm) REVERT: C 186 MET cc_start: 0.9166 (mmp) cc_final: 0.8898 (mmp) REVERT: C 220 PHE cc_start: 0.9579 (m-10) cc_final: 0.9328 (m-10) REVERT: C 252 HIS cc_start: 0.9329 (m-70) cc_final: 0.9099 (m170) REVERT: C 306 LEU cc_start: 0.9371 (mm) cc_final: 0.8831 (tt) REVERT: C 476 TRP cc_start: 0.9536 (t60) cc_final: 0.9025 (t60) REVERT: D 72 MET cc_start: 0.9385 (ppp) cc_final: 0.9044 (ppp) REVERT: D 139 MET cc_start: 0.9600 (mmm) cc_final: 0.9366 (mmm) REVERT: D 186 MET cc_start: 0.9295 (mmp) cc_final: 0.9005 (mmp) REVERT: D 220 PHE cc_start: 0.9596 (m-10) cc_final: 0.9337 (m-10) REVERT: D 252 HIS cc_start: 0.9283 (m-70) cc_final: 0.9064 (m170) REVERT: D 293 MET cc_start: 0.9651 (tmm) cc_final: 0.9358 (tpp) REVERT: D 306 LEU cc_start: 0.9346 (mm) cc_final: 0.8759 (tt) outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.1203 time to fit residues: 47.9393 Evaluate side-chains 179 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** 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 83 GLN C 284 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037111 restraints weight = 170878.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038017 restraints weight = 122556.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038685 restraints weight = 96230.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039197 restraints weight = 80366.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039577 restraints weight = 70054.530| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20934 Z= 0.157 Angle : 0.632 7.895 28424 Z= 0.314 Chirality : 0.043 0.173 3264 Planarity : 0.004 0.048 3548 Dihedral : 4.563 25.726 2746 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.61 (0.17), residues: 2522 helix: 1.08 (0.18), residues: 898 sheet: -2.56 (0.31), residues: 270 loop : -0.95 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 736 TYR 0.016 0.001 TYR C 248 PHE 0.026 0.001 PHE D 483 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 0.00333 / 0.16 (20912) covalent geometry : angle 0.63034 / 0.31 (28374) SS BOND : bond 0.00390 / 0.21 ( 16) SS BOND : angle 1.12212 / 0.63 ( 32) hydrogen bonds : bond 0.03400 / 2.30 ( 684) hydrogen bonds : angle 4.34835 / 2.97 ( 1902) link_BETA1-4 : bond 0.00023 / 0.02 ( 2) link_BETA1-4 : angle 1.08142 / 0.76 ( 6) link_NAG-ASN : bond 0.00280 / 0.17 ( 4) link_NAG-ASN : angle 1.83941 / 1.31 ( 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 247 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.792 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: 0.6295 (mmm) cc_final: 0.6025 (mmm) REVERT: A 402 LEU cc_start: 0.9645 (tp) cc_final: 0.9443 (tp) REVERT: A 417 PHE cc_start: 0.9531 (m-80) cc_final: 0.9229 (m-80) REVERT: A 498 LEU cc_start: 0.9800 (tp) cc_final: 0.9540 (tp) REVERT: A 549 PHE cc_start: 0.9064 (t80) cc_final: 0.8268 (t80) REVERT: A 602 MET cc_start: 0.8867 (mpp) cc_final: 0.8523 (mpp) REVERT: A 635 TRP cc_start: 0.9186 (m-90) cc_final: 0.8975 (m-90) REVERT: A 743 LEU cc_start: 0.9680 (mm) cc_final: 0.9458 (mt) REVERT: A 777 MET cc_start: 0.9168 (tpt) cc_final: 0.8913 (tpp) REVERT: B 111 MET cc_start: 0.7534 (mmm) cc_final: 0.7331 (mmm) REVERT: B 417 PHE cc_start: 0.9569 (m-80) cc_final: 0.9313 (m-80) REVERT: B 498 LEU cc_start: 