Starting phenix.real_space_refine on Thu Mar 5 07:41:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyn_30501/03_2026/7cyn_30501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyn_30501/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyn_30501/03_2026/7cyn_30501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyn_30501/03_2026/7cyn_30501.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyn_30501/03_2026/7cyn_30501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyn_30501/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, D, F Time building chain proxies: 7.08, per 1000 atoms: 0.35 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: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 3.64 Time building geometry restraints manager: 2.11 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: 11560 17.22 - 34.44: 868 34.44 - 51.66: 170 51.66 - 68.88: 20 68.88 - 86.10: 18 Dihedral angle restraints: 12636 sinusoidal: 5166 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 12633 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: 0.03 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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 : 12.509 86.102 7760 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 covalent geometry : bond 0.00202 (20912) covalent geometry : angle 0.51911 (28374) SS BOND : bond 0.00122 ( 16) SS BOND : angle 0.39036 ( 32) hydrogen bonds : bond 0.15422 ( 684) hydrogen bonds : angle 5.60707 ( 1902) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 0.72373 ( 6) link_NAG-ASN : bond 0.00234 ( 4) link_NAG-ASN : angle 0.99871 ( 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 : 0.719 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: 0.1251 time to fit residues: 91.0890 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 : 0.628 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3423 r_free = 0.3423 target = 0.056283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.044635 restraints weight = 148049.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.045579 restraints weight = 115828.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046184 restraints weight = 95658.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046757 restraints weight = 83159.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047099 restraints weight = 74348.567| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20934 Z= 0.128 Angle : 0.625 9.180 28424 Z= 0.306 Chirality : 0.043 0.229 3264 Planarity : 0.004 0.056 3548 Dihedral : 3.970 22.697 2872 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.54 % 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: -1.60 (0.17), residues: 2522 helix: 0.23 (0.17), residues: 906 sheet: -2.59 (0.32), residues: 274 loop : -1.66 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 376 TYR 0.011 0.001 TYR A 751 PHE 0.023 0.001 PHE C 346 TRP 0.022 0.001 TRP D 476 HIS 0.006 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00282 (20912) covalent geometry : angle 0.62450 (28374) SS BOND : bond 0.00754 ( 16) SS BOND : angle 0.70871 ( 32) hydrogen bonds : bond 0.03568 ( 684) hydrogen bonds : angle 4.20777 ( 1902) link_BETA1-4 : bond 0.00882 ( 2) link_BETA1-4 : angle 1.00400 ( 6) link_NAG-ASN : bond 0.00368 ( 4) link_NAG-ASN : angle 0.99970 ( 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 : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.9451 (m-30) cc_final: 0.9149 (p0) REVERT: A 309 TRP cc_start: 0.8569 (m-10) cc_final: 0.7907 (m-10) REVERT: A 417 PHE cc_start: 0.9490 (m-80) cc_final: 0.9066 (m-80) REVERT: A 498 LEU cc_start: 0.9813 (tp) cc_final: 0.9570 (tp) REVERT: A 602 MET cc_start: 0.8887 (mpp) cc_final: 0.8621 (mpp) REVERT: A 603 MET cc_start: 0.9379 (tmm) cc_final: 0.9100 (tmm) REVERT: A 714 VAL cc_start: 0.8153 (m) cc_final: 0.7718 (m) REVERT: A 779 LEU cc_start: 0.9141 (mp) cc_final: 0.8554 (mp) REVERT: B 275 ASN cc_start: 0.9587 (m110) cc_final: 0.9367 (p0) REVERT: B 302 LEU cc_start: 0.9622 (mt) cc_final: 0.9329 (mt) REVERT: B 309 TRP cc_start: 0.8734 (m-10) cc_final: 0.8143 (m-10) REVERT: B 402 LEU cc_start: 0.9488 (tp) cc_final: 0.9236 (tp) REVERT: B 417 PHE cc_start: 0.9346 (m-80) cc_final: 0.8918 (m-80) REVERT: B 498 LEU cc_start: 0.9728 (tp) cc_final: 0.9486 (tp) REVERT: B 603 MET cc_start: 0.9384 (tmm) cc_final: 0.9088 (tmm) REVERT: B 761 MET cc_start: 0.7947 (tmm) cc_final: 0.7301 (tmm) REVERT: B 777 MET cc_start: 0.8873 (tpt) cc_final: 0.8667 (tpp) REVERT: B 779 LEU cc_start: 0.9093 (mp) cc_final: 0.8539 (mp) REVERT: B 785 PHE cc_start: 0.8145 (m-80) cc_final: 0.7895 (m-80) REVERT: C 72 MET cc_start: 0.9334 (ppp) cc_final: 0.8498 (tmm) REVERT: C 73 LEU cc_start: 0.9759 (tp) cc_final: 0.9495 (tp) REVERT: C 84 MET cc_start: 0.9589 (tmm) cc_final: 0.9370 (tmm) REVERT: C 102 MET cc_start: 0.7785 (mpp) cc_final: 0.7403 (ppp) REVERT: C 108 ASP cc_start: 0.9360 (m-30) cc_final: 0.9031 (m-30) REVERT: C 220 PHE cc_start: 0.9471 (m-10) cc_final: 0.9266 (m-10) REVERT: C 306 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8597 (tp) REVERT: C 476 TRP cc_start: 0.9286 (t60) cc_final: 0.8822 (t60) REVERT: D 108 ASP cc_start: 0.9347 (m-30) cc_final: 0.8990 (m-30) REVERT: D 181 ASN cc_start: 0.9593 (t0) cc_final: 0.9165 (m-40) REVERT: D 306 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 384 LEU cc_start: 0.9055 (mt) cc_final: 0.8724 (pp) REVERT: D 476 TRP cc_start: 0.9229 (t60) cc_final: 0.8964 (t60) outliers start: 4 outliers final: 1 residues processed: 356 average time/residue: 0.1212 time to fit residues: 70.7718 Evaluate side-chains 260 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 7.9990 chunk 128 optimal weight: 0.0030 chunk 199 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 140 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 overall best weight: 9.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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 ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.040281 restraints weight = 175991.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041169 restraints weight = 128814.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041823 restraints weight = 102442.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042317 restraints weight = 86317.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042704 restraints weight = 75594.246| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 20934 Z= 0.312 Angle : 0.886 11.630 28424 Z= 0.433 Chirality : 0.047 0.247 3264 Planarity : 0.006 0.083 3548 Dihedral : 4.930 24.961 2872 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 0.18 % Allowed : 6.01 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2522 helix: 0.46 (0.17), residues: 912 sheet: -2.59 (0.31), residues: 272 loop : -1.35 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 622 TYR 0.021 0.002 TYR B 751 PHE 0.025 0.003 PHE D 224 TRP 0.021 0.002 TRP C 176 HIS 0.013 0.002 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00640 (20912) covalent geometry : angle 0.88306 (28374) SS BOND : bond 0.00937 ( 16) SS BOND : angle 1.62217 ( 32) hydrogen bonds : bond 0.04140 ( 684) hydrogen bonds : angle 4.69102 ( 1902) link_BETA1-4 : bond 0.01889 ( 2) link_BETA1-4 : angle 2.48044 ( 6) link_NAG-ASN : bond 0.01191 ( 4) link_NAG-ASN : angle 2.01778 ( 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 267 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.738 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 417 PHE cc_start: 0.9426 (m-80) cc_final: 0.9161 (m-80) REVERT: A 602 MET cc_start: 0.8836 (mpp) cc_final: 0.8533 (mpp) REVERT: A 761 MET cc_start: 0.8777 (tmm) cc_final: 0.8502 (tmm) REVERT: A 767 PHE cc_start: 0.9347 (m-10) cc_final: 0.9145 (p90) REVERT: A 779 LEU cc_start: 0.9361 (mp) cc_final: 0.9047 (mp) REVERT: B 402 LEU cc_start: 0.9600 (tp) cc_final: 0.9384 (tp) REVERT: B 417 PHE cc_start: 0.9499 (m-80) cc_final: 0.9225 (m-80) REVERT: B 603 MET cc_start: 0.9266 (tmm) cc_final: 0.9029 (tmm) REVERT: B 690 PHE cc_start: 0.8866 (t80) cc_final: 0.8575 (t80) REVERT: B 761 MET cc_start: 0.8762 (tmm) cc_final: 0.8508 (tmm) REVERT: B 777 MET cc_start: 0.9023 (tpt) cc_final: 0.8780 (tpp) REVERT: B 847 ILE cc_start: 0.9433 (tt) cc_final: 0.9222 (pt) REVERT: C 72 MET cc_start: 0.9434 (ppp) cc_final: 0.9080 (ppp) REVERT: C 84 MET cc_start: 0.9527 (tmm) cc_final: 0.9318 (tmm) REVERT: C 108 ASP cc_start: 0.9480 (m-30) cc_final: 0.9100 (m-30) REVERT: C 138 MET cc_start: 0.9565 (tpp) cc_final: 0.9054 (tpt) REVERT: C 139 MET cc_start: 0.9652 (mmm) cc_final: 0.9299 (mmm) REVERT: C 179 MET cc_start: 0.9550 (ptm) cc_final: 0.9316 (ptt) REVERT: C 186 MET cc_start: 0.9078 (mmp) cc_final: 0.8870 (mmp) REVERT: C 220 PHE cc_start: 0.9450 (m-10) cc_final: 0.9237 (m-10) REVERT: C 476 TRP cc_start: 0.9567 (t60) cc_final: 0.9145 (t60) REVERT: C 514 MET cc_start: 0.8778 (mmt) cc_final: 0.8369 (mmm) REVERT: D 72 MET cc_start: 0.9379 (ppp) cc_final: 0.8979 (ppp) REVERT: D 84 MET cc_start: 0.9494 (tmm) cc_final: 0.9256 (tmm) REVERT: D 138 MET cc_start: 0.9572 (tpt) cc_final: 0.9163 (tpt) REVERT: D 139 MET cc_start: 0.9781 (mmm) cc_final: 0.9410 (mmm) REVERT: D 179 MET cc_start: 0.9498 (ptm) cc_final: 0.9256 (ptm) REVERT: D 186 MET cc_start: 0.9282 (mmp) cc_final: 0.9038 (mmp) REVERT: D 220 PHE cc_start: 0.9543 (m-10) cc_final: 0.9270 (m-10) outliers start: 4 outliers final: 3 residues processed: 267 average time/residue: 0.1234 time to fit residues: 54.3980 Evaluate side-chains 187 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 85 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** 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 83 GLN D 85 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.050447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.039834 restraints weight = 161527.