Starting phenix.real_space_refine on Fri Sep 11 19:49:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.map" model { file = "/net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vfx_65041/09_2026/9vfx_65041.cif" } resolution = 2.8 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= 0.015 sd= 0.304 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 48 5.16 5 C 6981 2.51 5 N 1796 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10923 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2410 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 286} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2956 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 21, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2955 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 364} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2406 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 286} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10923 At special positions: 0 Unit cell: (133.276, 103.452, 137.936, 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 48 16.00 O 2098 8.00 N 1796 7.00 C 6981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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 NAG-ASN " NAG A 401 " - " ASN A 17 " " NAG A 402 " - " ASN A 61 " " NAG A 403 " - " ASN A 74 " " NAG A 404 " - " ASN A 122 " " NAG A 405 " - " ASN A 165 " " NAG A 406 " - " ASN A 234 " " NAG B 701 " - " ASN B 343 " " NAG B 702 " - " ASN B 616 " " NAG C 401 " - " ASN C 17 " " NAG C 402 " - " ASN C 61 " " NAG C 403 " - " ASN C 122 " " NAG C 404 " - " ASN C 149 " " NAG C 405 " - " ASN C 165 " " NAG C 406 " - " ASN C 234 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 438.7 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 21 sheets defined 6.0% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.695A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.651A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.567A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.755A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.801A pdb=" N SER B 477 " --> pdb=" O GLN B 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 301 removed outlier: 3.862A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 removed outlier: 3.954A pdb=" N ASN D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 removed outlier: 4.078A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.543A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.116A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.522A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.334A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.633A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.595A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.643A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.504A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.569A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.530A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 311 through 314 removed outlier: 3.881A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 324 through 325 removed outlier: 6.761A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 354 through 357 removed outlier: 3.651A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 354 through 357 removed outlier: 3.651A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU D 516 " --> pdb=" O ASN D 394 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 512 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'D' and resid 664 through 665 Processing sheet with id=AB8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.650A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.650A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.605A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.003A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.779A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 696 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: 1.80 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3457 1.34 - 1.46: 2530 1.46 - 1.58: 5154 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 11194 Sorted by residual: bond pdb=" C1 NAG C 405 " pdb=" O5 NAG C 405 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C1 NAG C 403 " pdb=" O5 NAG C 403 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 11189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15067 1.88 - 3.77: 184 3.77 - 5.65: 5 5.65 - 7.54: 0 7.54 - 9.42: 1 Bond angle restraints: 