Starting phenix.real_space_refine on Sat Aug 23 15:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.map" model { file = "/net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on9_16983/08_2025/8on9_16983.cif" } resolution = 2.4 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= 0.035 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 8289 2.51 5 N 2163 2.21 5 O 2457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 13014 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain breaks: 1 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 29, 'TRANS': 494} 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': 29, 'TRANS': 494} Chain breaks: 1 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: "J" 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: "K" 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: "L" 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: 3.54, per 1000 atoms: 0.27 Number of scatterers: 13014 At special positions: 0 Unit cell: (107.31, 108.332, 134.904, 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 2457 8.00 N 2163 7.00 C 8289 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=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 G 1 " - " ASN A 180 " " NAG H 1 " - " ASN A 299 " " NAG I 1 " - " ASN B 180 " " NAG J 1 " - " ASN B 299 " " NAG K 1 " - " ASN C 180 " " NAG L 1 " - " ASN C 299 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 678.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 46.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 27 through 57 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.565A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.506A 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 509 Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 27 through 57 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.564A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.506A 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 509 Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 27 through 57 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.565A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.506A 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 509 Processing helix chain 'C' and resid 514 through 530 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 171 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 224 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.303A 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: 9.246A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 9.039A 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 189 removed outlier: 6.411A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.511A 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: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 171 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 224 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.302A 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: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 9.039A 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 189 removed outlier: 6.411A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.511A 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: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 171 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 224 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.303A 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: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 9.039A 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 189 removed outlier: 6.411A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1884 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: 2.20 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2896 1.33 - 1.45: 3189 1.45 - 1.58: 7100 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 13341 Sorted by residual: bond pdb=" CA SER B 58 " pdb=" CB SER B 58 " ideal model delta sigma weight residual 1.534 1.481 0.053 1.71e-02 3.42e+03 9.46e+00 bond pdb=" CA SER C 58 " pdb=" CB SER C 58 