0.9747 (tp) cc_final: 0.9477 (tp) REVERT: B 571 LEU cc_start: 0.9779 (tp) cc_final: 0.9476 (tt) REVERT: B 602 MET cc_start: 0.9009 (mpp) cc_final: 0.8791 (mpp) REVERT: B 635 TRP cc_start: 0.9149 (m-90) cc_final: 0.8939 (m-90) REVERT: B 743 LEU cc_start: 0.9694 (mm) cc_final: 0.9483 (mt) REVERT: B 761 MET cc_start: 0.8935 (tmm) cc_final: 0.8683 (tmm) REVERT: B 777 MET cc_start: 0.9149 (tpt) cc_final: 0.8755 (tpt) REVERT: B 785 PHE cc_start: 0.8797 (m-80) cc_final: 0.8330 (m-80) REVERT: C 73 LEU cc_start: 0.9831 (tp) cc_final: 0.9624 (tp) REVERT: C 138 MET cc_start: 0.9729 (tpp) cc_final: 0.9353 (tpp) REVERT: C 139 MET cc_start: 0.9532 (mmm) cc_final: 0.9288 (mmm) REVERT: C 146 TYR cc_start: 0.9587 (m-80) cc_final: 0.9380 (m-80) REVERT: C 186 MET cc_start: 0.9125 (mmp) cc_final: 0.8878 (mmp) REVERT: C 220 PHE cc_start: 0.9591 (m-10) cc_final: 0.9339 (m-10) REVERT: C 450 LYS cc_start: 0.9675 (mmtt) cc_final: 0.9436 (mmtm) REVERT: C 476 TRP cc_start: 0.9477 (t60) cc_final: 0.8845 (t60) REVERT: D 72 MET cc_start: 0.9373 (ppp) cc_final: 0.9102 (ppp) REVERT: D 139 MET cc_start: 0.9623 (mmm) cc_final: 0.9408 (mmm) REVERT: D 186 MET cc_start: 0.9289 (mmp) cc_final: 0.9017 (mmp) REVERT: D 220 PHE cc_start: 0.9586 (m-10) cc_final: 0.9329 (m-10) REVERT: D 252 HIS cc_start: 0.9304 (m-70) cc_final: 0.9048 (m170) REVERT: D 293 MET cc_start: 0.9629 (tmm) cc_final: 0.9300 (tpp) REVERT: D 297 PHE cc_start: 0.9503 (t80) cc_final: 0.9076 (t80) REVERT: D 301 LEU cc_start: 0.9676 (mt) cc_final: 0.9432 (mt) REVERT: D 306 LEU cc_start: 0.9307 (mm) cc_final: 0.8714 (tt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1194 time to fit residues: 50.0548 Evaluate side-chains 191 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 173 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 394 HIS ** 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 412 HIS ** 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 = 0.3162 r_free = 0.3162 target = 0.046164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036389 restraints weight = 175121.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.037251 restraints weight = 124764.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037883 restraints weight = 98005.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.038356 restraints weight = 82072.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038694 restraints weight = 71709.003| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20934 Z= 0.238 Angle : 0.748 9.320 28424 Z= 0.368 Chirality : 0.045 0.359 3264 Planarity : 0.005 0.044 3548 Dihedral : 4.864 24.637 2746 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -0.77 (0.17), residues: 2522 helix: 0.87 (0.17), residues: 916 sheet: -2.75 (0.30), residues: 268 loop : -0.97 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 466 TYR 0.018 0.002 TYR D 146 PHE 0.029 0.002 PHE C 483 TRP 0.032 0.002 TRP C 176 HIS 0.008 0.002 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (20912) covalent geometry : angle 0.74543 / 0.37 (28374) SS BOND : bond 0.00815 / 0.32 ( 16) SS BOND : angle 1.38519 / 0.79 ( 32) hydrogen bonds : bond 0.03729 / 2.54 ( 684) hydrogen bonds : angle 4.67944 / 3.21 ( 1902) link_BETA1-4 : bond 0.00504 / 0.35 ( 2) link_BETA1-4 : angle 1.46783 / 1.10 ( 6) link_NAG-ASN : bond 0.00680 / 0.42 ( 4) link_NAG-ASN : angle 2.19802 / 1.50 ( 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 231 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 PHE cc_start: 0.9465 (m-80) cc_final: 0.9165 (m-80) REVERT: A 498 LEU cc_start: 0.9777 (tp) cc_final: 0.9542 (tp) REVERT: A 602 MET cc_start: 0.8880 (mpp) cc_final: 0.8578 (mpp) REVERT: A 635 TRP cc_start: 0.9227 (m-90) cc_final: 0.8743 (m-90) REVERT: A 777 MET cc_start: 0.9213 (tpt) cc_final: 0.8944 (tpp) REVERT: B 498 LEU cc_start: 0.9701 (tp) cc_final: 0.9483 (tp) REVERT: B 571 LEU cc_start: 0.9771 (tp) cc_final: 0.9428 (tt) REVERT: B 635 TRP cc_start: 0.9198 (m-90) cc_final: 0.8996 (m-90) REVERT: B 761 MET cc_start: 0.8910 (tmm) cc_final: 0.8634 (tmm) REVERT: B 777 MET cc_start: 0.9104 (tpt) cc_final: 0.8777 (tpt) REVERT: B 785 PHE cc_start: 0.9018 (m-80) cc_final: 0.8468 (m-80) REVERT: C 84 MET cc_start: 0.9400 (tmm) cc_final: 0.9194 (tmm) REVERT: C 138 MET cc_start: 0.9703 (tpp) cc_final: 0.9414 (tpp) REVERT: C 139 MET cc_start: 0.9626 (mmm) cc_final: 0.9387 (mmm) REVERT: C 186 MET cc_start: 0.9154 (mmp) cc_final: 0.8900 (mmp) REVERT: C 220 PHE cc_start: 0.9593 (m-10) cc_final: 0.9371 (m-10) REVERT: C 450 LYS cc_start: 0.9696 (mmtt) cc_final: 0.9426 (mmtm) REVERT: C 476 TRP cc_start: 0.9547 (t60) cc_final: 0.8939 (t60) REVERT: C 483 PHE cc_start: 0.9744 (t80) cc_final: 0.9393 (t80) REVERT: D 72 MET cc_start: 0.9399 (ppp) cc_final: 0.9063 (ppp) REVERT: D 84 MET cc_start: 0.9373 (tmm) cc_final: 0.9170 (tmm) REVERT: D 139 MET cc_start: 0.9589 (mmm) cc_final: 0.9344 (mmm) REVERT: D 186 MET cc_start: 0.9265 (mmp) cc_final: 0.9023 (mmp) REVERT: D 220 PHE cc_start: 0.9605 (m-10) cc_final: 0.9372 (m-10) REVERT: D 252 HIS cc_start: 0.9352 (m-70) cc_final: 0.9113 (m170) REVERT: D 293 MET cc_start: 0.9621 (tmm) cc_final: 0.9259 (tpp) REVERT: D 297 PHE cc_start: 0.9481 (t80) cc_final: 0.8846 (t80) REVERT: D 301 LEU cc_start: 0.9668 (mt) cc_final: 0.9224 (mt) REVERT: D 306 LEU cc_start: 0.9368 (mm) cc_final: 0.8740 (tt) REVERT: D 450 LYS cc_start: 0.9718 (mmtt) cc_final: 0.9429 (mmtm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1173 time to fit residues: 45.9706 Evaluate side-chains 174 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 203 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 419 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036378 restraints weight = 174598.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037277 restraints weight = 122977.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037942 restraints weight = 95604.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038441 restraints weight = 79504.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038804 restraints weight = 68994.494| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20934 Z= 0.180 Angle : 0.681 10.208 28424 Z= 0.336 Chirality : 0.044 0.257 3264 Planarity : 0.004 0.047 3548 Dihedral : 4.751 25.239 2746 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -0.74 (0.17), residues: 2522 helix: 0.87 (0.17), residues: 914 sheet: -2.74 (0.30), residues: 272 loop : -0.92 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 736 TYR 0.019 0.002 TYR D 474 PHE 