15257 Sorted by residual: angle pdb=" CA LEU C 56 " pdb=" CB LEU C 56 " pdb=" CG LEU C 56 " ideal model delta sigma weight residual 116.30 125.72 -9.42 3.50e+00 8.16e-02 7.25e+00 angle pdb=" C VAL B 635 " pdb=" N TYR B 636 " pdb=" CA TYR B 636 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.04e+00 angle pdb=" N ALA C 123 " pdb=" CA ALA C 123 " pdb=" C ALA C 123 " ideal model delta sigma weight residual 114.75 112.13 2.62 1.26e+00 6.30e-01 4.33e+00 angle pdb=" C THR C 19 " pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta sigma weight residual 122.61 125.85 -3.24 1.56e+00 4.11e-01 4.31e+00 angle pdb=" C ALA D 570 " pdb=" N ASP D 571 " pdb=" CA ASP D 571 " ideal model delta sigma weight residual 121.54 125.43 -3.89 1.91e+00 2.74e-01 4.16e+00 ... (remaining 15252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 6544 15.51 - 31.01: 223 31.01 - 46.52: 21 46.52 - 62.03: 4 62.03 - 77.53: 1 Dihedral angle restraints: 6793 sinusoidal: 2781 harmonic: 4012 Sorted by residual: dihedral pdb=" N ARG D 454 " pdb=" CA ARG D 454 " pdb=" CB ARG D 454 " pdb=" CG ARG D 454 " ideal model delta sinusoidal sigma weight residual -180.00 -126.79 -53.21 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CA ASP D 571 " pdb=" CB ASP D 571 " pdb=" CG ASP D 571 " pdb=" OD1 ASP D 571 " ideal model delta sinusoidal sigma weight residual -30.00 -81.30 51.30 1 2.00e+01 2.50e-03 8.99e+00 dihedral pdb=" N CYS B 361 " pdb=" CA CYS B 361 " pdb=" CB CYS B 361 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 60.00 109.60 -49.60 3 1.50e+01 4.44e-03 8.80e+00 ... (remaining 6790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1142 0.032 - 0.063: 385 0.063 - 0.095: 118 0.095 - 0.126: 109 0.126 - 0.158: 5 Chirality restraints: 1759 Sorted by residual: chirality pdb=" CG LEU C 56 " pdb=" CB LEU C 56 " pdb=" CD1 LEU C 56 " pdb=" CD2 LEU C 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" C1 NAG C 405 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C 405 " pdb=" O5 NAG C 405 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1756 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 630 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 631 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 462 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO D 463 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 664 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO D 665 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 665 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 665 " -0.016 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1430 2.76 - 3.29: 10109 3.29 - 3.83: 17527 3.83 - 4.36: 19951 4.36 - 4.90: 35289 Nonbonded interactions: 84306 Sorted by model distance: nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR C 22 " pdb=" O LYS C 77 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR D 323 " pdb=" O CYS D 538 " model vdw 2.317 3.040 ... (remaining 84301 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 155 or (resid 1 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 157 through \ 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or r \ esid 188 through 406)) selection = (chain 'C' and (resid 14 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 through 289 or (resid 2 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 291 through \ 406)) } ncs_group { reference = (chain 'B' and (resid 291 through 292 or resid 294 through 406 or (resid 407 and \ (name N or name CA or name C or name O or name CB )) or resid 408 through 417 o \ r (resid 418 through 419 and (name N or name CA or name C or name O or name CB ) \ ) or resid 420 through 457 or (resid 458 and (name N or name CA or name C or nam \ e O or name CB )) or resid 459 through 491 or (resid 492 and (name N or name CA \ or name C or name O or name CB )) or resid 493 through 508 or (resid 509 and (na \ me N or name CA or name C or name O or name CB )) or resid 510 through 515 or (r \ esid 516 and (name N or name CA or name C or name O or name CB )) or resid 517 t \ hrough 613 or (resid 614 and (name N or name CA or name C or name O or name CB ) \ ) or resid 615 through 651 or resid 653 through 656 or resid 663 through 697)) selection = (chain 'D' and (resid 291 through 348 or (resid 349 and (name N or name CA or na \ me C or name O or name CB )) or resid 350 through 408 or (resid 409 and (name N \ or name CA or name C or name O or name CB )) or resid 410 through 439 or (resid \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throug \ h 443 or resid 451 through 485 or (resid 486 and (name N or name CA or name C or \ name O or name CB )) or resid 487 through 500 or (resid 501 and (name N or name \ CA or name C or name O or name CB )) or resid 502 through 507 or (resid 508 thr \ ough 509 and (name N or name CA or name C or name O or name CB )) or resid 510 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 through 653 or (resid 654 and (name N or name CA or name C or nam \ e O or name CB )) or resid 655 through 696 or (resid 697 and (name N or name CA \ or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 0.030 11228 Z= 0.117 Angle : 0.452 9.422 15339 Z= 0.233 Chirality : 0.043 0.158 1759 Planarity : 0.003 0.042 1950 Dihedral : 7.179 77.534 4157 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.52 % Allowed : 4.48 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.19), residues: 1357 helix: -3.02 (0.42), residues: 83 sheet: -0.85 (0.28), residues: 326 loop : -2.51 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 454 TYR 0.006 0.001 TYR B 636 PHE 0.005 0.001 PHE B 400 TRP 0.005 0.001 TRP B 633 HIS 0.001 0.000 HIS D 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (11194) covalent geometry : angle 0.45044 / 0.23 (15257) SS BOND : bond 0.00082 / 0.06 ( 20) SS BOND : angle 0.35501 / 0.25 ( 40) hydrogen bonds : bond 0.30084 / 19.55 ( 254) hydrogen bonds : angle 11.03468 / 7.99 ( 696) link_NAG-ASN : bond 0.00251 / 0.16 ( 14) link_NAG-ASN : angle 0.93103 / 0.65 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 314 time to evaluate : 0.423 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: B 574 ASP cc_start: 0.7431 (t70) cc_final: 0.7194 (t0) REVERT: D 369 TYR cc_start: 0.6320 (m-10) cc_final: 0.5405 (m-80) REVERT: D 377 PHE cc_start: 0.5662 (t80) cc_final: 0.5400 (p90) REVERT: D 574 ASP cc_start: 0.7789 (t70) cc_final: 0.7469 (t0) REVERT: C 66 HIS cc_start: 0.6553 (m-70) cc_final: 0.6299 (m90) outliers start: 18 outliers final: 5 residues processed: 327 average time/residue: 0.5322 time to fit residues: 188.5919 Evaluate side-chains 203 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain C residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 239 GLN A 314 GLN B 370 ASN B 498 GLN B 544 ASN B 690 GLN D 321 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 493 GLN D 613 GLN D 655 HIS C 52 GLN C 239 GLN C 271 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.087938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079868 restraints weight = 34861.876| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.73 r_work: 0.3505 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11228 Z= 0.192 Angle : 0.661 11.266 15339 Z= 0.345 Chirality : 0.048 0.218 1759 Planarity : 0.005 0.047 1950 Dihedral : 5.773 117.858 1787 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.74 % Allowed : 14.21 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.21), residues: 1357 helix: -2.43 (0.50), residues: 77 sheet: -0.41 (0.28), residues: 339 loop : -2.11 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 214 TYR 0.018 0.002 TYR C 265 PHE 0.021 0.002 PHE A 79 TRP 0.015 0.002 TRP D 436 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (11194) covalent geometry : angle 0.65451 / 0.34 (15257) SS BOND : bond 0.00870 / 0.67 ( 20) SS BOND : angle 1.51390 / 1.22 ( 40) hydrogen bonds : bond 0.04240 / 2.94 ( 254) hydrogen bonds : angle 7.56604 / 5.36 ( 696) link_NAG-ASN : bond 0.00292 / 0.19 ( 14) link_NAG-ASN : angle 1.33663 / 0.93 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.428 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: B 321 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: B 473 TYR cc_start: 0.3052 (OUTLIER) cc_final: 0.0686 (p90) REVERT: D 369 TYR cc_start: 0.6702 (m-10) cc_final: 0.5557 (m-80) REVERT: D 454 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4806 (mmt180) REVERT: D 481 ASN cc_start: 0.8568 (p0) cc_final: 0.8352 (p0) REVERT: C 198 ASP cc_start: 0.6344 (m-30) cc_final: 0.5993 (m-30) outliers start: 56 outliers final: 19 residues processed: 255 average time/residue: 0.5432 time to fit residues: 149.9955 Evaluate side-chains 203 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN D 354 ASN C 99 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.083918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075996 restraints weight = 35115.941| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.70 r_work: 0.3424 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11228 