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.71e-02 3.42e+03 9.19e+00 bond pdb=" CA SER A 58 " pdb=" CB SER A 58 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.71e-02 3.42e+03 9.19e+00 bond pdb=" N PRO C 266 " pdb=" CA PRO C 266 " ideal model delta sigma weight residual 1.465 1.431 0.034 1.15e-02 7.56e+03 8.50e+00 bond pdb=" N PRO A 266 " pdb=" CA PRO A 266 " ideal model delta sigma weight residual 1.465 1.431 0.033 1.15e-02 7.56e+03 8.40e+00 ... (remaining 13336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17550 2.09 - 4.18: 438 4.18 - 6.27: 69 6.27 - 8.37: 6 8.37 - 10.46: 6 Bond angle restraints: 18069 Sorted by residual: angle pdb=" N SER B 58 " pdb=" CA SER B 58 " pdb=" C SER B 58 " ideal model delta sigma weight residual 113.38 104.51 8.87 1.23e+00 6.61e-01 5.20e+01 angle pdb=" N SER C 58 " pdb=" CA SER C 58 " pdb=" C SER C 58 " ideal model delta sigma weight residual 113.38 104.51 8.87 1.23e+00 6.61e-01 5.20e+01 angle pdb=" N SER A 58 " pdb=" CA SER A 58 " pdb=" C SER A 58 " ideal model delta sigma weight residual 113.38 104.53 8.85 1.23e+00 6.61e-01 5.18e+01 angle pdb=" CA PHE B 188 " pdb=" CB PHE B 188 " pdb=" CG PHE B 188 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" CA PHE C 188 " pdb=" CB PHE C 188 " pdb=" CG PHE C 188 " ideal model delta sigma weight residual 113.80 119.05 -5.25 1.00e+00 1.00e+00 2.76e+01 ... (remaining 18064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 7611 16.79 - 33.58: 522 33.58 - 50.36: 114 50.36 - 67.15: 45 67.15 - 83.94: 15 Dihedral angle restraints: 8307 sinusoidal: 3666 harmonic: 4641 Sorted by residual: dihedral pdb=" CB CYS B 80 " pdb=" SG CYS B 80 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.81 -32.81 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS C 80 " pdb=" SG CYS C 80 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.79 -32.79 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 80 " pdb=" SG CYS A 80 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.78 -32.78 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 8304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1473 0.049 - 0.099: 366 0.099 - 0.148: 123 0.148 - 0.197: 18 0.197 - 0.246: 9 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.35e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.31e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.21e+01 ... (remaining 1986 not shown) Planarity restraints: 2334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" C7 NAG C 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" C7 NAG A 602 " -0.031 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" C7 NAG B 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.130 2.00e-02 2.50e+03 ... (remaining 2331 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 425 2.72 - 3.26: 12904 3.26 - 3.81: 21443 3.81 - 4.35: 26422 4.35 - 4.90: 45406 Nonbonded interactions: 106600 Sorted by model distance: nonbonded pdb=" O ASP A 302 " pdb=" OD1 ASP A 302 " model vdw 2.175 3.040 nonbonded pdb=" O ASP C 302 " pdb=" OD1 ASP C 302 " model vdw 2.175 3.040 nonbonded pdb=" O ASP B 302 " pdb=" OD1 ASP B 302 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR C 192 " pdb=" O VAL C 249 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 192 " pdb=" O VAL A 249 " model vdw 2.283 3.040 ... (remaining 106595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.720 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.005 0.101 13389 Z= 0.312 Angle : 0.772 10.458 18180 Z= 0.445 Chirality : 0.050 0.246 1989 Planarity : 0.009 0.144 2319 Dihedral : 12.861 83.940 5241 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: 1.48 (0.22), residues: 1569 helix: 1.49 (0.21), residues: 678 sheet: 1.74 (0.30), residues: 273 loop : 0.15 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 183 TYR 0.013 0.001 TYR B 452 PHE 0.036 0.001 PHE A 188 TRP 0.017 0.002 TRP B 419 HIS 0.002 0.000 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00451 (13341) covalent geometry : angle 0.74443 (18069) SS BOND : bond 0.00361 ( 24) SS BOND : angle 1.01450 ( 48) hydrogen bonds : bond 0.17589 ( 637) hydrogen