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040652 restraints weight = 120907.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041320 restraints weight = 98621.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041808 restraints weight = 83895.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042112 restraints weight = 74109.671| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20934 Z= 0.132 Angle : 0.622 7.970 28424 Z= 0.307 Chirality : 0.043 0.230 3264 Planarity : 0.004 0.049 3548 Dihedral : 4.380 23.683 2872 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: -0.84 (0.17), residues: 2522 helix: 0.93 (0.18), residues: 898 sheet: -2.59 (0.31), residues: 272 loop : -1.14 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 736 TYR 0.015 0.001 TYR D 349 PHE 0.025 0.001 PHE D 346 TRP 0.017 0.001 TRP A 796 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00285 (20912) covalent geometry : angle 0.61672 (28374) SS BOND : bond 0.00766 ( 16) SS BOND : angle 1.79160 ( 32) hydrogen bonds : bond 0.03319 ( 684) hydrogen bonds : angle 4.22969 ( 1902) link_BETA1-4 : bond 0.00804 ( 2) link_BETA1-4 : angle 1.48464 ( 6) link_NAG-ASN : bond 0.00273 ( 4) link_NAG-ASN : angle 2.95837 ( 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 271 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.616 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: 0.9540 (m-80) cc_final: 0.9238 (m-80) REVERT: A 498 LEU cc_start: 0.9813 (tp) cc_final: 0.9568 (tp) REVERT: A 602 MET cc_start: 0.8891 (mpp) cc_final: 0.8584 (mpp) REVERT: A 779 LEU cc_start: 0.9238 (mp) cc_final: 0.8944 (mp) REVERT: B 111 MET cc_start: 0.7482 (mmm) cc_final: 0.7173 (mmm) REVERT: B 417 PHE cc_start: 0.9496 (m-80) cc_final: 0.9172 (m-80) REVERT: B 498 LEU cc_start: 0.9784 (tp) cc_final: 0.9481 (tp) REVERT: B 602 MET cc_start: 0.9231 (mpp) cc_final: 0.9000 (mpp) REVERT: B 603 MET cc_start: 0.9293 (tmm) cc_final: 0.9020 (tmm) REVERT: B 690 PHE cc_start: 0.8850 (t80) cc_final: 0.8577 (t80) REVERT: B 777 MET cc_start: 0.9087 (tpt) cc_final: 0.8858 (tpp) REVERT: B 785 PHE cc_start: 0.8777 (m-80) cc_final: 0.8325 (m-10) REVERT: C 73 LEU cc_start: 0.9826 (tp) cc_final: 0.9624 (tp) REVERT: C 84 MET cc_start: 0.9495 (tmm) cc_final: 0.9260 (tmm) REVERT: C 102 MET cc_start: 0.8411 (mmp) cc_final: 0.8086 (mmt) REVERT: C 138 MET cc_start: 0.9642 (tpp) cc_final: 0.9114 (tpt) REVERT: C 139 MET cc_start: 0.9587 (mmm) cc_final: 0.9289 (mmm) REVERT: C 179 MET cc_start: 0.9501 (ptm) cc_final: 0.9279 (ptm) REVERT: C 183 ILE cc_start: 0.9878 (mm) cc_final: 0.9649 (tt) REVERT: C 306 LEU cc_start: 0.9348 (mm) cc_final: 0.8724 (tt) REVERT: C 476 TRP cc_start: 0.9458 (t60) cc_final: 0.8806 (t60) REVERT: D 72 MET cc_start: 0.9374 (ppp) cc_final: 0.9087 (ppp) REVERT: D 138 MET cc_start: 0.9530 (tpt) cc_final: 0.9247 (tpt) REVERT: D 139 MET cc_start: 0.9770 (mmm) cc_final: 0.9436 (mmm) REVERT: D 186 MET cc_start: 0.9297 (mmp) cc_final: 0.9057 (mmp) REVERT: D 220 PHE cc_start: 0.9488 (m-10) cc_final: 0.9207 (m-10) REVERT: D 293 MET cc_start: 0.9632 (tmm) cc_final: 0.9404 (tpp) REVERT: D 306 LEU cc_start: 0.9316 (mm) cc_final: 0.8698 (tt) REVERT: D 476 TRP cc_start: 0.9376 (t60) cc_final: 0.8892 (t60) REVERT: D 483 PHE cc_start: 0.9691 (t80) cc_final: 0.9410 (t80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1216 time to fit residues: 55.0044 Evaluate side-chains 190 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** 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 167 ASN B 298 HIS B 337 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037692 restraints weight = 170019.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038594 restraints weight = 124308.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039223 restraints weight = 98588.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.039730 restraints weight = 83469.