Z= 0.198 Angle : 0.673 10.287 15339 Z= 0.354 Chirality : 0.048 0.174 1759 Planarity : 0.005 0.055 1950 Dihedral : 4.829 34.348 1782 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.31 % Allowed : 15.82 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.21), residues: 1357 helix: -2.18 (0.51), residues: 76 sheet: -0.51 (0.27), residues: 350 loop : -2.00 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 214 TYR 0.022 0.002 TYR B 636 PHE 0.025 0.002 PHE D 377 TRP 0.014 0.002 TRP D 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (11194) covalent geometry : angle 0.66584 / 0.35 (15257) SS BOND : bond 0.00670 / 0.51 ( 20) SS BOND : angle 1.33014 / 1.08 ( 40) hydrogen bonds : bond 0.04395 / 3.00 ( 254) hydrogen bonds : angle 7.12536 / 5.02 ( 696) link_NAG-ASN : bond 0.00279 / 0.19 ( 14) link_NAG-ASN : angle 1.65069 / 1.14 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.328 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: B 473 TYR cc_start: 0.3556 (OUTLIER) cc_final: 0.1278 (p90) REVERT: B 628 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6693 (tm-30) REVERT: D 369 TYR cc_start: 0.6884 (m-10) cc_final: 0.5644 (m-80) outliers start: 51 outliers final: 21 residues processed: 225 average time/residue: 0.5518 time to fit residues: 134.6225 Evaluate side-chains 198 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 218 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN C 121 ASN C 218 GLN ** C 271 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.082235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074373 restraints weight = 34926.352| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.69 r_work: 0.3389 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11228 Z= 0.202 Angle : 0.658 9.636 15339 Z= 0.348 Chirality : 0.048 0.170 1759 Planarity : 0.005 0.059 1950 Dihedral : 5.061 36.242 1782 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.15 % Allowed : 18.36 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.21), residues: 1357 helix: -2.18 (0.48), residues: 82 sheet: -0.53 (0.27), residues: 362 loop : -2.00 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.022 0.002 TYR B 636 PHE 0.022 0.002 PHE A 157 TRP 0.018 0.002 TRP D 353 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (11194) covalent geometry : angle 0.64921 / 0.35 (15257) SS BOND : bond 0.00640 / 0.48 ( 20) SS BOND : angle 1.45367 / 1.07 ( 40) hydrogen bonds : bond 0.03998 / 2.75 ( 254) hydrogen bonds : angle 6.92633 / 4.88 ( 696) link_NAG-ASN : bond 0.00252 / 0.17 ( 14) link_NAG-ASN : angle 1.69223 / 1.15 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.437 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: B 314 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8573 (mm110) REVERT: B 473 TYR cc_start: 0.3850 (OUTLIER) cc_final: 0.1557 (p90) REVERT: B 484 GLU cc_start: 0.7382 (tp30) cc_final: 0.7062 (pm20) REVERT: B 628 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6892 (tm130) REVERT: D 369 TYR cc_start: 0.6907 (m-10) cc_final: 0.5681 (m-80) REVERT: C 34 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7343 (ttm-80) REVERT: C 115 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8485 (mt0) outliers start: 49 outliers final: 22 residues processed: 228 average time/residue: 0.5304 time to fit residues: 131.1346 Evaluate side-chains 191 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 52 optimal weight: 0.0060 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 66 HIS B 580 GLN B 607 GLN D 354 ASN C 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.082912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.075270 restraints weight = 34729.562| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.65 r_work: 0.3412 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11228 Z= 0.148 Angle : 0.632 9.835 15339 Z= 0.330 Chirality : 0.047 0.190 1759 Planarity : 0.005 0.064 1950 Dihedral : 4.999 36.515 1782 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.15 % Allowed : 20.22 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.21), residues: 1357 helix: -1.94 (0.50), residues: 83 sheet: -0.50 (0.27), residues: 361 loop : -1.95 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.015 0.001 TYR B 636 PHE 0.033 0.002 PHE B 347 TRP 0.013 0.001 TRP D 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11194) covalent geometry : angle 0.62381 / 0.33 (15257) SS BOND : bond 0.00703 / 0.58 ( 20) SS BOND : angle 1.56545 / 1.30 ( 40) hydrogen bonds : bond 0.03507 / 