0.023 0.002 PHE C 483 TRP 0.020 0.002 TRP B 796 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (20912) covalent geometry : angle 0.67884 / 0.34 (28374) SS BOND : bond 0.00416 / 0.21 ( 16) SS BOND : angle 1.22363 / 0.70 ( 32) hydrogen bonds : bond 0.03603 / 2.43 ( 684) hydrogen bonds : angle 4.58949 / 3.15 ( 1902) link_BETA1-4 : bond 0.00146 / 0.10 ( 2) link_BETA1-4 : angle 1.22061 / 0.80 ( 6) link_NAG-ASN : bond 0.00447 / 0.28 ( 4) link_NAG-ASN : angle 2.11572 / 1.53 ( 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 235 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 PHE cc_start: 0.9465 (m-80) cc_final: 0.9226 (m-80) REVERT: A 498 LEU cc_start: 0.9765 (tp) cc_final: 0.9548 (tp) REVERT: A 549 PHE cc_start: 0.9119 (t80) cc_final: 0.8335 (t80) REVERT: A 602 MET cc_start: 0.8856 (mpp) cc_final: 0.8532 (mpp) REVERT: A 777 MET cc_start: 0.9234 (tpt) cc_final: 0.8949 (tpp) REVERT: A 785 PHE cc_start: 0.8903 (m-10) cc_final: 0.8608 (m-10) REVERT: B 498 LEU cc_start: 0.9712 (tp) cc_final: 0.9492 (tp) REVERT: B 571 LEU cc_start: 0.9772 (tp) cc_final: 0.9411 (tt) REVERT: B 602 MET cc_start: 0.8879 (mpp) cc_final: 0.8656 (mpp) REVERT: B 743 LEU cc_start: 0.9730 (mm) cc_final: 0.9438 (mt) REVERT: B 761 MET cc_start: 0.8921 (tmm) cc_final: 0.8654 (tmm) REVERT: B 777 MET cc_start: 0.9104 (tpt) cc_final: 0.8773 (tpt) REVERT: B 785 PHE cc_start: 0.8974 (m-80) cc_final: 0.8392 (m-80) REVERT: C 73 LEU cc_start: 0.9827 (tp) cc_final: 0.9615 (tp) REVERT: C 138 MET cc_start: 0.9729 (tpp) cc_final: 0.9451 (tpp) REVERT: C 139 MET cc_start: 0.9636 (mmm) cc_final: 0.9235 (mmm) REVERT: C 179 MET cc_start: 0.9346 (pmm) cc_final: 0.9014 (pmm) REVERT: C 186 MET cc_start: 0.9135 (mmp) cc_final: 0.8920 (mmp) REVERT: C 220 PHE cc_start: 0.9615 (m-10) cc_final: 0.9395 (m-10) REVERT: C 252 HIS cc_start: 0.9038 (m-70) cc_final: 0.8774 (m-70) REVERT: C 476 TRP cc_start: 0.9501 (t60) cc_final: 0.8779 (t60) REVERT: D 72 MET cc_start: 0.9399 (ppp) cc_final: 0.9124 (ppp) REVERT: D 84 MET cc_start: 0.9340 (tmm) cc_final: 0.9123 (tmm) REVERT: D 139 MET cc_start: 0.9579 (mmm) cc_final: 0.9339 (mmm) REVERT: D 186 MET cc_start: 0.9248 (mmp) cc_final: 0.9012 (mmp) REVERT: D 220 PHE cc_start: 0.9606 (m-10) cc_final: 0.9371 (m-10) REVERT: D 293 MET cc_start: 0.9630 (tmm) cc_final: 0.9277 (tpp) REVERT: D 297 PHE cc_start: 0.9481 (t80) cc_final: 0.8897 (t80) REVERT: D 301 LEU cc_start: 0.9682 (mt) cc_final: 0.9266 (mt) REVERT: D 306 LEU cc_start: 0.9347 (mm) cc_final: 0.8702 (tt) REVERT: D 450 LYS cc_start: 0.9714 (mmtt) cc_final: 0.9427 (mmtm) REVERT: D 483 PHE cc_start: 0.9700 (t80) cc_final: 0.9298 (t80) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1219 time to fit residues: 48.7200 Evaluate side-chains 174 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 0.0670 chunk 237 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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 419 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** 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 412 HIS ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036130 restraints weight = 175064.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.037030 restraints weight = 123005.