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.040112 restraints weight = 73309.398| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20934 Z= 0.186 Angle : 0.666 8.059 28424 Z= 0.328 Chirality : 0.043 0.190 3264 Planarity : 0.004 0.043 3548 Dihedral : 4.480 24.326 2872 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2522 helix: 0.99 (0.18), residues: 912 sheet: -2.58 (0.31), residues: 270 loop : -0.98 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 519 TYR 0.014 0.002 TYR C 248 PHE 0.018 0.001 PHE D 483 TRP 0.045 0.002 TRP A 635 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00392 (20912) covalent geometry : angle 0.66378 (28374) SS BOND : bond 0.00552 ( 16) SS BOND : angle 1.49154 ( 32) hydrogen bonds : bond 0.03333 ( 684) hydrogen bonds : angle 4.26537 ( 1902) link_BETA1-4 : bond 0.00224 ( 2) link_BETA1-4 : angle 1.31378 ( 6) link_NAG-ASN : bond 0.00550 ( 4) link_NAG-ASN : angle 1.71874 ( 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 247 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6604 (mmm) cc_final: 0.6241 (mmm) REVERT: A 402 LEU cc_start: 0.9683 (tp) cc_final: 0.9477 (tp) REVERT: A 417 PHE cc_start: 0.9543 (m-80) cc_final: 0.9248 (m-80) REVERT: A 498 LEU cc_start: 0.9796 (tp) cc_final: 0.9522 (tp) REVERT: A 602 MET cc_start: 0.8867 (mpp) cc_final: 0.8561 (mpp) REVERT: A 635 TRP cc_start: 0.9200 (m-90) cc_final: 0.8813 (m-90) REVERT: A 777 MET cc_start: 0.9076 (tpt) cc_final: 0.8866 (tpp) REVERT: A 779 LEU cc_start: 0.9288 (mp) cc_final: 0.9023 (mp) REVERT: B 111 MET cc_start: 0.7470 (mmm) cc_final: 0.7218 (mmm) REVERT: B 402 LEU cc_start: 0.9703 (tp) cc_final: 0.9488 (tp) REVERT: B 417 PHE cc_start: 0.9558 (m-80) cc_final: 0.9278 (m-80) REVERT: B 498 LEU cc_start: 0.9737 (tp) cc_final: 0.9454 (tp) REVERT: B 571 LEU cc_start: 0.9828 (tp) cc_final: 0.9570 (tt) REVERT: B 602 MET cc_start: 0.9102 (mpp) cc_final: 0.8873 (mpp) REVERT: B 777 MET cc_start: 0.9163 (tpt) cc_final: 0.8920 (tpp) REVERT: C 72 MET cc_start: 0.9399 (ppp) cc_final: 0.9174 (ppp) REVERT: C 73 LEU cc_start: 0.9826 (tp) cc_final: 0.9619 (tp) REVERT: C 102 MET cc_start: 0.8576 (mmp) cc_final: 0.8021 (mmt) REVERT: C 138 MET cc_start: 0.9738 (tpp) cc_final: 0.9199 (tpt) REVERT: C 139 MET cc_start: 0.9483 (mmm) cc_final: 0.9237 (mmm) REVERT: C 186 MET cc_start: 0.9132 (mmp) cc_final: 0.8888 (mmp) REVERT: C 220 PHE cc_start: 0.9525 (m-10) cc_final: 0.9300 (m-10) REVERT: C 306 LEU cc_start: 0.9349 (mm) cc_final: 0.8830 (tt) REVERT: C 450 LYS cc_start: 0.9685 (mmtt) cc_final: 0.9359 (mmtm) REVERT: C 476 TRP cc_start: 0.9504 (t60) cc_final: 0.8940 (t60) REVERT: D 72 MET cc_start: 0.9376 (ppp) cc_final: 0.9071 (ppp) REVERT: D 139 MET cc_start: 0.9626 (mmm) cc_final: 0.9380 (mmm) REVERT: D 186 MET cc_start: 0.9303 (mmp) cc_final: 0.9023 (mmp) REVERT: D 220 PHE cc_start: 0.9568 (m-10) cc_final: 0.9290 (m-10) REVERT: D 293 MET cc_start: 0.9675 (tmm) cc_final: 0.9412 (tpp) REVERT: D 306 LEU cc_start: 0.9317 (mm) cc_final: 0.8731 (tt) REVERT: D 483 PHE cc_start: 0.9731 (t80) cc_final: 0.9455 (t80) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1169 time to fit residues: 48.8757 Evaluate side-chains 184 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.037102 restraints weight = 171088.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037944 restraints weight = 123725.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038585 restraints weight = 98593.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.039068 restraints weight = 82788.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039429 restraints weight = 72534.170| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20934 Z= 0.188 Angle : 0.662 7.161 28424 Z= 0.330 Chirality : 0.044 0.314 3264 Planarity : 0.004 0.042 3548 Dihedral : 4.547 25.267 2872 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -0.63 (0.17), residues: 2522 helix: 0.99 (0.17), residues: 918 sheet: -2.55 (0.31), residues: 270 loop : -0.93 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 736 TYR 0.016 0.001 TYR D 248 PHE 0.018 0.001 PHE D 483 TRP 0.038 0.002 TRP B 793 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00392 (20912) covalent geometry : angle 0.65867 (28374) SS BOND : bond 0.00516 ( 16) SS BOND : angle 1.61382 ( 32) hydrogen bonds : bond 0.03478 ( 684) hydrogen bonds : angle 4.35799 ( 1902) link_BETA1-4 : bond 0.00209 ( 2) link_BETA1-4 : angle 1.26224 ( 6) link_NAG-ASN : bond 0.00323 ( 4) link_NAG-ASN : angle 2.05373 ( 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 241 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.765 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: 0.6385 (mmm) cc_final: 0.6106 (mmm) REVERT: A 402 LEU cc_start: 0.9637 (tp) cc_final: 0.9435 (tp) REVERT: A 417 PHE cc_start: 0.9520 (m-80) cc_final: 0.9218 (m-80) REVERT: A 498 LEU