2.40 ( 254) hydrogen bonds : angle 6.68438 / 4.72 ( 696) link_NAG-ASN : bond 0.00250 / 0.17 ( 14) link_NAG-ASN : angle 1.54061 / 1.06 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.457 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: B 314 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8540 (mm110) REVERT: B 360 ASN cc_start: 0.8034 (t0) cc_final: 0.7583 (t0) REVERT: B 473 TYR cc_start: 0.3760 (OUTLIER) cc_final: 0.1630 (p90) REVERT: B 484 GLU cc_start: 0.7359 (tp30) cc_final: 0.7004 (pm20) REVERT: B 607 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: B 628 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6826 (tm-30) REVERT: D 356 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8857 (tptp) REVERT: D 369 TYR cc_start: 0.6857 (m-10) cc_final: 0.5715 (m-80) REVERT: D 558 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8891 (mmmm) REVERT: C 34 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7154 (ttm170) REVERT: C 271 GLN cc_start: 0.8026 (pt0) cc_final: 0.7748 (pt0) outliers start: 49 outliers final: 22 residues processed: 214 average time/residue: 0.5283 time to fit residues: 122.5763 Evaluate side-chains 194 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 GLN D 321 GLN D 354 ASN C 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.074181 restraints weight = 35165.276| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.66 r_work: 0.3390 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11228 Z= 0.165 Angle : 0.643 9.918 15339 Z= 0.338 Chirality : 0.047 0.165 1759 Planarity : 0.005 0.068 1950 Dihedral : 5.079 36.766 1782 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.06 % Allowed : 20.73 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.21), residues: 1357 helix: -1.81 (0.51), residues: 83 sheet: -0.40 (0.28), residues: 349 loop : -1.92 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 577 TYR 0.017 0.002 TYR B 636 PHE 0.014 0.002 PHE B 392 TRP 0.017 0.002 TRP D 353 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (11194) covalent geometry : angle 0.63507 / 0.34 (15257) SS BOND : bond 0.00623 / 0.49 ( 20) SS BOND : angle 1.28069 / 1.04 ( 40) hydrogen bonds : bond 0.03625 / 2.47 ( 254) hydrogen bonds : angle 6.58472 / 4.65 ( 696) link_NAG-ASN : bond 0.00221 / 0.15 ( 14) link_NAG-ASN : angle 1.71807 / 1.25 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.485 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: B 314 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8554 (mm110) REVERT: B 473 TYR cc_start: 0.3834 (OUTLIER) cc_final: 0.1769 (p90) REVERT: B 484 GLU cc_start: 0.7192 (tp30) cc_final: 0.6842 (pm20) REVERT: D 369 TYR cc_start: 0.6852 (m-10) cc_final: 0.5694 (m-80) REVERT: D 454 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4939 (tpt170) REVERT: D 558 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8900 (mmmm) outliers start: 48 outliers final: 23 residues processed: 209 average time/residue: 0.5829 time to fit residues: 131.6790 Evaluate side-chains 185 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 354 ASN C 121 ASN C 218 GLN C 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073459 restraints weight = 35040.155| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.64 r_work: 0.3374 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11228 Z= 0.180 Angle : 0.663 10.017 15339 Z= 0.351 Chirality : 0.047 0.180 1759 Planarity : 0.005 0.064 1950 Dihedral : 5.259 37.474 1782 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.23 % Allowed : 22.17 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.21), residues: 1357 helix: -1.95 (0.49), residues: 89 sheet: -0.42 (0.27), residues: 359 loop : -1.91 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 577 TYR 0.018 0.002 TYR B 636 PHE 0.027 0.002 PHE A 157 TRP 0.018 0.002 TRP D 353 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (11194) covalent geometry : angle 0.65551 / 0.35 (15257) SS BOND : bond 0.00644 / 0.51 ( 20) SS BOND : angle 1.35227 / 1.11 ( 40) hydrogen bonds : bond 0.03678 / 2.52 ( 254) hydrogen bonds : angle 6.56671 / 4.63 ( 696) link_NAG-ASN : bond 0.00232 / 0.16 ( 14) link_NAG-ASN : angle 1.63300 / 1.12 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.436 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 169 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: B 298 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: B 314 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8562 (mm110) REVERT: B 408 ARG cc_start: 