bonds : angle 6.24260 ( 1884) Misc. bond : bond 0.10066 ( 3) link_BETA1-4 : bond 0.00638 ( 6) link_BETA1-4 : angle 1.42116 ( 18) link_NAG-ASN : bond 0.00195 ( 15) link_NAG-ASN : angle 4.07367 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8061 (mttt) cc_final: 0.7484 (mtmm) REVERT: A 66 GLU cc_start: 0.8307 (pt0) cc_final: 0.8028 (pt0) REVERT: A 111 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 125 TYR cc_start: 0.7534 (m-80) cc_final: 0.7159 (m-80) REVERT: A 145 SER cc_start: 0.8284 (p) cc_final: 0.8025 (m) REVERT: A 156 GLU cc_start: 0.7629 (tt0) cc_final: 0.7277 (tt0) REVERT: A 166 GLU cc_start: 0.8035 (tt0) cc_final: 0.7426 (tt0) REVERT: A 232 LYS cc_start: 0.8555 (mttm) cc_final: 0.8347 (mttp) REVERT: A 235 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 289 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7594 (ttt180) REVERT: A 311 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 319 GLN cc_start: 0.7440 (mt0) cc_final: 0.7226 (mt0) REVERT: A 357 PRO cc_start: 0.7847 (Cg_exo) cc_final: 0.7639 (Cg_endo) REVERT: A 396 MET cc_start: 0.7595 (mmm) cc_final: 0.7284 (mmp) REVERT: A 407 GLU cc_start: 0.7759 (tt0) cc_final: 0.7539 (tt0) REVERT: A 465 GLU cc_start: 0.7874 (mp0) cc_final: 0.7614 (mp0) REVERT: A 494 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6790 (ttm110) REVERT: A 525 ASP cc_start: 0.6887 (m-30) cc_final: 0.6553 (t0) REVERT: B 15 THR cc_start: 0.6444 (p) cc_final: 0.5946 (p) REVERT: B 29 MET cc_start: 0.6947 (mmm) cc_final: 0.6638 (mmm) REVERT: B 48 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7181 (mm-40) REVERT: B 57 PHE cc_start: 0.7927 (m-80) cc_final: 0.7624 (m-80) REVERT: B 86 ASP cc_start: 0.8027 (t0) cc_final: 0.7779 (t0) REVERT: B 124 LYS cc_start: 0.7986 (mttt) cc_final: 0.7748 (mtpm) REVERT: B 145 SER cc_start: 0.8237 (p) cc_final: 0.7957 (m) REVERT: B 156 GLU cc_start: 0.7655 (tt0) cc_final: 0.7376 (tt0) REVERT: B 166 GLU cc_start: 0.8050 (tt0) cc_final: 0.7632 (tt0) REVERT: B 177 HIS cc_start: 0.7384 (m-70) cc_final: 0.7132 (m-70) REVERT: B 303 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8190 (ptpp) REVERT: B 308 ASP cc_start: 0.7631 (m-30) cc_final: 0.7374 (p0) REVERT: B 311 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6548 (mm-30) REVERT: B 329 GLU cc_start: 0.7592 (tt0) cc_final: 0.7098 (mm-30) REVERT: B 357 PRO cc_start: 0.7788 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8246 (m-80) cc_final: 0.7952 (m-80) REVERT: B 377 ASN cc_start: 0.7654 (m-40) cc_final: 0.7389 (m110) REVERT: B 407 GLU cc_start: 0.7769 (tt0) cc_final: 0.7222 (tt0) REVERT: B 449 GLN cc_start: 0.7939 (tp40) cc_final: 0.7730 (tp40) REVERT: B 465 GLU cc_start: 0.7823 (mp0) cc_final: 0.7553 (mp0) REVERT: B 469 LYS cc_start: 0.8549 (mttt) cc_final: 0.8301 (mttm) REVERT: B 481 SER cc_start: 0.8242 (t) cc_final: 0.7950 (p) REVERT: B 511 ILE cc_start: 0.7723 (mt) cc_final: 0.7484 (mm) REVERT: B 525 ASP cc_start: 0.6820 (m-30) cc_final: 0.6550 (t70) REVERT: C 29 MET cc_start: 0.7549 (mmm) cc_final: 0.7221 (mmm) REVERT: C 49 MET cc_start: 0.7782 (tpp) cc_final: 0.7545 (tpp) REVERT: C 66 GLU cc_start: 0.8165 (pt0) cc_final: 0.7795 (pt0) REVERT: C 142 GLU cc_start: 0.7449 (tt0) cc_final: 0.7222 (tt0) REVERT: C 145 SER cc_start: 0.8200 (p) cc_final: 0.7945 (m) REVERT: C 166 GLU cc_start: 0.7994 (tt0) cc_final: 0.7582 (tt0) REVERT: C 301 SER cc_start: 0.7761 (t) cc_final: 0.7481 (p) REVERT: C 311 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6590 (mm-30) REVERT: C 329 GLU cc_start: 0.7805 (tt0) cc_final: 0.7322 (mp0) REVERT: C 407 GLU cc_start: 0.7813 (tt0) cc_final: 0.7507 (tt0) REVERT: C 465 GLU cc_start: 0.7953 (mp0) cc_final: 0.7645 (mp0) REVERT: C 480 ASP cc_start: 0.7342 (m-30) cc_final: 0.6947 (m-30) REVERT: C 481 SER cc_start: 0.8135 (t) cc_final: 0.7785 (p) REVERT: C 511 ILE cc_start: 0.7780 (mt) cc_final: 0.7531 (mm) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.7394 time to fit residues: 350.2780 Evaluate side-chains 373 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 400 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN B 54 GLN