cc_start: 0.9783 (tp) cc_final: 0.9517 (tp) REVERT: A 602 MET cc_start: 0.8910 (mpp) cc_final: 0.8558 (mpp) REVERT: A 635 TRP cc_start: 0.9179 (m-90) cc_final: 0.8958 (m-90) REVERT: A 777 MET cc_start: 0.9163 (tpt) cc_final: 0.8905 (tpp) REVERT: B 111 MET cc_start: 0.7415 (mmm) cc_final: 0.7213 (mmm) REVERT: B 417 PHE cc_start: 0.9513 (m-80) cc_final: 0.9217 (m-80) REVERT: B 498 LEU cc_start: 0.9755 (tp) cc_final: 0.9466 (tp) REVERT: B 571 LEU cc_start: 0.9795 (tp) cc_final: 0.9481 (tt) REVERT: B 602 MET cc_start: 0.9055 (mpp) cc_final: 0.8810 (mpp) REVERT: B 779 LEU cc_start: 0.9420 (mp) cc_final: 0.9192 (mp) REVERT: C 73 LEU cc_start: 0.9827 (tp) cc_final: 0.9619 (tp) REVERT: C 102 MET cc_start: 0.8666 (mmp) cc_final: 0.8113 (mmt) REVERT: C 138 MET cc_start: 0.9716 (tpp) cc_final: 0.9356 (tpp) REVERT: C 139 MET cc_start: 0.9459 (mmm) cc_final: 0.9167 (mmm) REVERT: C 186 MET cc_start: 0.9114 (mmp) cc_final: 0.8882 (mmp) REVERT: C 220 PHE cc_start: 0.9529 (m-10) cc_final: 0.9288 (m-10) REVERT: C 252 HIS cc_start: 0.9299 (m-70) cc_final: 0.9080 (m-70) REVERT: C 450 LYS cc_start: 0.9673 (mmtt) cc_final: 0.9442 (mmtm) REVERT: C 476 TRP cc_start: 0.9509 (t60) cc_final: 0.8935 (t60) REVERT: D 72 MET cc_start: 0.9372 (ppp) cc_final: 0.9091 (ppp) REVERT: D 139 MET cc_start: 0.9668 (mmm) cc_final: 0.9455 (mmm) REVERT: D 146 TYR cc_start: 0.9605 (m-80) cc_final: 0.9244 (m-80) REVERT: D 186 MET cc_start: 0.9270 (mmp) cc_final: 0.9000 (mmp) REVERT: D 220 PHE cc_start: 0.9575 (m-10) cc_final: 0.9313 (m-10) REVERT: D 293 MET cc_start: 0.9626 (tmm) cc_final: 0.9295 (tpp) REVERT: D 297 PHE cc_start: 0.9475 (t80) cc_final: 0.9045 (t80) REVERT: D 301 LEU cc_start: 0.9665 (mt) cc_final: 0.9410 (mt) REVERT: D 306 LEU cc_start: 0.9315 (mm) cc_final: 0.8729 (tt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1183 time to fit residues: 48.2538 Evaluate side-chains 182 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 5.9990 chunk 189 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 475 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037164 restraints weight = 170223.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038013 restraints weight = 121821.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.038695 restraints weight = 96554.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039209 restraints weight = 80937.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.039578 restraints weight = 70652.152| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20934 Z= 0.126 Angle : 0.602 8.391 28424 Z= 0.297 Chirality : 0.043 0.222 3264 Planarity : 0.004 0.041 3548 Dihedral : 4.357 24.286 2872 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2522 helix: 1.13 (0.18), residues: 914 sheet: -2.57 (0.31), residues: 274 loop : -0.86 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 736 TYR 0.014 0.001 TYR D 248 PHE 0.027 0.001 PHE C 483 TRP 0.030 0.001 TRP B 793 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00279 (20912) covalent geometry : angle 0.59974 (28374) SS BOND : bond 0.00393 ( 16) SS BOND : angle 1.18285 ( 32) hydrogen bonds : bond 0.03239 ( 684) hydrogen bonds : angle 4.20966 ( 1902) link_BETA1-4 : bond 0.00175 ( 2) link_BETA1-4 : angle 0.99265 ( 6) link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 1.68446 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.747 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: 0.6356 (mmm) cc_final: 0.6095 (mmm) REVERT: A 417 PHE cc_start: 0.9512 (m-80) cc_final: 0.9162 (m-80) REVERT: A 498 LEU cc_start: 0.9779 (tp) cc_final: 0.9501 (tp) REVERT: A 549 PHE cc_start: 0.9043 (t80) cc_final: 0.8232 (t80) REVERT: A 602 MET cc_start: 0.8829 (mpp) cc_final: 0.8508 (mpp) REVERT: A 777 MET cc_start: 0.9170 (tpt) cc_final: 0.8903 (tpp) REVERT: B 417 PHE cc_start: 0.9560 (m-80) cc_final: 0.9287 (m-80) REVERT: B 498 LEU cc_start: 0.9793 (tp) cc_final: 0.9554 (tp) REVERT: B 571 LEU cc_start: 0.9782 (tp) cc_final: 0.9568 (tt) REVERT: B 602 MET cc_start: 0.8931 (mpp) cc_final: 0.8719 (mpp) REVERT: B 777 MET cc_start: 0.9054 (tpt) cc_final: 0.8639 (tpt) REVERT: B 779 LEU cc_start: 0.9367 (mp) cc_final: 0.9151 (mp) REVERT: B 785 PHE cc_start: 0.8808 (m-80) cc_final: 0.8442 (m-80) REVERT: C 73 LEU cc_start: 0.9820 (tp) cc_final: 0.9604 (tp) REVERT: C 84 MET cc_start: 0.9414 (tmm) cc_final: 0.9184 (tmm) REVERT: C 102 MET cc_start: 0.8595 (mmp) cc_final: 0.8044 (mmt) REVERT: C 138 MET cc_start: 0.9727 (tpp) cc_final: 0.9343 (tpp) REVERT: C 139 MET cc_start: 0.9513 (mmm) cc_final: 0.9239 (mmm) REVERT: C 186 MET cc_start: 0.9111 (mmp) cc_final: 0.8869 (mmp) REVERT: C 220 PHE cc_start: 