Starting phenix.real_space_refine on Sat Aug 23 14:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.map" model { file = "/net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on8_16982/08_2025/8on8_16982.cif" } resolution = 2.7 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= 0.002 sd= 0.034 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 105 5.16 5 C 8190 2.51 5 N 2142 2.21 5 O 2454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12891 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "B" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.58, per 1000 atoms: 0.20 Number of scatterers: 12891 At special positions: 0 Unit cell: (112.42, 110.376, 136.948, 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 105 16.00 O 2454 8.00 N 2142 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.04 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 444 " " NAG A 603 " - " ASN A 460 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 444 " " NAG B 603 " - " ASN B 460 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 444 " " NAG C 603 " - " ASN C 460 " " NAG D 1 " - " ASN A 180 " " NAG E 1 " - " ASN A 299 " " NAG F 1 " - " ASN B 180 " " NAG G 1 " - " ASN B 299 " " NAG H 1 " - " ASN C 180 " " NAG I 1 " - " ASN C 299 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 587.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 49.5% alpha, 19.8% 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 2 through 14 Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER A 105 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.883A pdb=" N LEU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA A 345 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.560A pdb=" N CYS A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.600A pdb=" N MET A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 425' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.519A pdb=" N ASN A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER B 105 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 107 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.884A pdb=" N LEU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA B 345 " --> pdb=" O PRO B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.561A pdb=" N CYS B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 392 Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.600A pdb=" N MET B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU B 425 " --> pdb=" O ALA B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 422 through 425' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.518A pdb=" N ASN B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER C 105 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 107 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 133 Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.884A pdb=" N LEU C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 332 Processing helix chain 'C' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.560A pdb=" N CYS C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 392 Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.601A pdb=" N MET C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU C 425 " --> pdb=" O ALA C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing helix chain 'C' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR C 430 " --> pdb=" O GLY C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.519A pdb=" N ASN C 444 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'C' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU C 518 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 224 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 169 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.987A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 224 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 169 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.986A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 224 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 169 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.987A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1893 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: 1.85 Time building geometry restraints manager: 1.38 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: 4146 1.34 - 1.46: 3264 1.46 - 1.59: 5649 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 13215 Sorted by residual: bond pdb=" CA SER C 512 " pdb=" CB SER C 512 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.98e+00 bond pdb=" CA SER B 512 " pdb=" CB SER B 512 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.85e+00 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.530 1.478 0.053 1.69e-02 3.50e+03 9.69e+00 bond pdb=" N THR C 515 " pdb=" CA THR C 515 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.33e-02 5.65e+03 8.22e+00 bond pdb=" N THR B 515 " pdb=" CA THR B 515 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.33e-02 5.65e+03 8.10e+00 ... (remaining 13210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 17569 2.13 - 4.26: 287 4.26 - 6.39: 24 6.39 - 8.52: 12 8.52 - 10.65: 9 Bond angle restraints: 17901 Sorted by residual: angle pdb=" N ALA B 517 " pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 111.69 104.65 7.04 1.23e+00 6.61e-01 3.28e+01 angle pdb=" N ALA C 517 " pdb=" CA ALA C 517 " pdb=" C ALA C 517 " ideal model delta sigma weight residual 111.69 104.70 6.99 1.23e+00 6.61e-01 3.23e+01 angle pdb=" N ALA A 517 " pdb=" CA ALA A 517 " pdb=" C ALA A 517 " ideal model delta sigma weight residual 111.69 104.71 6.98 1.23e+00 6.61e-01 3.22e+01 angle pdb=" N LEU C 516 " pdb=" CA LEU C 516 " pdb=" C LEU C 516 " ideal model delta sigma weight residual 113.20 106.75 6.45 1.21e+00 6.83e-01 2.84e+01 angle pdb=" N LEU A 516 " pdb=" CA LEU A 516 " pdb=" C LEU A 516 " ideal model delta sigma weight residual 113.20 106.75 6.45 1.21e+00 6.83e-01 2.84e+01 ... (remaining 17896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 7518 15.84 - 31.67: 525 31.67 - 47.51: 141 47.51 - 63.34: 48 63.34 - 79.18: 12 Dihedral angle restraints: 8244 sinusoidal: 3639 harmonic: 4605 Sorted by residual: dihedral pdb=" CA ILE C 293 " pdb=" C ILE C 293 " pdb=" N GLY C 294 " pdb=" CA GLY C 294 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ILE A 293 " pdb=" C ILE A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ILE B 293 " pdb=" C ILE B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 8241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1386 0.039 - 0.079: 373 0.079 - 0.118: 184 0.118 - 0.157: 19 0.157 - 0.196: 6 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA ALA B 517 " pdb=" N ALA B 517 " pdb=" C ALA B 517 " pdb=" CB ALA B 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA ALA A 517 " pdb=" N ALA A 517 " pdb=" C ALA A 517 " pdb=" CB ALA A 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ALA C 517 " pdb=" N ALA C 517 " pdb=" C ALA C 517 " pdb=" CB ALA C 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1965 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 34 " 0.023 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP B 34 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 34 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 34 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 34 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 34 " -0.022 2.00e-02 2.50e+03 1.78e-02 7.90e+00 pdb=" CG TRP C 34 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 34 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 34 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " -0.022 2.00e-02 2.50e+03 1.78e-02 7.90e+00 pdb=" CG TRP A 34 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " -0.013 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3583 2.82 - 3.34: 11821 3.34 - 3.86: 21064 3.86 - 4.38: 24387 4.38 - 4.90: 42932 Nonbonded interactions: 103787 Sorted by model distance: nonbonded pdb=" OH TYR C 492 " pdb=" OD2 ASP C 500 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 492 " pdb=" OD2 ASP B 500 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 492 " pdb=" OD2 ASP A 500 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR C 265 " pdb=" OE2 GLU C 311 " model vdw 2.375 3.040 nonbonded pdb=" OG1 THR A 265 " pdb=" OE2 GLU A 311 " model vdw 2.375 3.040 ... (remaining 103782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.140 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.003 0.053 13260 Z= 0.185 Angle : 0.662 10.654 18012 Z= 0.339 Chirality : 0.044 0.196 1968 Planarity : 0.004 0.041 2304 Dihedral : 12.578 79.181 5202 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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 aren not related in a simple way. whole: 1.34 (0.22), residues: 1560 helix: 1.25 (0.21), residues: 681 sheet: 1.62 (0.32), residues: 279 loop : 0.24 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 237 TYR 0.009 0.001 TYR A 136 PHE 0.019 0.001 PHE B 33 TRP 0.045 0.003 TRP A 34 HIS 0.008 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00348 (13215) covalent geometry : angle 0.64824 (17901) SS BOND : bond 0.00283 ( 24) SS BOND : angle 1.17169 ( 48) hydrogen bonds : bond 0.17501 ( 649) hydrogen bonds : angle 6.64732 ( 1893) link_BETA1-4 : bond 0.00793 ( 6) link_BETA1-4 : angle 1.77118 ( 18) link_NAG-ASN : bond 0.00409 ( 15) link_NAG-ASN : angle 2.35435 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.7265 (t0) cc_final: 0.7000 (m-40) REVERT: A 33 PHE cc_start: 0.6618 (t80) cc_final: 0.6403 (t80) REVERT: A 54 GLN cc_start: 0.7473 (tt0) cc_final: 0.7272 (tt0) REVERT: A 100 ASP cc_start: 0.7206 (t0) cc_final: 0.6501 (t0) REVERT: A 101 ASP cc_start: 0.7859 (t0) cc_final: 0.7569 (t0) REVERT: A 108 ASN cc_start: 0.8048 (m-40) cc_final: 0.7826 (m110) REVERT: A 111 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 129 PHE cc_start: 0.7559 (t80) cc_final: 0.7149 (t80) REVERT: A 136 TYR cc_start: 0.7159 (m-80) cc_final: 0.6815 (m-10) REVERT: A 138 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 166 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 178 ARG cc_start: 0.7447 (mtp85) cc_final: 0.6777 (mtp85) REVERT: A 186 TYR cc_start: 0.8039 (m-80) cc_final: 0.7339 (m-80) REVERT: A 200 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7882 (ttpt) REVERT: A 211 LEU cc_start: 0.7156 (mt) cc_final: 0.6905 (mt) REVERT: A 216 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 217 ASN cc_start: 0.8142 (m-40) cc_final: 0.7860 (m-40) REVERT: A 235 GLU cc_start: 0.7900 (tt0) cc_final: 0.7353 (tt0) REVERT: A 269 PHE cc_start: 0.8359 (m-80) cc_final: 0.7818 (m-80) REVERT: A 274 ASP cc_start: 0.8117 (m-30) cc_final: 0.7781 (m-30) REVERT: A 288 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7494 (mtp85) REVERT: A 301 SER cc_start: 0.7761 (t) cc_final: 0.7530 (p) REVERT: A 335 ASP cc_start: 0.7561 (t0) cc_final: 0.7257 (t0) REVERT: A 350 CYS cc_start: 0.6513 (m) cc_final: 0.6306 (m) REVERT: A 352 ASP cc_start: 0.7498 (t0) cc_final: 0.7273 (t0) REVERT: A 354 ASP cc_start: 0.7850 (t0) cc_final: 0.7365 (t0) REVERT: A 361 MET cc_start: 0.7187 (mtp) cc_final: 0.6880 (mtm) REVERT: A 362 PHE cc_start: 0.7641 (m-80) cc_final: 0.7413 (m-80) REVERT: A 373 MET cc_start: 0.7008 (mmt) cc_final: 0.6750 (mmm) REVERT: A 380 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6992 (mtmt) REVERT: A 388 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6864 (ttpp) REVERT: A 391 LYS cc_start: 0.7769 (mttt) cc_final: 0.7535 (mttt) REVERT: A 427 ASP cc_start: 0.7696 (m-30) cc_final: 0.7402 (m-30) REVERT: A 437 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 449 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7438 (mm-40) REVERT: A 485 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7326 (ttpp) REVERT: A 491 ASP cc_start: 0.7828 (t70) cc_final: 0.7494 (t0) REVERT: A 493 THR cc_start: 0.7507 (p) cc_final: 0.7240 (p) REVERT: A 496 GLN cc_start: 0.7312 (mt0) cc_final: 0.6609 (mt0) REVERT: A 500 ASP cc_start: 0.7190 (m-30) cc_final: 0.6599 (m-30) REVERT: B 24 ASN cc_start: 0.7321 (t0) cc_final: 0.7050 (t0) REVERT: B 51 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 54 GLN cc_start: 0.7499 (tt0) cc_final: 0.7240 (tt0) REVERT: B 108 ASN cc_start: 0.8059 (m-40) cc_final: 0.7739 (m110) REVERT: B 129 PHE cc_start: 0.7608 (t80) cc_final: 0.7367 (t80) REVERT: B 131 ASN cc_start: 0.7668 (m-40) cc_final: 0.7398 (m110) REVERT: B 136 TYR cc_start: 0.7196 (m-80) cc_final: 0.6159 (m-80) REVERT: B 138 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6800 (mt-10) REVERT: B 144 PHE cc_start: 0.8362 (m-80) cc_final: 0.7755 (m-80) REVERT: B 166 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 178 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6557 (mtp85) REVERT: B 186 TYR cc_start: 0.8087 (m-80) cc_final: 0.7808 (m-80) REVERT: B 235 GLU cc_start: 0.7981 (tt0) cc_final: 0.7738 (tt0) REVERT: B 249 VAL cc_start: 0.7532 (t) cc_final: 0.7276 (m) REVERT: B 269 PHE cc_start: 0.8470 (m-80) cc_final: 0.8135 (m-80) REVERT: B 273 TYR cc_start: 0.8513 (m-80) cc_final: 0.8115 (m-80) REVERT: B 274 ASP cc_start: 0.8167 (m-30) cc_final: 0.7714 (m-30) REVERT: B 340 LYS cc_start: 0.7959 (tppp) cc_final: 0.7579 (tppp) REVERT: B 354 ASP cc_start: 0.7795 (t0) cc_final: 0.7470 (t0) REVERT: B 373 MET cc_start: 0.7060 (mmt) cc_final: 0.6715 (mmm) REVERT: B 388 LYS