B 173 HIS B 286 HIS B 374 GLN B 463 ASN B 475 ASN B 495 ASN C 141 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 319 GLN C 449 GLN C 482 ASN C 495 ASN C 496 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120348 restraints weight = 17331.408| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.64 r_work: 0.3604 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13389 Z= 0.145 Angle : 0.653 11.897 18180 Z= 0.321 Chirality : 0.046 0.244 1989 Planarity : 0.004 0.040 2319 Dihedral : 6.481 59.965 2172 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.13 % Allowed : 11.47 % Favored : 85.40 % 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: 1.43 (0.21), residues: 1569 helix: 1.45 (0.20), residues: 705 sheet: 1.43 (0.29), residues: 273 loop : 0.21 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.013 0.001 TYR A 414 PHE 0.015 0.001 PHE C 439 TRP 0.014 0.002 TRP B 419 HIS 0.003 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00333 (13341) covalent geometry : angle 0.62896 (18069) SS BOND : bond 0.00534 ( 24) SS BOND : angle 2.45005 ( 48) hydrogen bonds : bond 0.04222 ( 637) hydrogen bonds : angle 4.63945 ( 1884) Misc. bond : bond 0.00236 ( 3) link_BETA1-4 : bond 0.00601 ( 6) link_BETA1-4 : angle 1.08488 ( 18) link_NAG-ASN : bond 0.00364 ( 15) link_NAG-ASN : angle 2.60549 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 401 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ASP cc_start: 0.7657 (p0) cc_final: 0.7422 (p0) REVERT: A 359 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 487 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: B 44 MET cc_start: 0.7883 (mmm) cc_final: 0.7526 (mmm) REVERT: B 57 PHE cc_start: 0.8536 (m-80) cc_final: 0.8261 (m-80) REVERT: B 362 PHE cc_start: 0.8917 (m-80) cc_final: 0.8556 (m-80) REVERT: B 377 ASN cc_start: 0.8584 (m-40) cc_final: 0.8291 (m110) REVERT: C 142 GLU cc_start: 0.7704 (tt0) cc_final: 0.7460 (tt0) REVERT: C 321 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7926 (mtt) outliers start: 44 outliers final: 13 residues processed: 416 average time/residue: 0.7462 time to fit residues: 333.5524 Evaluate side-chains 361 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 127 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 324 GLN A 400 ASN A 495 ASN B 374 GLN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 475 ASN C 496 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121148 restraints weight = 17605.001| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.65 r_work: 0.3622 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13389 Z= 0.118 Angle : 0.619 9.459 18180 Z= 0.299 Chirality : 0.045 0.237 1989 Planarity : 0.004 0.033 2319 Dihedral : 6.197 57.389 2172 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.49 % Allowed : 13.60 % Favored : 82.91 % 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: 1.40 (0.21), residues: 1569 helix: 1.53 (0.20), residues: 711 sheet: 1.18 (0.29), residues: 276 loop : 0.16 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 246 TYR 0.011 0.001 TYR C 273 PHE 0.015 0.001 PHE C 188 TRP 0.013 0.002 TRP B 419 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00258 (13341) covalent geometry : angle 0.59723 (18069) SS BOND : bond 0.01007 ( 24) SS BOND : angle 2.24872 ( 48) hydrogen bonds : bond 0.03692 ( 637) hydrogen bonds : angle 4.32345 ( 1884) Misc. bond : bond 0.00096 ( 3) link_BETA1-4 : bond 0.00472 ( 6) link_BETA1-4 : angle 0.76430 ( 18) link_NAG-ASN : bond 0.00152 ( 15) link_NAG-ASN : angle 2.47008 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8187 (mm-40) REVERT: A 121 LYS cc_start: 0.8452 (tppt) cc_final: 0.8160 (tptt) REVERT: B 57 PHE cc_start: 0.8503 (m-80) cc_final: 0.8227 (m-80) REVERT: B 253 GLU cc_start: 0.7831 (tt0) cc_final: 0.7620 (tt0) REVERT: B 362 PHE cc_start: 0.8931 (m-80) cc_final: 0.8521 (m-80) REVERT: B 377 ASN cc_start: 0.8555 (m-40) cc_final: 0.8272 (m110) REVERT: C 142 GLU cc_start: 0.7603 (tt0) cc_final: 0.7377 (tt0) REVERT: C 246 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8228 (mtt180) REVERT: C 321 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7817 (mtt) REVERT: C 377 ASN cc_start: 0.8591 (m-40) cc_final: 0.8327 (m110) REVERT: C 495 ASN cc_start: 0.7971 (t0) cc_final: 0.7624 (t0) outliers start: 49 outliers final: 16 residues processed: 389 average time/residue: 0.7670 time to fit residues: 320.0531 Evaluate side-chains 366 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 348 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 374 GLN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN C 48 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 496 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120475 restraints weight = 17435.015| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.64 r_work: 0.3611 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13389 Z= 0.143 Angle : 0.632 10.043 18180 Z= 0.307 Chirality : 0.046 0.240 1989 Planarity : 0.004 0.041 2319 Dihedral : 6.165 57.756 2172 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.63 % Allowed : 14.10 % Favored : 82.26 % 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: 1.40 (0.21), residues: 1569 helix: 1.53 (0.20), residues: 711 sheet: 1.16 (0.29), residues: 276 loop : 0.17 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.015 0.001 PHE B 188 TRP 0.011 0.002 TRP C 349 HIS 0.003 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00335 (13341) covalent geometry : angle 0.60410 (18069) SS BOND : bond 0.00551 ( 24) SS BOND : angle 2.86624 ( 48) hydrogen bonds : bond 0.03765 ( 637) hydrogen bonds : angle 4.20013 ( 1884) Misc. bond : bond 0.00041 ( 3) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 0.81829 ( 18) link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 2.36338 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8489 (m-80) cc_final: 0.8231 (m-80) REVERT: B 362 PHE cc_start: 0.8924 (m-80) cc_final: 0.8533 (m-80) REVERT: B 377 ASN cc_start: 0.8580 (m-40) cc_final: 0.8284 (m110) REVERT: C 238 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: C 321 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7837 (mtt) outliers start: 51 outliers final: 23 residues processed: 384 average time/residue: 0.7371 time to fit residues: 303.2836 Evaluate side-chains 378 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 353 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 482 ASN C 48 GLN C 106 ASN C 319 GLN C 374 GLN C 475 ASN C 482 ASN C 496 GLN C 504 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120409 restraints weight = 17495.691| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.66 r_work: 0.3603 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13389 Z= 0.141 Angle : 0.624 9.541 18180 Z= 0.303 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.042 2319 Dihedral : 6.133 57.839 2172 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.56 % Allowed : 15.03 % Favored : 81.41 % 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: 1.43 (0.21), residues: 1569 helix: 1.52 (0.20), residues: 711 sheet: 1.20 (0.30), residues: 273 loop : 0.24 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.015 0.001 PHE C 45 TRP 0.011 0.002 TRP C 349 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00329 (13341) covalent geometry : angle 0.59772 (18069) SS BOND : bond 0.00617 ( 24) SS BOND : angle 2.74138 ( 48) hydrogen bonds : bond 0.03734 ( 637) hydrogen bonds : angle 4.17237 ( 1884) Misc. bond : bond 0.00023 ( 3) link_BETA1-4 : bond 0.00538 ( 6) link_BETA1-4 : angle 0.82738 ( 18) link_NAG-ASN : bond 0.00104 ( 15) link_NAG-ASN : angle 2.30458 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8525 (mmtp) REVERT: A 518 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: B 82 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7477 (mtt) REVERT: B 178 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8122 (ttm170) REVERT: B 362 PHE cc_start: 0.8937 (m-80) cc_final: 0.8549 (m-80) REVERT: B 377 ASN cc_start: 0.8574 (m-40) cc_final: 0.8291 (m110) REVERT: C 238 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7740 (ttp) REVERT: C 321 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: C 380 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7917 (mttm) REVERT: C 437 GLU cc_start: 0.7617 (tp30) cc_final: 0.7345 (tp30) outliers start: 50 outliers final: 27 residues processed: 376 average time/residue: 0.7954 time to fit residues: 319.6007 Evaluate side-chains 370 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 400 ASN A 495 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 482 ASN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 475 ASN C 482 ASN C 496 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120983 restraints weight = 17247.502| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.63 r_work: 0.3616 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13389 Z= 0.129 Angle : 0.620 10.152 18180 Z= 0.300 Chirality : 0.045 0.238 1989 Planarity : 0.004 0.039 2319 Dihedral : 6.074 57.827 2172 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.56 % Allowed : 15.60 % Favored : 80.84 % 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: 1.44 (0.21), residues: 1569 helix: 1.54 (0.20), residues: 711 sheet: 1.19 (0.30), residues: 273 loop : 0.23 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.013 0.001 PHE B 188 TRP 0.011 0.002 TRP A 419 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00297 (13341) covalent geometry : angle 0.59631 (18069) SS BOND : bond 0.00592 ( 24) SS BOND : angle 2.68893 ( 48) hydrogen bonds : bond 0.03625 ( 637) hydrogen bonds : angle 4.14643 ( 1884) Misc. bond : bond 0.00016 ( 3) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 0.82952 ( 18) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 2.17113 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 358 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8672 (mt) cc_final: 0.8391 (mt) REVERT: B 178 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8098 (ttm170) REVERT: B 362 PHE cc_start: 0.8933 (m-80) cc_final: 0.8548 (m-80) REVERT: B 377 ASN cc_start: 0.8581 (m-40) cc_final: 0.8310 (m110) REVERT: C 238 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7703 (ttp) REVERT: C 306 PHE cc_start: 0.8621 (m-80) cc_final: 0.8363 (m-80) REVERT: C 321 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7838 (mtt) REVERT: C 437 GLU cc_start: 0.7621 (tp30) cc_final: 0.7355 (tp30) outliers start: 50 outliers final: 31 residues processed: 373 average time/residue: 0.7948 time to fit residues: 316.6166 Evaluate side-chains 385 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 352 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 400 ASN A 495 ASN B 297 HIS B 319 GLN B 374 GLN B 482 ASN B 495 ASN C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 496 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119081 restraints weight = 17288.302| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.63 r_work: 0.3590 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13389 Z= 0.207 Angle : 0.657 13.782 18180 Z= 0.321 Chirality : 0.047 0.243 1989 Planarity : 0.004 0.044 2319 Dihedral : 6.138 58.269 2172 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.56 % Allowed : 16.52 % Favored : 79.91 % 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 (0.21), residues: 1569 helix: 1.44 (0.20), residues: 711 sheet: 1.28 (0.30), residues: 264 loop : 0.14 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 31 TYR 0.015 0.002 TYR A 414 PHE 0.015 0.002 PHE B 188 TRP 0.012 0.002 TRP C 349 HIS 0.006 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00492 (13341) covalent geometry : angle 0.63252 (18069) SS BOND : bond 0.00570 ( 24) SS BOND : angle 2.80755 ( 48) hydrogen bonds : bond 0.04125 ( 637) hydrogen bonds : angle 4.22187 ( 1884) Misc. bond : bond 0.00039 ( 3) link_BETA1-4 : bond 0.00427 ( 6) link_BETA1-4 : angle 0.90889 ( 18) link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 2.29085 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8526 (mmm) cc_final: 0.8207 (mmt) REVERT: A 242 LEU cc_start: 0.8692 (mt) cc_final: 0.8393 (mt) REVERT: A 381 CYS cc_start: 0.6739 (m) cc_final: 0.6291 (t) REVERT: B 178 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8073 (ttm170) REVERT: B 362 PHE cc_start: 0.8953 (m-80) cc_final: 