0.9525 (m-10) cc_final: 0.9319 (m-10) REVERT: C 252 HIS cc_start: 0.9296 (m-70) cc_final: 0.9079 (m-70) REVERT: C 476 TRP cc_start: 0.9478 (t60) cc_final: 0.8843 (t60) REVERT: C 483 PHE cc_start: 0.9710 (t80) cc_final: 0.9375 (t80) REVERT: D 72 MET cc_start: 0.9388 (ppp) cc_final: 0.9130 (ppp) REVERT: D 139 MET cc_start: 0.9684 (mmm) cc_final: 0.9466 (mmm) REVERT: D 146 TYR cc_start: 0.9556 (m-80) cc_final: 0.9191 (m-10) REVERT: D 186 MET cc_start: 0.9266 (mmp) cc_final: 0.8986 (mmp) REVERT: D 220 PHE cc_start: 0.9586 (m-10) cc_final: 0.9320 (m-10) REVERT: D 293 MET cc_start: 0.9634 (tmm) cc_final: 0.9304 (tpp) REVERT: D 306 LEU cc_start: 0.9288 (mm) cc_final: 0.8634 (tt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1153 time to fit residues: 49.2364 Evaluate side-chains 183 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 GLN ** 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 = 0.3203 r_free = 0.3203 target = 0.047362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037221 restraints weight = 170413.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038096 restraints weight = 122901.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038774 restraints weight = 96384.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039279 restraints weight = 80963.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.039657 restraints weight = 70678.339| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20934 Z= 0.142 Angle : 0.621 7.241 28424 Z= 0.307 Chirality : 0.043 0.209 3264 Planarity : 0.004 0.043 3548 Dihedral : 4.392 24.740 2872 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -0.47 (0.18), residues: 2522 helix: 1.14 (0.18), residues: 914 sheet: -2.53 (0.31), residues: 272 loop : -0.82 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 723 TYR 0.027 0.001 TYR D 146 PHE 0.022 0.001 PHE C 483 TRP 0.052 0.002 TRP A 635 HIS 0.006 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00309 (20912) covalent geometry : angle 0.61830 (28374) SS BOND : bond 0.00316 ( 16) SS BOND : angle 1.28594 ( 32) hydrogen bonds : bond 0.03231 ( 684) hydrogen bonds : angle 4.22822 ( 1902) link_BETA1-4 : bond 0.00074 ( 2) link_BETA1-4 : angle 1.13536 ( 6) link_NAG-ASN : bond 0.00217 ( 4) link_NAG-ASN : angle 1.76722 ( 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 239 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.848 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: A 111 MET cc_start: 0.6518 (mmm) cc_final: 0.6307 (mmm) REVERT: A 417 PHE cc_start: 0.9542 (m-80) cc_final: 0.9237 (m-80) REVERT: A 498 LEU cc_start: 0.9799 (tp) cc_final: 0.9529 (tp) REVERT: A 549 PHE cc_start: 0.9068 (t80) cc_final: 0.8255 (t80) REVERT: A 602 MET cc_start: 0.8826 (mpp) cc_final: 0.8504 (mpp) REVERT: A 777 MET cc_start: 0.9197 (tpt) cc_final: 0.8944 (tpp) REVERT: B 417 PHE cc_start: 0.9528 (m-80) cc_final: 0.9269 (m-80) REVERT: B 498 LEU cc_start: 0.9779 (tp) cc_final: 0.9528 (tp) REVERT: B 571 LEU cc_start: 0.9776 (tp) cc_final: 0.9554 (tt) REVERT: B 602 MET cc_start: 0.8883 (mpp) cc_final: 0.8672 (mpp) REVERT: B 761 MET cc_start: 0.8917 (tmm) cc_final: 0.8560 (tmm) REVERT: B 777 MET cc_start: 0.9038 (tpt) cc_final: 0.8703 (tpt) REVERT: B 779 LEU cc_start: 0.9349 (mp) cc_final: 0.9146 (mp) REVERT: B 785 PHE cc_start: 0.8795 (m-80) cc_final: 0.8359 (m-80) REVERT: C 73 LEU cc_start: 0.9822 (tp) cc_final: 0.9608 (tp) REVERT: C 102 MET cc_start: 0.8648 (mmp) cc_final: 0.8138 (mmm) REVERT: C 138 MET cc_start: 0.9728 (tpp) cc_final: 0.9359 (tpp) REVERT: C 139 MET cc_start: 0.9512 (mmm) cc_final: 0.9231 (mmm) REVERT: C 186 MET cc_start: 0.9123 (mmp) cc_final: 0.8883 (mmp) REVERT: C 220 PHE cc_start: 0.9520 (m-10) cc_final: 0.9320 (m-10) REVERT: C 467 GLN cc_start: 0.9443 (pt0) cc_final: 0.9226 (pt0) REVERT: C 476 TRP cc_start: 0.9497 (t60) cc_final: 0.8868 (t60) REVERT: C 483 PHE cc_start: 0.9733 (t80) cc_final: 0.9338 (t80) REVERT: D 72 MET cc_start: 0.9392 (ppp) cc_final: 0.9141 (ppp) REVERT: D 73 LEU cc_start: 0.9786 (tp) cc_final: 0.9580 (tp) REVERT: D 139 MET cc_start: 0.9657 (mmm) cc_final: 0.9422 (mmm) REVERT: D 186 MET cc_start: 0.9216 (mmp) cc_final: 0.8941 (mmp) REVERT: D 220 PHE cc_start: 0.9581 (m-10) cc_final: 0.9324 (m-10) REVERT: D 293 MET cc_start: 0.9648 (tmm) cc_final: 0.9273 (tpp) REVERT: D 306 LEU cc_start: 0.9283 (mm) cc_final: 0.8635 (tt) REVERT: D 483 PHE cc_start: 0.9673 (t80) cc_final: 0.9348 (t80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1117 time to fit residues: 45.3657 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 : 0.769 ------------------------------------------------------------------------------- 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: 30.0000 chunk 3 optimal weight: 0.0770 chunk 232 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN A 757 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** 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 763 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.048466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038331 restraints weight = 165793.