cc_start: 0.7152 (ttpp) cc_final: 0.6878 (ttpp) REVERT: B 407 GLU cc_start: 0.7756 (tt0) cc_final: 0.7450 (tt0) REVERT: B 425 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 438 LYS cc_start: 0.8229 (mttt) cc_final: 0.8016 (mttt) REVERT: B 492 TYR cc_start: 0.8089 (t80) cc_final: 0.7878 (t80) REVERT: B 493 THR cc_start: 0.7434 (p) cc_final: 0.7078 (t) REVERT: C 31 ARG cc_start: 0.6587 (ttm170) cc_final: 0.6017 (ttm170) REVERT: C 100 ASP cc_start: 0.7177 (t0) cc_final: 0.6578 (t0) REVERT: C 111 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 129 PHE cc_start: 0.7345 (t80) cc_final: 0.6890 (t80) REVERT: C 131 ASN cc_start: 0.7847 (m-40) cc_final: 0.7645 (m110) REVERT: C 136 TYR cc_start: 0.7004 (m-80) cc_final: 0.6350 (m-80) REVERT: C 138 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 142 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6597 (mm-30) REVERT: C 177 HIS cc_start: 0.7100 (m-70) cc_final: 0.6777 (m-70) REVERT: C 186 TYR cc_start: 0.8033 (m-80) cc_final: 0.7739 (m-80) REVERT: C 200 LYS cc_start: 0.8270 (ttpt) cc_final: 0.8025 (ttpt) REVERT: C 235 GLU cc_start: 0.8043 (tt0) cc_final: 0.7740 (tt0) REVERT: C 237 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7347 (mtp-110) REVERT: C 269 PHE cc_start: 0.8382 (m-80) cc_final: 0.8161 (m-80) REVERT: C 274 ASP cc_start: 0.8204 (m-30) cc_final: 0.7815 (m-30) REVERT: C 301 SER cc_start: 0.7965 (t) cc_final: 0.7694 (p) REVERT: C 333 CYS cc_start: 0.4950 (p) cc_final: 0.3713 (p) REVERT: C 354 ASP cc_start: 0.7647 (t0) cc_final: 0.7227 (t0) REVERT: C 361 MET cc_start: 0.6966 (mtp) cc_final: 0.6758 (mtm) REVERT: C 391 LYS cc_start: 0.7563 (mttt) cc_final: 0.7146 (mttt) REVERT: C 396 MET cc_start: 0.7444 (mmm) cc_final: 0.7104 (mmm) REVERT: C 399 CYS cc_start: 0.6487 (m) cc_final: 0.6224 (m) REVERT: C 407 GLU cc_start: 0.7576 (tt0) cc_final: 0.7275 (tt0) REVERT: C 425 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 449 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7636 (mm110) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.5811 time to fit residues: 302.1473 Evaluate side-chains 387 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 106 ASN A 141 GLN A 319 GLN A 355 ASN A 495 ASN B 48 GLN B 141 GLN B 173 HIS B 217 ASN B 355 ASN C 48 GLN C 141 GLN C 164 GLN C 217 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116180 restraints weight = 17575.368| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.88 r_work: 0.3432 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13260 Z= 0.183 Angle : 0.635 13.107 18012 Z= 0.321 Chirality : 0.045 0.322 1968 Planarity : 0.005 0.052 2304 Dihedral : 5.615 54.036 2157 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 11.78 % Favored : 85.56 % 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 aren not related in a simple way. whole: 1.41 (0.21), residues: 1560 helix: 1.54 (0.20), residues: 687 sheet: 1.35 (0.30), residues: 279 loop : 0.11 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 383 TYR 0.013 0.001 TYR A 414 PHE 0.024 0.002 PHE A 356 TRP 0.016 0.002 TRP A 34 HIS 0.005 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00423 (13215) covalent geometry : angle 0.61109 (17901) SS BOND : bond 0.00526 ( 24) SS BOND : angle 2.60410 ( 48) hydrogen bonds : bond 0.04916 ( 649) hydrogen bonds : angle 4.88117 ( 1893) link_BETA1-4 : bond 0.00731 ( 6) link_BETA1-4 : angle 1.38387 ( 18) link_NAG-ASN : bond 0.00701 ( 15) link_NAG-ASN : angle 2.16110 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7975 (t0) cc_final: 0.7610 (t0) REVERT: A 129 PHE cc_start: 0.8329 (t80) cc_final: 0.8048 (t80) REVERT: A 142 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 164 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: A 186 TYR cc_start: 0.8612 (m-80) cc_final: 0.8204 (m-80) REVERT: A 200 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8152 (ttpp) REVERT: A 217 ASN cc_start: 0.8497 (m-40) cc_final: 0.8238 (m-40) REVERT: A 235 GLU cc_start: 0.8292 (tt0) cc_final: 0.8065 (tt0) REVERT: A 269 PHE cc_start: 0.8464 (m-80) cc_final: 0.8051 (m-80) REVERT: A 289 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8080 (ttm-80) REVERT: A 354 ASP cc_start: 0.8086 (t0) cc_final: 0.7725 (t0) REVERT: A 361 MET cc_start: 0.8057 (mtp) cc_final: 0.7753 (mtm) REVERT: A 391 LYS cc_start: 0.8280 (mttt) cc_final: 0.8000 (mttt) REVERT: A 396 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7800 (mmp) REVERT: A 449 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7867 (mm110) REVERT: B 24 ASN cc_start: 0.7941 (t0) cc_final: 0.7688 (t0) REVERT: B 47 LEU cc_start: 0.8051 (mt) cc_final: 0.7847 (mp) REVERT: B 129 PHE cc_start: 0.8487 (t80) cc_final: 0.8251 (t80) REVERT: B 131 ASN cc_start: 0.8479 (m-40) cc_final: 0.8237 (m110) REVERT: B 138 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 164 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: B 178 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7440 (mtp85) REVERT: B 249 VAL cc_start: 0.8348 (t) cc_final: 0.8013 (m) REVERT: B 273 TYR cc_start: 0.8692 (m-80) cc_final: 0.8244 (m-80) REVERT: B 288 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7934 (mtp-110) REVERT: B 354 ASP cc_start: 0.7989 (t0) cc_final: 0.7657 (t0) REVERT: B 388 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7820 (ttmm) REVERT: B 396 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7850 (mmt) REVERT: B 425 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 493 THR cc_start: 0.8610 (p) cc_final: 0.8320 (t) REVERT: C 21 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7641 (mmtp) REVERT: C 31 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6925 (mtt90) REVERT: C 84 ASN cc_start: 0.8273 (p0) cc_final: 0.8048 (p0) REVERT: C 100 ASP cc_start: 0.8205 (t0) cc_final: 0.7819 (t0) REVERT: C 129 PHE cc_start: 0.8438 (t80) cc_final: 0.7918 (t80) REVERT: C 131 ASN cc_start: 0.8589 (m-40) cc_final: 0.8374 (m110) REVERT: C 177 HIS cc_start: 0.7595 (m-70) cc_final: 0.7370 (m-70) REVERT: C 274 ASP cc_start: 0.7407 (m-30) cc_final: 0.7197 (m-30) REVERT: C 301 SER cc_start: 0.8519 (t) cc_final: 0.8264 (p) REVERT: C 303 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8487 (ptmm) REVERT: C 354 ASP cc_start: 0.8018 (t0) cc_final: 0.7617 (t0) REVERT: C 386 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8243 (mttt) REVERT: C 387 SER cc_start: 0.8462 (t) cc_final: 0.8245 (m) REVERT: C 388 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8160 (ttmm) outliers start: 37 outliers final: 9 residues processed: 414 average time/residue: 0.5744 time to fit residues: 254.7672 Evaluate side-chains 388 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 516 