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037710 restraints weight = 95716.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038204 restraints weight = 79187.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038561 restraints weight = 68770.882| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20934 Z= 0.161 Angle : 0.676 9.836 28424 Z= 0.333 Chirality : 0.044 0.236 3264 Planarity : 0.004 0.047 3548 Dihedral : 4.706 24.886 2746 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.66 (0.17), residues: 2522 helix: 0.99 (0.18), residues: 890 sheet: -2.65 (0.31), residues: 272 loop : -0.89 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 736 TYR 0.030 0.002 TYR C 474 PHE 0.019 0.001 PHE C 346 TRP 0.018 0.001 TRP B 796 HIS 0.008 0.001 HIS C 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (20912) covalent geometry : angle 0.67315 / 0.33 (28374) SS BOND : bond 0.00537 / 0.31 ( 16) SS BOND : angle 1.69694 / 0.95 ( 32) hydrogen bonds : bond 0.03570 / 2.43 ( 684) hydrogen bonds : angle 4.59708 / 3.15 ( 1902) link_BETA1-4 : bond 0.00203 / 0.15 ( 2) link_BETA1-4 : angle 1.00083 / 0.60 ( 6) link_NAG-ASN : bond 0.00348 / 0.22 ( 4) link_NAG-ASN : angle 1.97447 / 1.39 ( 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 236 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9315 (m-30) cc_final: 0.9089 (p0) REVERT: A 417 PHE cc_start: 0.9490 (m-80) cc_final: 0.9213 (m-80) REVERT: A 498 LEU cc_start: 0.9764 (tp) cc_final: 0.9550 (tp) REVERT: A 549 PHE cc_start: 0.9095 (t80) cc_final: 0.8293 (t80) REVERT: A 602 MET cc_start: 0.8780 (mpp) cc_final: 0.8465 (mpp) REVERT: A 761 MET cc_start: 0.8755 (tmm) cc_final: 0.8378 (tmm) REVERT: A 777 MET cc_start: 0.9256 (tpt) cc_final: 0.8969 (tpp) REVERT: B 571 LEU cc_start: 0.9765 (tp) cc_final: 0.9420 (tt) REVERT: B 602 MET cc_start: 0.8855 (mpp) cc_final: 0.8617 (mpp) REVERT: B 743 LEU cc_start: 0.9741 (mm) cc_final: 0.9471 (mt) REVERT: B 761 MET cc_start: 0.8916 (tmm) cc_final: 0.8636 (tmm) REVERT: B 777 MET cc_start: 0.9106 (tpt) cc_final: 0.8830 (tpt) REVERT: B 785 PHE cc_start: 0.8925 (m-80) cc_final: 0.8301 (m-80) REVERT: B 856 MET cc_start: 0.9531 (tmm) cc_final: 0.9055 (ppp) REVERT: B 857 MET cc_start: 0.8580 (tpt) cc_final: 0.8278 (tpp) REVERT: C 73 LEU cc_start: 0.9822 (tp) cc_final: 0.9616 (tp) REVERT: C 138 MET cc_start: 0.9713 (tpp) cc_final: 0.9435 (tpp) REVERT: C 139 MET cc_start: 0.9636 (mmm) cc_final: 0.9240 (mmm) REVERT: C 179 MET cc_start: 0.9355 (pmm) cc_final: 0.9065 (pmm) REVERT: C 186 MET cc_start: 0.9139 (mmp) cc_final: 0.8932 (mmp) REVERT: C 220 PHE cc_start: 0.9605 (m-10) cc_final: 0.9382 (m-10) REVERT: C 252 HIS cc_start: 0.8972 (m-70) cc_final: 0.8703 (m-70) REVERT: C 467 GLN cc_start: 0.9494 (pt0) cc_final: 0.9256 (pt0) REVERT: C 476 TRP cc_start: 0.9489 (t60) cc_final: 0.8716 (t60) REVERT: C 483 PHE cc_start: 0.9700 (t80) cc_final: 0.9409 (t80) REVERT: D 72 MET cc_start: 0.9382 (ppp) cc_final: 0.9130 (ppp) REVERT: D 102 MET cc_start: 0.8603 (mmp) cc_final: 0.8230 (mmm) REVERT: D 139 MET cc_start: 0.9590 (mmm) cc_final: 0.9307 (mmm) REVERT: D 186 MET cc_start: 0.9231 (mmp) cc_final: 0.8966 (mmp) REVERT: D 220 PHE cc_start: 0.9606 (m-10) cc_final: 0.9381 (m-10) REVERT: D 293 MET cc_start: 0.9619 (tmm) cc_final: 