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.039211 restraints weight = 119813.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039876 restraints weight = 93632.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040260 restraints weight = 79463.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040674 restraints weight = 70731.854| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20934 Z= 0.117 Angle : 0.621 9.769 28424 Z= 0.304 Chirality : 0.043 0.183 3264 Planarity : 0.004 0.045 3548 Dihedral : 4.309 24.390 2872 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % 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: -0.44 (0.18), residues: 2522 helix: 1.19 (0.18), residues: 902 sheet: -2.50 (0.32), residues: 272 loop : -0.80 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 736 TYR 0.030 0.001 TYR C 474 PHE 0.029 0.001 PHE D 297 TRP 0.038 0.001 TRP A 635 HIS 0.009 0.001 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00258 (20912) covalent geometry : angle 0.61970 (28374) SS BOND : bond 0.00422 ( 16) SS BOND : angle 1.11212 ( 32) hydrogen bonds : bond 0.03286 ( 684) hydrogen bonds : angle 4.19542 ( 1902) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 1.01691 ( 6) link_NAG-ASN : bond 0.00149 ( 4) link_NAG-ASN : angle 1.66756 ( 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 248 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9749 (tp) cc_final: 0.9525 (pp) REVERT: A 417 PHE cc_start: 0.9544 (m-80) cc_final: 0.9208 (m-80) REVERT: A 498 LEU cc_start: 0.9805 (tp) cc_final: 0.9545 (tp) REVERT: A 549 PHE cc_start: 0.9033 (t80) cc_final: 0.8212 (t80) REVERT: A 602 MET cc_start: 0.8826 (mpp) cc_final: 0.8507 (mpp) REVERT: A 743 LEU cc_start: 0.9683 (mm) cc_final: 0.9436 (mt) REVERT: A 777 MET cc_start: 0.9189 (tpt) cc_final: 0.8930 (tpp) REVERT: A 785 PHE cc_start: 0.8815 (m-80) cc_final: 0.8285 (m-10) REVERT: B 417 PHE cc_start: 0.9575 (m-80) cc_final: 0.9224 (m-80) REVERT: B 498 LEU cc_start: 0.9779 (tp) cc_final: 0.9537 (tp) REVERT: B 571 LEU cc_start: 0.9791 (tp) cc_final: 0.9460 (tt) REVERT: B 743 LEU cc_start: 0.9583 (mm) cc_final: 0.9338 (mt) REVERT: B 761 MET cc_start: 0.8878 (tmm) cc_final: 0.8490 (tmm) REVERT: B 777 MET cc_start: 0.9012 (tpt) cc_final: 0.8690 (tpt) REVERT: B 785 PHE cc_start: 0.8716 (m-80) cc_final: 0.8281 (m-80) REVERT: C 73 LEU cc_start: 0.9824 (tp) cc_final: 0.9610 (tp) REVERT: C 84 MET cc_start: 0.9429 (tmm) cc_final: 0.9215 (tmm) REVERT: C 102 MET cc_start: 0.8653 (mmp) cc_final: 0.8047 (mmt) REVERT: C 138 MET cc_start: 0.9689 (tpp) cc_final: 0.9336 (tpp) REVERT: C 139 MET cc_start: 0.9530 (mmm) cc_final: 0.9265 (mmm) REVERT: C 186 MET cc_start: 0.9057 (mmp) cc_final: 0.8846 (mmp) REVERT: C 220 PHE cc_start: 0.9509 (m-10) cc_final: 0.9308 (m-10) REVERT: C 252 HIS cc_start: 0.9290 (m-70) cc_final: 0.9032 (m-70) REVERT: C 467 GLN cc_start: 0.9421 (pt0) cc_final: 0.9183 (pt0) REVERT: C 476 TRP cc_start: 0.9380 (t60) cc_final: 0.8843 (t60) REVERT: C 483 PHE cc_start: 0.9727 (t80) cc_final: 0.9376 (t80) REVERT: D 72 MET cc_start: 0.9394 (ppp) cc_final: 0.9184 (ppp) REVERT: D 139 MET cc_start: 0.9620 (mmm) cc_final: 0.9380 (mmm) REVERT: D 186 MET cc_start: 0.9165 (mmp) cc_final: 0.8905 (mmp) REVERT: D 220 PHE cc_start: 0.9588 (m-10) cc_final: 0.9375 (m-10) REVERT: D 293 MET cc_start: 0.9642 (tmm) cc_final: 0.9281 (tpp) REVERT: D 306 LEU cc_start: 0.9233 (mm) cc_final: 0.8571 (tt) REVERT: D 483 PHE cc_start: 0.9654 (t80) cc_final: 0.9306 (t80) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1115 time to fit residues: 47.5083 Evaluate side-chains 197 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 0.9990 chunk 251 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 389 ASN ** 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** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.036626 restraints weight = 173320.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037473 restraints weight = 123460.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038150 restraints weight = 97556.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038657 restraints weight = 81110.