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 319 GLN A 355 ASN A 495 ASN A 496 GLN B 48 GLN B 108 ASN B 217 ASN C 24 ASN C 48 GLN C 164 GLN C 173 HIS C 355 ASN C 370 GLN C 449 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115561 restraints weight = 17727.212| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.90 r_work: 0.3437 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13260 Z= 0.150 Angle : 0.584 8.880 18012 Z= 0.294 Chirality : 0.043 0.266 1968 Planarity : 0.004 0.046 2304 Dihedral : 5.456 53.309 2157 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.80 % Allowed : 15.45 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 1.42 (0.21), residues: 1560 helix: 1.60 (0.20), residues: 690 sheet: 1.17 (0.30), residues: 279 loop : 0.15 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.009 0.001 TYR A 414 PHE 0.020 0.001 PHE B 33 TRP 0.011 0.002 TRP A 34 HIS 0.005 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00349 (13215) covalent geometry : angle 0.56399 (17901) SS BOND : bond 0.00424 ( 24) SS BOND : angle 1.99172 ( 48) hydrogen bonds : bond 0.04499 ( 649) hydrogen bonds : angle 4.54406 ( 1893) link_BETA1-4 : bond 0.00662 ( 6) link_BETA1-4 : angle 1.32384 ( 18) link_NAG-ASN : bond 0.00534 ( 15) link_NAG-ASN : angle 2.29056 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 378 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7710 (mmm) cc_final: 0.7436 (mmm) REVERT: A 101 ASP cc_start: 0.7889 (t0) cc_final: 0.7515 (t0) REVERT: A 129 PHE cc_start: 0.8303 (t80) cc_final: 0.7942 (t80) REVERT: A 164 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: A 186 TYR cc_start: 0.8618 (m-80) cc_final: 0.8204 (m-80) REVERT: A 200 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8118 (ttpp) REVERT: A 217 ASN cc_start: 0.8527 (m-40) cc_final: 0.8245 (m-40) REVERT: A 235 GLU cc_start: 0.8305 (tt0) cc_final: 0.8070 (tt0) REVERT: A 269 PHE cc_start: 0.8501 (m-80) cc_final: 0.8100 (m-80) REVERT: A 354 ASP cc_start: 0.8070 (t0) cc_final: 0.7693 (t0) REVERT: A 361 MET cc_start: 0.7984 (mtp) cc_final: 0.7679 (mtm) REVERT: A 391 LYS cc_start: 0.8206 (mttt) cc_final: 0.7932 (mttt) REVERT: A 425 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 24 ASN cc_start: 0.7960 (t0) cc_final: 0.7702 (t0) REVERT: B 129 PHE cc_start: 0.8449 (t80) cc_final: 0.8181 (t80) REVERT: B 131 ASN cc_start: 0.8467 (m-40) cc_final: 0.8194 (m110) REVERT: B 138 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7261 (mt-10) REVERT: B 142 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7320 (mm-30) REVERT: B 164 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: B 171 ASN cc_start: 0.7738 (t0) cc_final: 0.7022 (m-40) REVERT: B 178 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7325 (mtp85) REVERT: B 249 VAL cc_start: 0.8372 (t) cc_final: 0.8044 (m) REVERT: B 273 TYR cc_start: 0.8703 (m-80) cc_final: 0.8270 (m-80) REVERT: B 354 ASP cc_start: 0.7999 (t0) cc_final: 0.7673 (t0) REVERT: B 388 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7880 (ttmm) REVERT: B 396 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: B 425 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 432 ASP cc_start: 0.8163 (t70) cc_final: 0.7910 (t0) REVERT: B 437 GLU cc_start: 0.7846 (mm-30) cc_final: 0.6950 (tp30) REVERT: B 493 THR cc_start: 0.8570 (p) cc_final: 0.8265 (t) REVERT: C 21 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7607 (mmtp) REVERT: C 31 ARG cc_start: 0.7538 (ttm170) cc_final: 0.6984 (ttm170) REVERT: C 47 LEU cc_start: 0.8126 (mt) cc_final: 0.7923 (mp) REVERT: C 84 ASN cc_start: 0.8251 (p0) cc_final: 0.8048 (p0) REVERT: C 129 PHE cc_start: 0.8456 (t80) cc_final: 0.7936 (t80) REVERT: C 131 ASN cc_start: 0.8620 (m-40) cc_final: 0.8403 (m110) REVERT: C 177 HIS cc_start: 0.7775 (m-70) cc_final: 0.7572 (m-70) REVERT: C 274 ASP cc_start: 0.7464 (m-30) cc_final: 0.7228 (m-30) REVERT: C 303 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8453 (ptmm) REVERT: C 354 ASP cc_start: 0.8036 (t0) cc_final: 0.7740 (t70) REVERT: C 387 SER cc_start: 0.8483 (t) cc_final: 0.8274 (m) REVERT: C 388 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8213 (ttmm) outliers start: 39 outliers final: 16 residues processed: 393 average time/residue: 0.6100 time to fit residues: 256.5604 Evaluate side-chains 386 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 366 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 243 HIS A 495 ASN A 496 GLN B 217 ASN C 24 ASN C 164 GLN C 217 ASN C 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115308 restraints weight = 17802.302| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.88 r_work: 0.3427 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13260 Z= 0.142 Angle : 0.580 8.783 18012 Z= 0.290 Chirality : 0.042 0.207 1968 Planarity : 0.004 0.045 2304 Dihedral : 5.332 53.502 2157 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.16 % Allowed : 15.80 % Favored : 81.03 % 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 aren not related in a simple way. whole: 1.41 (0.21), residues: 1560 helix: 1.60 (0.20), residues: 690 sheet: 1.09 (0.30), residues: 279 loop : 0.17 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 288 TYR 0.020 0.001 TYR C 132 PHE 0.021 0.001 PHE C 33 TRP 0.010 0.002 TRP C 34 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00330 (13215) covalent geometry : angle 0.56307 (17901) SS BOND : bond 0.00330 ( 24) SS BOND : angle 1.74817 ( 48) hydrogen bonds : bond 0.04233 ( 649) hydrogen bonds : angle 4.41112 ( 1893) link_BETA1-4 : bond 0.00561 ( 6) link_BETA1-4 : angle 1.22550 ( 18) link_NAG-ASN : bond 0.00485 ( 15) link_NAG-ASN : angle 2.19764 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 383 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7692 (mmm) cc_final: 0.7433 (mmm) REVERT: A 101 ASP cc_start: 0.7874 (t0) cc_final: 0.7514 (t0) REVERT: A 129 PHE cc_start: 0.8294 (t80) cc_final: 0.7881 (t80) REVERT: A 164 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: A 186 TYR cc_start: 0.8618 (m-80) cc_final: 0.8219 (m-80) REVERT: A 217 ASN cc_start: 0.8529 (m-40) cc_final: 0.8248 (m-40) REVERT: A 235 GLU cc_start: 0.8265 (tt0) cc_final: 0.8040 (tt0) REVERT: A 269 PHE cc_start: 0.8500 (m-80) cc_final: 0.8102 (m-80) REVERT: A 354 ASP cc_start: 0.8061 (t0) cc_final: 0.7466 (t0) REVERT: A 361 MET cc_start: 0.7979 (mtp) cc_final: 0.7769 (mtm) REVERT: A 388 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8036 (ttpp) REVERT: A 391 LYS cc_start: 0.8132 (mttt) cc_final: 0.7848 (mttt) REVERT: A 396 MET cc_start: 0.7976 (mmp) cc_final: 0.7649 (mpp) REVERT: A 425 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 491 ASP cc_start: 0.8060 (t70) cc_final: 0.7766 (t0) REVERT: B 24 ASN cc_start: 0.7972 (t0) cc_final: 0.7702 (t0) REVERT: B 129 PHE cc_start: 0.8523 (t80) cc_final: 0.8269 (t80) REVERT: B 131 ASN cc_start: 0.8455 (m-40) cc_final: 0.8172 (m110) REVERT: B 138 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 142 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 164 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: B 171 ASN cc_start: 0.7739 (t0) cc_final: 0.7225 (m-40) REVERT: B 178 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7303 (mtp85) REVERT: B 223 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 249 VAL cc_start: 0.8388 (t) cc_final: 0.8056 (m) REVERT: B 273 TYR cc_start: 0.8717 (m-80) cc_final: 0.8265 (m-80) REVERT: B 288 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7958 (mtp-110) REVERT: B 347 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 354 ASP cc_start: 0.7989 (t0) cc_final: 0.7675 (t0) REVERT: B 388 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7929 (ttmm) REVERT: B 396 MET cc_start: 0.8156 (mmm) cc_final: 0.7848 (mmt) REVERT: B 425 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 432 ASP cc_start: 0.8178 (t70) cc_final: 0.7931 (t0) REVERT: B 437 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7129 (tp30) REVERT: B 493 THR cc_start: 0.8539 (p) cc_final: 0.8253 (t) REVERT: C 16 MET cc_start: 0.8082 (mmm) cc_final: 0.7842 (mtp) REVERT: C 24 ASN cc_start: 0.7955 (t0) cc_final: 0.7692 (t0) REVERT: C 47 LEU cc_start: 0.8138 (mt) cc_final: 0.7934 (mp) REVERT: C 129 PHE cc_start: 0.8497 (t80) cc_final: 0.7994 (t80) REVERT: C 131 ASN cc_start: 0.8590 (m-40) cc_final: 0.8365 (m110) REVERT: C 142 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 303 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8416 (ptmm) REVERT: C 354 ASP cc_start: 0.7992 (t0) cc_final: 0.7704 (t70) REVERT: C 373 MET cc_start: 0.8104 (mmm) cc_final: 0.7807 (mmt) REVERT: C 387 SER cc_start: 0.8464 (t) cc_final: 0.8259 (m) REVERT: C 388 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8222 (ttmm) REVERT: C 507 LEU cc_start: 0.8823 (tm) cc_final: 0.8601 (tp) outliers start: 44 outliers final: 16 residues processed: 400 average time/residue: 0.5912 time to fit residues: 253.0913 Evaluate side-chains 389 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 368 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 319 GLN A 355 ASN A 377 ASN A 495 ASN A 496 GLN B 108 ASN B 217 ASN C 217 ASN C 355 ASN C 377 ASN C 449 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113717 restraints weight = 17809.695| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.89 r_work: 0.3408 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13260 Z= 0.178 Angle : 0.585 8.564 18012 Z= 0.293 Chirality : 0.043 0.205 1968 Planarity : 0.004 0.060 2304 Dihedral : 5.308 53.499 2157 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 16.45 % Favored : 80.82 % 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 aren not related in a simple way. whole: 1.31 (0.21), residues: 1560 helix: 1.60 (0.20), residues: 690 sheet: 0.99 (0.30), residues: 273 loop : 0.03 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 383 TYR 0.017 0.001 TYR C 132 PHE 0.022 0.001 PHE C 33 TRP 0.009 0.002 TRP C 34 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00420 (13215) covalent geometry : angle 0.56861 (17901) SS BOND : bond 0.00543 ( 24) SS BOND : angle 1.65097 ( 48) hydrogen bonds : bond 0.04365 ( 649) hydrogen bonds : angle 4.36962 ( 1893) link_BETA1-4 : bond 0.00593 ( 6) link_BETA1-4 : angle 1.25512 ( 18) link_NAG-ASN : bond 0.00430 ( 15) link_NAG-ASN : angle 2.15397 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 377 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7663 (mmm) cc_final: 0.7443 (mmm) REVERT: A 101 ASP cc_start: 0.7860 (t0) cc_final: 0.7492 (t0) REVERT: A 129 PHE cc_start: 0.8274 (t80) cc_final: 0.7884 (t80) REVERT: A 144 PHE cc_start: 0.8609 (m-80) cc_final: 0.8261 (m-80) REVERT: A 186 TYR cc_start: 0.8635 (m-80) cc_final: 0.8220 (m-80) REVERT: A 217 ASN cc_start: 0.8542 (m-40) cc_final: 0.8236 (m-40) REVERT: A 235 GLU cc_start: 0.8215 (tt0) cc_final: 0.8003 (tt0) REVERT: A 269 PHE cc_start: 0.8480 (m-80) cc_final: 0.8103 (m-80) REVERT: A 391 LYS cc_start: 0.8195 (mttt) cc_final: 0.7897 (mttt) REVERT: B 24 ASN cc_start: 0.8097 (t0) cc_final: 0.7782 (t0) REVERT: B 99 GLU cc_start: 0.7981 (tt0) cc_final: 0.7734 (tt0) REVERT: B 129 PHE cc_start: 0.8504 (t80) cc_final: 0.8202 (t80) REVERT: B 131 ASN cc_start: 0.8429 (m-40) cc_final: 0.8157 (m110) REVERT: B 142 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 164 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: B 171 ASN cc_start: 0.7764 (t0) cc_final: 0.7319 (m-40) REVERT: B 178 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7266 (mtp85) REVERT: B 223 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 249 VAL cc_start: 0.8422 (t) cc_final: 0.8080 (m) REVERT: B 273 TYR cc_start: 0.8700 (m-80) cc_final: 0.8283 (m-80) REVERT: B 347 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 354 ASP cc_start: 0.8001 (t0) cc_final: 0.7681 (t0) REVERT: B 388 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7932 (ttmm) REVERT: B 396 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: B 432 ASP cc_start: 0.8242 (t70) cc_final: 0.8020 (t0) REVERT: B 437 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7081 (tp30) REVERT: B 493 THR cc_start: 0.8558 (p) cc_final: 0.8284 (t) REVERT: C 16 MET cc_start: 0.8100 (mmm) cc_final: 0.7857 (mtp) REVERT: C 21 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7982 (mmtm) REVERT: C 129 PHE cc_start: 0.8534 (t80) cc_final: 0.8046 (t80) REVERT: C 354 ASP cc_start: 0.7993 (t0) cc_final: 0.7564 (t0) REVERT: C 373 MET cc_start: 0.8114 (mmm) cc_final: 0.7819 (mmt) REVERT: C 388 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8287 (ttmm) outliers start: 38 outliers final: 17 residues processed: 394 average time/residue: 0.5981 time to fit residues: 252.5731 Evaluate side-chains 393 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 371 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 319 GLN A 495 ASN A 496 GLN B 108 ASN B 217 ASN C 24 ASN C 131 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114619 restraints weight = 17646.543| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.88 r_work: 0.3421 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13260 Z= 0.136 Angle : 0.582 10.074 18012 Z= 0.289 Chirality : 0.042 0.194 1968 Planarity : 0.004 0.047 2304 Dihedral : 5.215 53.179 2157 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.44 % Allowed : 17.60 % Favored : 79.96 % 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 aren not related in a simple