0.9256 (tpp) REVERT: D 297 PHE cc_start: 0.9465 (t80) cc_final: 0.8882 (t80) REVERT: D 301 LEU cc_start: 0.9673 (mt) cc_final: 0.9270 (mt) REVERT: D 450 LYS cc_start: 0.9710 (mmtt) cc_final: 0.9426 (mmtm) REVERT: D 483 PHE cc_start: 0.9700 (t80) cc_final: 0.9376 (t80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1245 time to fit residues: 49.9098 Evaluate side-chains 179 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 0.3980 chunk 251 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 419 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN ** 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.045591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035965 restraints weight = 174701.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036850 restraints weight = 122029.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037519 restraints weight = 95614.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038002 restraints weight = 79358.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038278 restraints weight = 69079.825| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20934 Z= 0.133 Angle : 0.654 11.377 28424 Z= 0.320 Chirality : 0.043 0.236 3264 Planarity : 0.004 0.048 3548 Dihedral : 4.638 24.807 2746 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.62 (0.17), residues: 2522 helix: 1.00 (0.18), residues: 900 sheet: -2.61 (0.31), residues: 272 loop : -0.88 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 736 TYR 0.020 0.001 TYR C 474 PHE 0.020 0.001 PHE C 346 TRP 0.016 0.001 TRP B 796 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20912) covalent geometry : angle 0.65123 / 0.32 (28374) SS BOND : bond 0.00388 / 0.21 ( 16) SS BOND : angle 1.68793 / 0.92 ( 32) hydrogen bonds : bond 0.03530 / 2.41 ( 684) hydrogen bonds : angle 4.50370 / 3.08 ( 1902) link_BETA1-4 : bond 0.00209 / 0.14 ( 2) link_BETA1-4 : angle 1.00005 / 0.54 ( 6) link_NAG-ASN : bond 0.00195 / 0.11 ( 4) link_NAG-ASN : angle 1.87349 / 1.29 ( 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 237 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 PHE cc_start: 0.9515 (m-80) cc_final: 0.9227 (m-80) REVERT: A 498 LEU cc_start: 0.9761 (tp) cc_final: 0.9555 (tp) REVERT: A 549 PHE cc_start: 0.8938 (t80) cc_final: 0.8078 (t80) REVERT: A 602 MET cc_start: 0.8818 (mpp) cc_final: 0.8502 (mpp) REVERT: A 743 LEU cc_start: 0.9763 (mm) cc_final: 0.9511 (mt) REVERT: A 777 MET cc_start: 0.9280 (tpt) cc_final: 0.8976 (tpp) REVERT: B 498 LEU cc_start: 0.9747 (tp) cc_final: 0.9526 (tp) REVERT: B 571 LEU cc_start: 0.9756 (tp) cc_final: 0.9411 (tt) REVERT: B 602 MET cc_start: 0.8825 (mpp) cc_final: 0.8577 (mpp) REVERT: B 743 LEU cc_start: 0.9736 (mm) cc_final: 0.9461 (mt) REVERT: B 761 MET cc_start: 0.8875 (tmm) cc_final: 0.8593 (tmm) REVERT: B 777 MET cc_start: 0.9160 (tpt) cc_final: 0.8845 (tpt) REVERT: B 785 PHE cc_start: 0.8845 (m-80) cc_final: 0.8413 (m-80) REVERT: B 856 MET cc_start: 0.9540 (tmm) cc_final: 0.9104 (ppp) REVERT: B 857 MET cc_start: 0.8619 (tpt) cc_final: 0.8280 (tpp) REVERT: C 73 LEU cc_start: 0.9813 (tp) cc_final: 0.9609 (tp) REVERT: C 138 MET cc_start: 0.9687 (tpp) cc_final: 0.9382 (tpp) REVERT: C 139 MET cc_start: 0.9632 (mmm) cc_final: 0.9269 (mmm) REVERT: C 179 