0.4663 (ttt90) cc_final: 0.4418 (mmt180) REVERT: B 457 ARG cc_start: 0.7745 (ttp80) cc_final: 0.6999 (mtp-110) REVERT: B 473 TYR cc_start: 0.3928 (OUTLIER) cc_final: 0.1873 (p90) REVERT: B 484 GLU cc_start: 0.7111 (tp30) cc_final: 0.6847 (pm20) REVERT: B 580 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8234 (mm-40) REVERT: D 369 TYR cc_start: 0.6875 (m-10) cc_final: 0.5716 (m-80) REVERT: D 402 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8122 (mm) REVERT: D 558 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8875 (mmmm) REVERT: C 34 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7014 (ttm110) REVERT: C 176 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8992 (tp) outliers start: 50 outliers final: 23 residues processed: 204 average time/residue: 0.6033 time to fit residues: 132.7208 Evaluate side-chains 194 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 580 GLN B 607 GLN D 354 ASN C 14 GLN C 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.081681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.074035 restraints weight = 35069.218| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.66 r_work: 0.3388 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11228 Z= 0.155 Angle : 0.655 9.342 15339 Z= 0.345 Chirality : 0.047 0.218 1759 Planarity : 0.005 0.064 1950 Dihedral : 5.189 36.428 1780 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.38 % Allowed : 22.76 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.21), residues: 1357 helix: -1.84 (0.50), residues: 89 sheet: -0.35 (0.28), residues: 353 loop : -1.91 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 346 TYR 0.017 0.002 TYR A 248 PHE 0.027 0.002 PHE A 157 TRP 0.015 0.002 TRP D 353 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (11194) covalent geometry : angle 0.64795 / 0.34 (15257) SS BOND : bond 0.00572 / 0.46 ( 20) SS BOND : angle 1.28802 / 1.06 ( 40) hydrogen bonds : bond 0.03482 / 2.40 ( 254) hydrogen bonds : angle 6.46079 / 4.57 ( 696) link_NAG-ASN : bond 0.00221 / 0.14 ( 14) link_NAG-ASN : angle 1.55314 / 1.06 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.422 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 169 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: A 248 TYR cc_start: 0.7595 (m-10) cc_final: 0.7394 (p90) REVERT: B 314 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8543 (mm110) REVERT: B 408 ARG cc_start: 0.4680 (ttt90) cc_final: 0.4438 (mmt180) REVERT: B 473 TYR cc_start: 0.3835 (OUTLIER) cc_final: 0.1873 (p90) REVERT: B 484 GLU cc_start: 0.7073 (tp30) cc_final: 0.6818 (pm20) REVERT: B 580 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8184 (mm-40) REVERT: B 607 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7384 (pp30) REVERT: D 369 TYR cc_start: 0.6785 (m-10) cc_final: 0.5630 (m-80) REVERT: D 377 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5855 (p90) REVERT: D 558 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8856 (mmmm) outliers start: 40 outliers final: 22 residues processed: 202 average time/residue: 0.5891 time to fit residues: 128.4470 Evaluate side-chains 191 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 498 GLN B 580 GLN B 607 GLN D 354 ASN C 218 GLN C 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.073992 restraints weight = 34810.908| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.64 r_work: 0.3387 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11228 Z= 0.162 Angle : 0.674 9.231 15339 Z= 0.356 Chirality : 0.047 0.208 1759 Planarity : 0.005 0.060 1950 Dihedral : 5.252 36.201 1780 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.21 % Allowed : 23.86 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.21), residues: 1357 helix: -1.82 (0.50), residues: 90 sheet: -0.32 (0.28), residues: 353 loop : -1.88 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 357 TYR 0.015 0.002 TYR B 636 PHE 0.034 0.002 PHE B 347 TRP 0.014 0.002 TRP D 353 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (11194) covalent geometry : angle 0.66677 / 0.35 (15257) SS BOND : bond 0.00584 / 0.46 ( 20) SS BOND : angle 1.36081 / 1.11 ( 40) hydrogen bonds : bond 0.03498 / 2.40 ( 254) hydrogen bonds : angle 6.45074 / 4.56 ( 696) link_NAG-ASN : bond 0.00254 / 0.16 ( 14) link_NAG-ASN : angle 1.56743 / 1.10 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.548 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 169 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: B 314 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8534 (mm110) REVERT: B 328 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8644 (mmm160) REVERT: B 408 ARG cc_start: 0.4715 (ttt90) cc_final: 0.4451 (mmt180) REVERT: B 473 TYR cc_start: 0.3789 (OUTLIER) cc_final: 0.1889 (p90) REVERT: B 484 GLU cc_start: 0.7091 (tp30) cc_final: 0.6839 (pm20) REVERT: B 580 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8298 (mm110) REVERT: D 369 TYR cc_start: 0.6784 (m-10) cc_final: 0.5614 (m-80) REVERT: D 377 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5833 (p90) REVERT: D 558 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8840 (mmmm) outliers start: 38 outliers final: 24 residues processed: 195 average time/residue: 0.5883 time to fit residues: 124.1399 Evaluate side-chains 192 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 580 GLN B 607 GLN D 354 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.082111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074576 restraints weight = 34704.819| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.62 r_work: 0.3402 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11228 Z= 0.155 Angle : 0.684 8.822 15339 Z= 0.359 Chirality : 0.047 0.213 1759 Planarity : 0.005 0.058 1950 Dihedral : 5.305 36.459 1780 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.54 % Allowed : 24.20 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.06 (0.22), residues: 1357 helix: -1.72 (0.51), residues: 90 sheet: -0.36 (0.28), residues: 353 loop : -1.86 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 357 TYR 0.014 0.001 TYR B 636 PHE 0.028 0.002 PHE B 347 TRP 0.016 0.002 TRP B 633 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (11194) covalent geometry : angle 0.67748 / 0.36 (15257) SS BOND : bond 0.00560 / 0.45 ( 20) SS BOND : angle 1.36032 / 1.11 ( 40) hydrogen bonds : bond 0.03400 / 2.33 ( 254) hydrogen bonds : angle 6.46007 / 4.56 ( 696) link_NAG-ASN : bond 0.00245 / 0.16 ( 14) link_NAG-ASN : angle 1.54935 / 1.09 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.421 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 169 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: B 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8532 (mm110) REVERT: B 408 ARG cc_start: 0.4801 (ttt90) cc_final: 0.4487 (mmt180) REVERT: B 473 TYR cc_start: 0.3760 (OUTLIER) cc_final: 0.1823 (p90) REVERT: B 484 GLU cc_start: 0.7142 (tp30) cc_final: 0.6939 (pm20) REVERT: B 580 GLN cc_start: 0.8425 (mm110) cc_final: 0.8109 (mm-40) REVERT: B 607 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7508 (pp30) REVERT: D 369 TYR cc_start: 0.6782 (m-10) cc_final: 0.5610 (m-80) REVERT: D 377 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5823 (p90) REVERT: D 558 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8814 (mmmm) REVERT: C 14 GLN cc_start: 0.7354 (tp40) cc_final: 0.7153 (tp-100) REVERT: C 271 GLN cc_start: 0.8019 (pm20) cc_final: 0.7789 (pm20) REVERT: C 304 LYS cc_start: 0.7851 (tppt) cc_final: 0.7634 (tppp) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.5580 time to fit residues: 116.0932 Evaluate side-chains 191 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 607 GLN D 354 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN ** C 271 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.081200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073680 restraints weight = 34916.375| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.62 r_work: 0.3381 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11228 Z= 0.184 Angle : 0.706 9.265 15339 Z= 0.371 Chirality : 0.048 0.223 1759 Planarity : 0.005 0.058 1950 Dihedral : 5.428 37.101 1780 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.13 % Allowed : 23.86 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.08 (0.21), residues: 1357 helix: -1.78 (0.50), residues: 90 sheet: -0.35 (0.27), residues: 353 loop : -1.88 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 577 TYR 0.018 0.002 TYR B 636 PHE 0.028 0.002 PHE B 347 TRP 0.017 0.002 TRP B 633 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (11194) covalent geometry : angle 0.69644 / 0.37 (15257) SS BOND : bond 0.00653 / 0.51 ( 20) SS BOND : angle 1.88478 / 1.42 ( 40) hydrogen bonds : bond 0.03639 / 2.50 ( 254) hydrogen bonds : angle 6.54290 / 4.62 ( 696) link_NAG-ASN : bond 0.00213 / 0.15 ( 14) link_NAG-ASN : angle 1.61950 / 1.11 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.33 seconds wall clock time: 64 minutes 40.16 seconds (3880.16 seconds total)