way. whole: 1.22 (0.21), residues: 1560 helix: 1.48 (0.20), residues: 711 sheet: 0.98 (0.30), residues: 267 loop : -0.00 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 187 TYR 0.023 0.001 TYR A 132 PHE 0.021 0.001 PHE C 33 TRP 0.011 0.001 TRP C 34 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00317 (13215) covalent geometry : angle 0.56712 (17901) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.78070 ( 48) hydrogen bonds : bond 0.03986 ( 649) hydrogen bonds : angle 4.31833 ( 1893) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 1.15405 ( 18) link_NAG-ASN : bond 0.00439 ( 15) link_NAG-ASN : angle 1.95987 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7698 (mmm) cc_final: 0.7473 (mmm) REVERT: A 101 ASP cc_start: 0.7850 (t0) cc_final: 0.7474 (t0) REVERT: A 129 PHE cc_start: 0.8267 (t80) cc_final: 0.7847 (t80) REVERT: A 186 TYR cc_start: 0.8615 (m-80) cc_final: 0.8215 (m-80) REVERT: A 217 ASN cc_start: 0.8537 (m-40) cc_final: 0.8224 (m-40) REVERT: A 235 GLU cc_start: 0.8246 (tt0) cc_final: 0.8027 (tt0) REVERT: A 269 PHE cc_start: 0.8468 (m-80) cc_final: 0.8101 (m-80) REVERT: B 24 ASN cc_start: 0.8098 (t0) cc_final: 0.7777 (t0) REVERT: B 129 PHE cc_start: 0.8477 (t80) cc_final: 0.8177 (t80) REVERT: B 131 ASN cc_start: 0.8440 (m-40) cc_final: 0.8155 (m110) REVERT: B 142 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 164 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: B 171 ASN cc_start: 0.7733 (t0) cc_final: 0.7277 (m-40) REVERT: B 178 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7302 (mtp85) REVERT: B 223 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mt) REVERT: B 238 MET cc_start: 0.8837 (mtp) cc_final: 0.8303 (mtp) REVERT: B 249 VAL cc_start: 0.8418 (t) cc_final: 0.8075 (m) REVERT: B 273 TYR cc_start: 0.8691 (m-80) cc_final: 0.8274 (m-80) REVERT: B 319 GLN cc_start: 0.8452 (mt0) cc_final: 0.8240 (mt0) REVERT: B 347 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8207 (tt) REVERT: B 354 ASP cc_start: 0.8005 (t0) cc_final: 0.7686 (t0) REVERT: B 388 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7994 (ttmm) REVERT: B 396 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: B 432 ASP cc_start: 0.8185 (t70) cc_final: 0.7929 (t0) REVERT: B 437 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7047 (tp30) REVERT: B 493 THR cc_start: 0.8554 (p) cc_final: 0.8280 (t) REVERT: C 16 MET cc_start: 0.7984 (mmm) cc_final: 0.7765 (mtp) REVERT: C 21 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7965 (mmtm) REVERT: C 129 PHE cc_start: 0.8513 (t80) cc_final: 0.8003 (t80) REVERT: C 253 GLU cc_start: 0.7935 (pt0) cc_final: 0.7644 (pt0) REVERT: C 354 ASP cc_start: 0.7993 (t0) cc_final: 0.7643 (t0) REVERT: C 424 TYR cc_start: 0.8575 (p90) cc_final: 0.8267 (p90) REVERT: C 468 MET cc_start: 0.8890 (mmm) cc_final: 0.8669 (mmm) outliers start: 34 outliers final: 12 residues processed: 384 average time/residue: 0.5865 time to fit residues: 241.0244 Evaluate side-chains 381 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 364 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 495 ASN A 496 GLN B 108 ASN B 217 ASN B 344 GLN B 377 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114898 restraints weight = 17668.766| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.86 r_work: 0.3425 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13260 Z= 0.136 Angle : 0.566 8.127 18012 Z= 0.284 Chirality : 0.042 0.214 1968 Planarity : 0.004 0.048 2304 Dihedral : 5.146 53.409 2157 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.66 % Allowed : 18.39 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1560 helix: 1.47 (0.20), residues: 720 sheet: 0.97 (0.31), residues: 267 loop : -0.10 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 289 TYR 0.018 0.001 TYR C 132 PHE 0.023 0.001 PHE C 33 TRP 0.011 0.001 TRP C 34 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00318 (13215) covalent geometry : angle 0.55162 (17901) SS BOND : bond 0.00391 ( 24) SS BOND : angle 1.75010 ( 48) hydrogen bonds : bond 0.03956 ( 649) hydrogen bonds : angle 4.26553 ( 1893) link_BETA1-4 : bond 0.00532 ( 6) link_BETA1-4 : angle 1.16423 ( 18) link_NAG-ASN : bond 0.00311 ( 15) link_NAG-ASN : angle 1.86924 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 369 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.7720 (mmm) cc_final: 0.7512 (mmm) REVERT: A 82 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8069 (mtt) REVERT: A 101 ASP cc_start: 0.7855 (t0) cc_final: 0.7490 (t0) REVERT: A 129 PHE cc_start: 0.8243 (t80) cc_final: 0.7820 (t80) REVERT: A 186 TYR cc_start: 0.8636 (m-80) cc_final: 0.8249 (m-80) REVERT: A 217 ASN cc_start: 0.8532 (m-40) cc_final: 0.8223 (m-40) REVERT: A 223 LEU cc_start: 0.8426 (mt) cc_final: 0.8211 (mt) REVERT: A 235 GLU cc_start: 0.8258 (tt0) cc_final: 0.8040 (tt0) REVERT: A 269 PHE cc_start: 0.8451 (m-80) cc_final: 0.8085 (m-80) REVERT: B 24 ASN cc_start: 0.8124 (t0) cc_final: 0.7795 (t0) REVERT: B 47 LEU cc_start: 0.8187 (mt) cc_final: 0.7950 (mp) REVERT: B 129 PHE cc_start: 0.8445 (t80) cc_final: 0.8145 (t80) REVERT: B 131 ASN cc_start: 0.8491 (m-40) cc_final: 0.8235 (m110) REVERT: B 136 TYR cc_start: 0.7920 (m-80) cc_final: 0.7634 (m-80) REVERT: B 142 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 164 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: B 171 ASN cc_start: 0.7740 (t0) cc_final: 0.7334 (m-40) REVERT: B 223 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8110 (mt) REVERT: B 238 MET cc_start: 0.8825 (mtp) cc_final: 0.8299 (mtm) REVERT: B 249 VAL cc_start: 0.8435 (t) cc_final: 0.8098 (m) REVERT: B 273 TYR cc_start: 0.8691 (m-80) cc_final: 0.8279 (m-80) REVERT: B 303 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8618 (ptmm) REVERT: B 347 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 354 ASP cc_start: 0.8006 (t0) cc_final: 0.7687 (t0) REVERT: B 388 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7990 (ttmm) REVERT: B 396 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: B 432 ASP cc_start: 0.8191 (t70) cc_final: 0.7934 (t0) REVERT: B 437 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7385 (tp30) REVERT: B 493 THR cc_start: 0.8551 (p) cc_final: 0.8285 (t) REVERT: C 16 MET cc_start: 0.7981 (mmm) cc_final: 0.7727 (mtp) REVERT: C 21 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: C 47 LEU cc_start: 0.8222 (mt) cc_final: 0.8009 (mp) REVERT: C 129 PHE cc_start: 0.8506 (t80) cc_final: 0.8031 (t80) REVERT: C 253 GLU cc_start: 0.7893 (pt0) cc_final: 0.7661 (pt0) REVERT: C 354 ASP cc_start: 0.7993 (t0) cc_final: 0.7641 (t0) REVERT: C 373 MET cc_start: 0.8078 (mmm) cc_final: 0.7720 (mmm) REVERT: C 468 MET cc_start: 0.8863 (mmm) cc_final: 0.8650 (mmm) REVERT: C 481 SER cc_start: 0.8368 (t) cc_final: 0.8116 (m) outliers start: 37 outliers final: 21 residues processed: 383 average time/residue: 0.5893 time to fit residues: 241.8351 Evaluate side-chains 389 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 79 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 496 GLN B 48 GLN B 108 ASN B 112 HIS B 217 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115673 restraints weight = 17653.775| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.86 r_work: 0.3436 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13260 Z= 0.114 Angle : 0.579 10.317 18012 Z= 0.287 Chirality : 0.042 0.203 1968 Planarity : 0.004 0.048 2304 Dihedral : 5.090 53.196 2157 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.66 % Allowed : 18.89 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 1.21 (0.21), residues: 1560 helix: 1.49 (0.20), residues: 720 sheet: 0.99 (0.31), residues: 267 loop : -0.07 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.019 0.001 TYR C 132 PHE 0.023 0.001 PHE C 33 TRP 0.012 0.001 TRP C 34 HIS 0.003 0.000 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00261 (13215) covalent geometry : angle 0.56433 (17901) SS BOND : bond 0.00409 ( 24) SS BOND : angle 1.94833 ( 48) hydrogen bonds : bond 0.03713 ( 649) hydrogen bonds : angle 4.24893 ( 1893) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.11859 ( 18) link_NAG-ASN : bond 0.00306 ( 15) link_NAG-ASN : angle 1.77671 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 372 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7820 (t0) cc_final: 0.7458 (t0) REVERT: A 129 PHE cc_start: 0.8225 (t80) cc_final: 0.7797 (t80) REVERT: A 186 TYR cc_start: 0.8636 (m-80) cc_final: 0.8229 (m-80) REVERT: A 217 ASN cc_start: 0.8527 (m-40) cc_final: 0.8228 (m-40) REVERT: A 235 GLU cc_start: 0.8232 (tt0) cc_final: 0.8018 (tt0) REVERT: A 269 PHE cc_start: 0.8445 (m-80) cc_final: 0.8077 (m-80) REVERT: A 288 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7885 (mtp85) REVERT: A 388 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8052 (ttpp) REVERT: B 24 ASN cc_start: 0.8089 (t0) cc_final: 0.7748 (t0) REVERT: B 119 MET cc_start: 0.8882 (mmt) cc_final: 0.8658 (mmm) REVERT: B 129 PHE cc_start: 0.8415 (t80) cc_final: 0.8115 (t80) REVERT: B 131 ASN cc_start: 0.8452 (m-40) cc_final: 0.8181 (m110) REVERT: B 136 TYR cc_start: 0.7901 (m-80) cc_final: 0.7620 (m-80) REVERT: B 142 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 164 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: B 171 ASN cc_start: 0.7762 (t0) cc_final: 0.7349 (m-40) REVERT: B 238 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: B 249 VAL cc_start: 0.8411 (t) cc_final: 0.8072 (m) REVERT: B 273 TYR cc_start: 0.8693 (m-80) cc_final: 0.8220 (m-80) REVERT: B 303 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8604 (ptmm) REVERT: B 347 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8270 (tt) REVERT: B 354 ASP cc_start: 0.7958 (t0) cc_final: 0.7647 (t0) REVERT: B 383 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.8042 (ttm110) REVERT: B 388 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7972 (ttmm) REVERT: B 432 ASP cc_start: 0.8192 (t70) cc_final: 0.7934 (t0) REVERT: B 437 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7392 (tp30) REVERT: B 493 THR cc_start: 0.8507 (p) cc_final: 0.8242 (t) REVERT: C 16 MET cc_start: 0.7938 (mmm) cc_final: 0.7700 (mtp) REVERT: C 21 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8014 (mmtm) REVERT: C 31 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7129 (ttm170) REVERT: C 47 LEU cc_start: 0.8222 (mt) cc_final: 0.8015 (mp) REVERT: C 129 PHE cc_start: 0.8490 (t80) cc_final: 0.8016 (t80) REVERT: C 354 ASP cc_start: 0.7970 (t0) cc_final: 0.7611 (t0) REVERT: C 373 MET cc_start: 0.8079 (mmm) cc_final: 0.7710 (mmm) REVERT: C 481 SER cc_start: 0.8386 (t) cc_final: 0.8125 (m) outliers start: 37 outliers final: 21 residues processed: 387 average time/residue: 0.5886 time to fit residues: 244.8190 Evaluate side-chains 392 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN B 108 ASN B 217 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115093 restraints weight = 17736.011| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.87 r_work: 0.3430 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13260 Z= 0.133 Angle : 0.601 10.282 18012 Z= 0.297 Chirality : 0.042 0.186 1968 Planarity : 0.004 0.054 2304 Dihedral : 5.097 53.374 2157 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.94 % Allowed : 20.33 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1560 helix: 1.49 (0.20), residues: 717 sheet: 1.00 (0.31), residues: 267 loop : -0.13 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 237 TYR 0.018 0.001 TYR C 132 PHE 0.023 0.001 PHE C 33 TRP 0.011 0.002 TRP C 34 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00313 (13215) covalent geometry : angle 0.58092 (17901) SS BOND : bond 0.00400 ( 24) SS BOND : angle 2.45584 ( 48) hydrogen bonds : bond 0.03856 ( 649) hydrogen bonds : angle 4.28192 ( 1893) link_BETA1-4 : bond 0.00482 ( 6) link_BETA1-4 : angle 1.13727 ( 18) link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 1.77235 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 375 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7883 (t0) cc_final: 0.7523 (t0) REVERT: A 129 PHE cc_start: 0.8234 (t80) cc_final: 0.7823 (t80) REVERT: A 144 PHE cc_start: 0.8560 (m-80) cc_final: 0.8257 (m-80) REVERT: A 186 TYR cc_start: 0.8644 (m-80) cc_final: 0.8266 (m-80) REVERT: A 217 ASN cc_start: 0.8521 (m-40) cc_final: 0.8234 (m-40) REVERT: A 235 GLU cc_start: 0.8216 (tt0) cc_final: 0.8000 (tt0) REVERT: A 269 PHE cc_start: 0.8439 (m-80) cc_final: 0.8066 (m-80) REVERT: A 288 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7889 (mtp85) REVERT: A 380 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7948 (mtpp) REVERT: A 388 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8028 (ttpp) REVERT: B 24 ASN cc_start: 0.8142 (t0) cc_final: 0.7846 (t0) REVERT: B 129 PHE cc_start: 0.8420 (t80) cc_final: 0.8129 (t80) REVERT: B 131 ASN cc_start: 0.8465 (m-40) cc_final: 0.8195 (m110) REVERT: B 136 TYR cc_start: 0.7921 (m-80) cc_final: 0.7674 (m-80) REVERT: B 142 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 164 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: B 171 ASN cc_start: 0.7779 (t0) cc_final: 0.7356 (m-40) REVERT: B 238 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: B 249 VAL cc_start: 0.8431 (t) cc_final: 0.8101 (m) REVERT: B 273 TYR cc_start: 0.8698 (m-80) cc_final: 0.8296 (m-80) REVERT: B 303 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8609 (ptmm) REVERT: B 347 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 354 ASP cc_start: 0.7963 (t0) cc_final: 0.7648 (t0) REVERT: B 388 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7982 (ttmm) REVERT: B 424 TYR cc_start: 0.8645 (p90) cc_final: 0.8338 (p90) REVERT: B 432 ASP cc_start: 0.8199 (t70) cc_final: 0.7948 (t0) REVERT: B 437 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7384 (tp30) REVERT: B 493 THR cc_start: 0.8528 (p) cc_final: 0.8267 (t) REVERT: C 16 MET cc_start: 0.7942 (mmm) cc_final: 0.7642 (mtp) REVERT: C 21 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8021 (mmtm) REVERT: C 31 ARG cc_start: 0.7527 (ttm170) cc_final: 0.7144 (ttm170) REVERT: C 47 LEU cc_start: 0.8223 (mt) cc_final: 0.8013 (mp) REVERT: C 82 MET cc_start: 0.8404 (mmm) cc_final: 0.8148 (mtt) REVERT: C 129 PHE cc_start: 0.8497 (t80) cc_final: 0.8028 (t80) REVERT: C 354 ASP cc_start: 0.7977 (t0) cc_final: 0.7618 (t0) REVERT: C 373 MET cc_start: 0.8093 (mmm) cc_final: 0.7811 (mmt) REVERT: C 457 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8176 (ttpp) REVERT: C 481 SER cc_start: 0.8364 (t) cc_final: 0.8118 (m) outliers start: 27 outliers final: 17 residues processed: 386 average time/residue: 0.6106 time to fit residues: 252.2845 Evaluate side-chains 388 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 367 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 129 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 495 ASN B 108 ASN B 217 ASN C 112 HIS C 217 ASN C 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115966 restraints weight = 17826.972| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.87 r_work: 0.3438 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13260 Z= 0.124 Angle : 0.626 11.107 18012 Z= 0.306 Chirality : 0.042 0.174 1968 Planarity : 0.004 0.065 2304 Dihedral : 5.100 53.241 2157 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.65 % Allowed : 20.91 % Favored : 77.44 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1560 helix: 1.50 (0.20), residues: 717 sheet: 1.02 (0.31), residues: 267 loop : -0.15 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 237 TYR 0.018 0.001 TYR C 132 PHE 0.024 0.001 PHE C 33 TRP 0.011 0.002 TRP B 508 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00288 (13215) covalent geometry : angle 0.60520 (17901) SS BOND : bond 0.00439 ( 24) SS BOND : angle 2.67434 ( 48) hydrogen bonds : bond 0.03767 ( 649) hydrogen bonds : angle 4.30418 ( 1893) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 1.13795 ( 18) link_NAG-ASN : bond 0.00259 ( 15) link_NAG-ASN : angle 1.75435 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 365 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7869 (t0) cc_final: 0.7508 (t0) REVERT: A 129 PHE cc_start: 0.8227 (t80) cc_final: 0.7803 (t80) REVERT: A 186 TYR cc_start: 0.8631 (m-80) cc_final: 0.8228 (m-80) REVERT: A 217 ASN cc_start: 0.8534 (m-40) cc_final: 0.8252 (m-40) REVERT: A 235 GLU cc_start: 0.8184 (tt0) cc_final: 0.7974 (tt0) REVERT: A 269 PHE cc_start: 0.8436 (m-80) cc_final: 0.8070 (m-80) REVERT: A 288 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7898 (mtp85) REVERT: A 388 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8041 (ttpp) REVERT: B 24 ASN cc_start: 0.8146 (t0) cc_final: 0.7850 (t0) REVERT: B 95 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7954 (mtt180) REVERT: B 129 PHE cc_start: 0.8417 (t80) cc_final: 0.8165 (t80) REVERT: B 131 ASN cc_start: 0.8455 (m-40) cc_final: 0.8205 (m110) REVERT: B 136 TYR cc_start: 0.7904 (m-80) cc_final: 0.7672 (m-80) REVERT: B 142 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 164 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: B 171 ASN cc_start: 0.7756 (t0) cc_final: 0.7322 (m-40) REVERT: B 249 VAL cc_start: 0.8443 (t) cc_final: 0.8110 (m) REVERT: B 273 TYR cc_start: 0.8693 (m-80) cc_final: 0.8213 (m-80) REVERT: B 303 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8602 (ptmm) REVERT: B 347 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8262 (tt) REVERT: B 354 ASP cc_start: 0.7952 (t0) cc_final: 0.7638 (t0) REVERT: B 388 LYS cc_start: 0.8291 (ttpp) cc_final: 0.8000 (ttmm) REVERT: B 432 ASP cc_start: 0.8181 (t70) cc_final: 0.7925 (t0) REVERT: B 437 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7373 (tp30) REVERT: B 493 THR cc_start: 0.8515 (p) cc_final: 0.8260 (t) REVERT: C 16 MET cc_start: 0.7911 (mmm) cc_final: 0.7677 (mtp) REVERT: C 21 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8024 (mmtp) REVERT: C 31 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7089 (ttm170) REVERT: C 47 LEU cc_start: 0.8227 (mt) cc_final: 0.8010 (mp) REVERT: C 82 MET cc_start: 0.8408 (mmm) cc_final: 0.8197 (mtt) REVERT: C 129 PHE cc_start: 0.8497 (t80) cc_final: 0.8008 (t80) REVERT: C 354 ASP cc_start: 0.7957 (t0) cc_final: 0.7590 (t0) REVERT: C 373 MET cc_start: 0.8065 (mmm) cc_final: 0.7702 (mmm) REVERT: C 481 SER cc_start: 0.8362 (t) cc_final: 0.8112 (m) outliers start: 23 outliers final: 18 residues processed: 375 average time/residue: 0.6473 time to fit residues: 259.6819 Evaluate side-chains 385 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 364 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 65 optimal weight: 0.3980 chunk 76 optimal weight: 0.0070 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN B 108 ASN B 217 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116463 restraints weight = 17833.327| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.88 r_work: 0.3445 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13260 Z= 0.117 Angle : 0.610 11.541 18012 Z= 0.301 Chirality : 0.041 0.162 1968 Planarity : 0.005 0.108 2304 Dihedral : 5.044 53.164 2157 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.58 % Allowed : 21.12 % Favored : 77.30 % 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 aren not related in a simple way. whole: 1.24 (0.21), residues: 1560 helix: 1.56 (0.20), residues: 717 sheet: 1.06 (0.31), residues: 267 loop : -0.15 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 383 TYR 0.019 0.001 TYR A 132 PHE 0.024 0.001 PHE C 33 TRP 0.014 0.002 TRP C 219 HIS 0.004 0.000 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00269 (13215) covalent geometry : angle 0.58971 (17901) SS BOND : bond 0.00379 ( 24) SS BOND : angle 2.59630 ( 48) hydrogen bonds : bond 0.03719 ( 649) hydrogen bonds : angle 4.23624 ( 1893) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 1.09309 ( 18) link_NAG-ASN : bond 0.00263 ( 15) link_NAG-ASN : angle 1.68500 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5305.17 seconds wall clock time: 90 minutes 43.51 seconds (5443.51 seconds total)