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039012 restraints weight = 70450.973| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20934 Z= 0.169 Angle : 0.661 8.225 28424 Z= 0.324 Chirality : 0.043 0.192 3264 Planarity : 0.004 0.043 3548 Dihedral : 4.452 23.038 2872 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2522 helix: 1.22 (0.18), residues: 902 sheet: -2.56 (0.31), residues: 274 loop : -0.74 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 636 TYR 0.019 0.002 TYR C 474 PHE 0.021 0.001 PHE C 483 TRP 0.033 0.002 TRP A 635 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00359 (20912) covalent geometry : angle 0.65891 (28374) SS BOND : bond 0.00441 ( 16) SS BOND : angle 1.26197 ( 32) hydrogen bonds : bond 0.03321 ( 684) hydrogen bonds : angle 4.29886 ( 1902) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 1.23782 ( 6) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.98096 ( 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 236 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 PHE cc_start: 0.9527 (m-80) cc_final: 0.9222 (m-80) REVERT: A 498 LEU cc_start: 0.9770 (tp) cc_final: 0.9539 (tp) REVERT: A 549 PHE cc_start: 0.9103 (t80) cc_final: 0.8281 (t80) REVERT: A 602 MET cc_start: 0.8777 (mpp) cc_final: 0.8460 (mpp) REVERT: A 743 LEU cc_start: 0.9749 (mm) cc_final: 0.9535 (mt) REVERT: A 777 MET cc_start: 0.9284 (tpt) cc_final: 0.8992 (tpp) REVERT: A 785 PHE cc_start: 0.8917 (m-80) cc_final: 0.8354 (m-10) REVERT: B 417 PHE cc_start: 0.9594 (m-80) cc_final: 0.9263 (m-80) REVERT: B 571 LEU cc_start: 0.9787 (tp) cc_final: 0.9477 (tt) REVERT: B 602 MET cc_start: 0.8917 (mpp) cc_final: 0.8629 (mpp) REVERT: B 743 LEU cc_start: 0.9675 (mm) cc_final: 0.9452 (mt) REVERT: B 761 MET cc_start: 0.8816 (tmm) cc_final: 0.8434 (tmm) REVERT: B 777 MET cc_start: 0.9113 (tpt) cc_final: 0.8805 (tpt) REVERT: B 785 PHE cc_start: 0.8825 (m-80) cc_final: 0.8412 (m-80) REVERT: C 73 LEU cc_start: 0.9823 (tp) cc_final: 0.9606 (tp) REVERT: C 102 MET cc_start: 0.8738 (mmp) cc_final: 0.8209 (mmm) REVERT: C 138 MET cc_start: 0.9719 (tpp) cc_final: 0.9379 (tpp) REVERT: C 139 MET cc_start: 0.9541 (mmm) cc_final: 0.9256 (mmm) REVERT: C 186 MET cc_start: 0.9145 (mmp) cc_final: 0.8897 (mmp) REVERT: C 252 HIS cc_start: 0.9330 (m-70) cc_final: 0.9021 (m-70) REVERT: C 450 LYS cc_start: 0.9660 (mmtt) cc_final: 0.9418 (mmtm) REVERT: C 467 GLN cc_start: 0.9453 (pt0) cc_final: 0.9104 (mp10) REVERT: C 476 TRP cc_start: 0.9382 (t60) cc_final: 0.8752 (t60) REVERT: C 483 PHE cc_start: 0.9759 (t80) cc_final: 0.9385 (t80) REVERT: D 72 MET cc_start: 0.9398 (ppp) cc_final: 0.9105 (ppp) REVERT: D 113 MET cc_start: 0.9164 (mmm) cc_final: 0.8531 (tmm) REVERT: D 139 MET cc_start: 0.9631 (mmm) cc_final: 0.9387 (mmm) REVERT: D 186 MET cc_start: 0.9205 (mmp) cc_final: 0.8956 (mmp) REVERT: D 220 PHE cc_start: 0.9614 (m-10) cc_final: 0.9366 (m-10) REVERT: D 293 MET cc_start: 0.9639 (tmm) cc_final: 0.9272 (tpp) REVERT: D 483 PHE cc_start: 0.9704 (t80) cc_final: 0.9478 (t80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1128 time to fit residues: 45.3783 Evaluate side-chains 183 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 8.9990 chunk 212 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 177 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037081 restraints weight = 169414.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038016 restraints weight = 120878.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038686 restraints weight = 94473.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039208 restraints weight = 79072.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039560 restraints weight = 68905.357| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20934 Z= 0.111 Angle : 0.620 8.258 28424 Z= 0.303 Chirality : 0.043 0.179 3264 Planarity : 0.004 0.047 3548 Dihedral : 4.335 23.644 2872 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2522 helix: 1.32 (0.18), residues: 878 sheet: -2.50 (0.32), residues: 272 loop : -0.77 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.018 0.001 TYR C 474 PHE 0.030 0.001 PHE D 297 TRP 0.036 0.002 TRP A 635 HIS 0.006 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00247 (20912) covalent geometry : angle 0.61875 (28374) SS BOND : bond 0.00364 ( 16) SS BOND : angle 1.00910 ( 32) hydrogen bonds : bond 0.03260 ( 684) hydrogen bonds : angle 4.20849 ( 1902) link_BETA1-4 : bond 0.00279 ( 2) link_BETA1-4 : angle 0.95838 ( 6) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 1.76424 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.23 seconds wall clock time: 47 minutes 27.24 seconds (2847.24 seconds total)