0.8561 (m-80) REVERT: B 377 ASN cc_start: 0.8589 (m-40) cc_final: 0.8302 (m110) REVERT: B 393 THR cc_start: 0.8351 (p) cc_final: 0.8113 (m) REVERT: C 238 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7725 (ttp) REVERT: C 437 GLU cc_start: 0.7715 (tp30) cc_final: 0.7431 (tp30) outliers start: 50 outliers final: 32 residues processed: 379 average time/residue: 0.7458 time to fit residues: 302.9465 Evaluate side-chains 397 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 400 ASN A 495 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.120309 restraints weight = 17081.761| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.62 r_work: 0.3607 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13389 Z= 0.143 Angle : 0.637 12.197 18180 Z= 0.309 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.040 2319 Dihedral : 6.079 57.997 2172 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.71 % Allowed : 18.02 % Favored : 79.27 % 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: 1.36 (0.21), residues: 1569 helix: 1.49 (0.20), residues: 711 sheet: 1.23 (0.30), residues: 264 loop : 0.16 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.013 0.001 PHE B 188 TRP 0.016 0.002 TRP A 419 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00335 (13341) covalent geometry : angle 0.61016 (18069) SS BOND : bond 0.00571 ( 24) SS BOND : angle 3.02573 ( 48) hydrogen bonds : bond 0.03737 ( 637) hydrogen bonds : angle 4.21628 ( 1884) Misc. bond : bond 0.00023 ( 3) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 0.83032 ( 18) link_NAG-ASN : bond 0.00094 ( 15) link_NAG-ASN : angle 2.06293 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 363 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8682 (mt) cc_final: 0.8360 (mt) REVERT: A 381 CYS cc_start: 0.6636 (m) cc_final: 0.6225 (t) REVERT: B 44 MET cc_start: 0.7903 (mmm) cc_final: 0.7534 (mmm) REVERT: B 329 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7034 (mp0) REVERT: B 362 PHE cc_start: 0.8940 (m-80) cc_final: 0.8516 (m-80) REVERT: B 377 ASN cc_start: 0.8549 (m-40) cc_final: 0.8312 (m110) REVERT: B 381 CYS cc_start: 0.6263 (m) cc_final: 0.5739 (t) REVERT: B 393 THR cc_start: 0.8346 (p) cc_final: 0.8115 (m) REVERT: C 238 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7681 (ttp) REVERT: C 321 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7883 (mtt) REVERT: C 437 GLU cc_start: 0.7632 (tp30) cc_final: 0.7236 (tp30) outliers start: 38 outliers final: 24 residues processed: 373 average time/residue: 0.7753 time to fit residues: 309.6305 Evaluate side-chains 388 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120673 restraints weight = 17315.613| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.66 r_work: 0.3607 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13389 Z= 0.132 Angle : 0.649 9.964 18180 Z= 0.312 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.040 2319 Dihedral : 6.078 58.012 2172 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 18.45 % Favored : 79.13 % 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: 1.30 (0.21), residues: 1569 helix: 1.50 (0.20), residues: 711 sheet: 1.12 (0.30), residues: 267 loop : 0.06 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.016 0.001 PHE A 45 TRP 0.012 0.001 TRP A 419 HIS 0.006 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00306 (13341) covalent geometry : angle 0.62526 (18069) SS BOND : bond 0.00535 ( 24) SS BOND : angle 2.86321 ( 48) hydrogen bonds : bond 0.03641 ( 637) hydrogen bonds : angle 4.15351 ( 1884) Misc. bond : bond 0.00017 ( 3) link_BETA1-4 : bond 0.00513 ( 6) link_BETA1-4 : angle 0.86539 ( 18) link_NAG-ASN : bond 0.00094 ( 15) link_NAG-ASN : angle 2.00805 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.8273 (t80) cc_final: 0.8065 (t80) REVERT: A 242 LEU cc_start: 0.8687 (mt) cc_final: 0.8392 (mt) REVERT: A 381 CYS cc_start: 0.6659 (m) cc_final: 0.6262 (t) REVERT: B 44 MET cc_start: 0.7935 (mmm) cc_final: 0.7556 (mmm) REVERT: B 329 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7001 (mp0) REVERT: B 362 PHE cc_start: 0.8940 (m-80) cc_final: 0.8565 (m-80) REVERT: B 377 ASN cc_start: 0.8547 (m-40) cc_final: 0.8284 (m110) REVERT: B 381 CYS cc_start: 0.6302 (m) cc_final: 0.5713 (t) REVERT: B 393 THR cc_start: 0.8340 (p) cc_final: 0.8119 (m) REVERT: C 321 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: C 437 GLU cc_start: 0.7669 (tp30) cc_final: 0.7128 (tp30) outliers start: 34 outliers final: 24 residues processed: 371 average time/residue: 0.8023 time to fit residues: 318.7019 Evaluate side-chains 381 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 356 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 374 GLN A 400 ASN A 495 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.121315 restraints weight = 17434.612| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.65 r_work: 0.3613 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.042 13389 Z= 0.129 Angle : 0.643 9.527 18180 Z= 0.311 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.040 2319 Dihedral : 6.074 57.958 2172 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.35 % Allowed : 18.73 % Favored : 78.92 % 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: 1569 helix: 1.52 (0.20), residues: 711 sheet: 1.09 (0.30), residues: 267 loop : 0.06 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.012 0.001 TYR A 414 PHE 0.013 0.001 PHE C 188 TRP 0.013 0.001 TRP A 419 HIS 0.006 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00300 (13341) covalent geometry : angle 0.62060 (18069) SS BOND : bond 0.00463 ( 24) SS BOND : angle 2.79216 ( 48) hydrogen bonds : bond 0.03570 ( 637) hydrogen bonds : angle 4.14673 ( 1884) Misc. bond : bond 0.00016 ( 3) link_BETA1-4 : bond 0.00482 ( 6) link_BETA1-4 : angle 0.86513 ( 18) link_NAG-ASN : bond 0.00084 ( 15) link_NAG-ASN : angle 1.92502 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 363 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7961 (t80) cc_final: 0.7657 (t80) REVERT: A 242 LEU cc_start: 0.8678 (mt) cc_final: 0.8344 (mt) REVERT: A 381 CYS cc_start: 0.6610 (m) cc_final: 0.6190 (t) REVERT: B 44 MET cc_start: 0.7938 (mmm) cc_final: 0.7577 (mmm) REVERT: B 329 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6980 (mp0) REVERT: B 377 ASN cc_start: 0.8499 (m-40) cc_final: 0.8269 (m110) REVERT: B 381 CYS cc_start: 0.6220 (m) cc_final: 0.5673 (t) REVERT: B 393 THR cc_start: 0.8340 (p) cc_final: 0.8128 (m) REVERT: C 49 MET cc_start: 0.8048 (tpp) cc_final: 0.7746 (mpp) REVERT: C 437 GLU cc_start: 0.7525 (tp30) cc_final: 0.7141 (tp30) outliers start: 33 outliers final: 24 residues processed: 372 average time/residue: 0.7357 time to fit residues: 292.7299 Evaluate side-chains 370 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 346 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 149 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 116 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123060 restraints weight = 17365.217| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.65 r_work: 0.3631 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13389 Z= 0.113 Angle : 0.624 10.043 18180 Z= 0.300 Chirality : 0.044 0.239 1989 Planarity : 0.004 0.039 2319 Dihedral : 6.009 57.869 2172 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.07 % Allowed : 19.44 % Favored : 78.49 % 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: 1.36 (0.21), residues: 1569 helix: 1.61 (0.20), residues: 708 sheet: 1.11 (0.30), residues: 267 loop : 0.03 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.011 0.001 TYR A 273 PHE 0.016 0.001 PHE C 45 TRP 0.013 0.001 TRP C 419 HIS 0.005 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00257 (13341) covalent geometry : angle 0.60556 (18069) SS BOND : bond 0.00434 ( 24) SS BOND : angle 2.48267 ( 48) hydrogen bonds : bond 0.03302 ( 637) hydrogen bonds : angle 4.09474 ( 1884) Misc. bond : bond 0.00008 ( 3) link_BETA1-4 : bond 0.00472 ( 6) link_BETA1-4 : angle 0.83626 ( 18) link_NAG-ASN : bond 0.00157 ( 15) link_NAG-ASN : angle 1.81231 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7189.07 seconds wall clock time: 122 minutes 51.37 seconds (7371.37 seconds total)