MET cc_start: 0.9361 (pmm) cc_final: 0.9119 (pmm) REVERT: C 186 MET cc_start: 0.9171 (mmp) cc_final: 0.8929 (mmp) REVERT: C 220 PHE cc_start: 0.9618 (m-10) cc_final: 0.9395 (m-10) REVERT: C 252 HIS cc_start: 0.8927 (m-70) cc_final: 0.8670 (m-70) REVERT: C 467 GLN cc_start: 0.9465 (pt0) cc_final: 0.9222 (pt0) REVERT: C 476 TRP cc_start: 0.9438 (t60) cc_final: 0.8901 (t60) REVERT: C 483 PHE cc_start: 0.9700 (t80) cc_final: 0.9384 (t80) REVERT: D 72 MET cc_start: 0.9387 (ppp) cc_final: 0.9161 (ppp) REVERT: D 102 MET cc_start: 0.8618 (mmp) cc_final: 0.8244 (mmm) REVERT: D 139 MET cc_start: 0.9621 (mmm) cc_final: 0.9368 (mmm) REVERT: D 186 MET cc_start: 0.9236 (mmp) cc_final: 0.8966 (mmp) REVERT: D 220 PHE cc_start: 0.9612 (m-10) cc_final: 0.9377 (m-10) REVERT: D 293 MET cc_start: 0.9688 (tmm) cc_final: 0.9326 (tpp) REVERT: D 297 PHE cc_start: 0.9435 (t80) cc_final: 0.8997 (t80) REVERT: D 450 LYS cc_start: 0.9709 (mmtt) cc_final: 0.9425 (mmtm) REVERT: D 483 PHE cc_start: 0.9674 (t80) cc_final: 0.9342 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1222 time to fit residues: 49.2512 Evaluate side-chains 177 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 96 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 177 optimal weight: 0.0870 chunk 38 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 7.2166 ------------------------------------------------------------------------------- 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 419 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN ** 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 265 HIS ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 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 = 0.3138 r_free = 0.3138 target = 0.044906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.035460 restraints weight = 181760.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036363 restraints weight = 127582.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037006 restraints weight = 98147.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037485 restraints weight = 81629.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037828 restraints weight = 70955.043| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20934 Z= 0.215 Angle : 0.728 10.642 28424 Z= 0.359 Chirality : 0.044 0.236 3264 Planarity : 0.004 0.045 3548 Dihedral : 4.850 26.772 2746 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.73 (0.17), residues: 2522 helix: 0.90 (0.17), residues: 900 sheet: -2.78 (0.30), residues: 276 loop : -0.90 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 723 TYR 0.029 0.002 TYR D 146 PHE 0.016 0.002 PHE C 297 TRP 0.022 0.002 TRP A 796 HIS 0.006 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (20912) covalent geometry : angle 0.72493 / 0.36 (28374) SS BOND : bond 0.00478 / 0.22 ( 16) SS BOND : angle 1.63696 / 0.91 ( 32) hydrogen bonds : bond 0.03698 / 2.51 ( 684) hydrogen bonds : angle 4.68084 / 3.21 ( 1902) link_BETA1-4 : bond 0.00196 / 0.14 ( 2) link_BETA1-4 : angle 1.23913 / 0.82 ( 6) link_NAG-ASN : bond 0.00580 / 0.36 ( 4) link_NAG-ASN : angle 2.11427 / 1.47 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.89 seconds wall clock time: 51 minutes 4.59 seconds (3064.59 seconds total)