Starting phenix.real_space_refine on Thu May 15 07:05:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.map" model { file = "/net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on8_16982/05_2025/8on8_16982.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8190 2.51 5 N 2142 2.21 5 O 2454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12891 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "B" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 28, 'TRANS': 495} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.97, per 1000 atoms: 0.62 Number of scatterers: 12891 At special positions: 0 Unit cell: (112.42, 110.376, 136.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2454 8.00 N 2142 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.04 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 444 " " NAG A 603 " - " ASN A 460 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 444 " " NAG B 603 " - " ASN B 460 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 444 " " NAG C 603 " - " ASN C 460 " " NAG D 1 " - " ASN A 180 " " NAG E 1 " - " ASN A 299 " " NAG F 1 " - " ASN B 180 " " NAG G 1 " - " ASN B 299 " " NAG H 1 " - " ASN C 180 " " NAG I 1 " - " ASN C 299 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 49.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER A 105 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.883A pdb=" N LEU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA A 345 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.560A pdb=" N CYS A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.600A pdb=" N MET A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 425' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.519A pdb=" N ASN A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER B 105 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 107 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.884A pdb=" N LEU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA B 345 " --> pdb=" O PRO B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.561A pdb=" N CYS B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 392 Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.600A pdb=" N MET B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU B 425 " --> pdb=" O ALA B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 422 through 425' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.518A pdb=" N ASN B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.542A pdb=" N VAL C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.519A pdb=" N SER C 105 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 107 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 133 Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.770A pdb=" N PHE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.884A pdb=" N LEU C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 332 Processing helix chain 'C' and resid 341 through 345 removed outlier: 4.131A pdb=" N ALA C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.560A pdb=" N CYS C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 392 Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.601A pdb=" N MET C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 removed outlier: 4.032A pdb=" N GLU C 425 " --> pdb=" O ALA C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing helix chain 'C' and resid 426 through 435 removed outlier: 3.875A pdb=" N TYR C 430 " --> pdb=" O GLY C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.519A pdb=" N ASN C 444 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'C' and resid 514 through 528 removed outlier: 3.955A pdb=" N GLU C 518 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 224 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 169 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.987A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 224 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 169 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.986A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 224 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 169 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.396A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.987A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4146 1.34 - 1.46: 3264 1.46 - 1.59: 5649 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 13215 Sorted by residual: bond pdb=" CA SER C 512 " pdb=" CB SER C 512 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.98e+00 bond pdb=" CA SER B 512 " pdb=" CB SER B 512 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.85e+00 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.530 1.478 0.053 1.69e-02 3.50e+03 9.69e+00 bond pdb=" N THR C 515 " pdb=" CA THR C 515 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.33e-02 5.65e+03 8.22e+00 bond pdb=" N THR B 515 " pdb=" CA THR B 515 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.33e-02 5.65e+03 8.10e+00 ... (remaining 13210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 17569 2.13 - 4.26: 287 4.26 - 6.39: 24 6.39 - 8.52: 12 8.52 - 10.65: 9 Bond angle restraints: 17901 Sorted by residual: angle pdb=" N ALA B 517 " pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 111.69 104.65 7.04 1.23e+00 6.61e-01 3.28e+01 angle pdb=" N ALA C 517 " pdb=" CA ALA C 517 " pdb=" C ALA C 517 " ideal model delta sigma weight residual 111.69 104.70 6.99 1.23e+00 6.61e-01 3.23e+01 angle pdb=" N ALA A 517 " pdb=" CA ALA A 517 " pdb=" C ALA A 517 " ideal model delta sigma weight residual 111.69 104.71 6.98 1.23e+00 6.61e-01 3.22e+01 angle pdb=" N LEU C 516 " pdb=" CA LEU C 516 " pdb=" C LEU C 516 " ideal model delta sigma weight residual 113.20 106.75 6.45 1.21e+00 6.83e-01 2.84e+01 angle pdb=" N LEU A 516 " pdb=" CA LEU A 516 " pdb=" C LEU A 516 " ideal model delta sigma weight residual 113.20 106.75 6.45 1.21e+00 6.83e-01 2.84e+01 ... (remaining 17896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 7518 15.84 - 31.67: 525 31.67 - 47.51: 141 47.51 - 63.34: 48 63.34 - 79.18: 12 Dihedral angle restraints: 8244 sinusoidal: 3639 harmonic: 4605 Sorted by residual: dihedral pdb=" CA ILE C 293 " pdb=" C ILE C 293 " pdb=" N GLY C 294 " pdb=" CA GLY C 294 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ILE A 293 " pdb=" C ILE A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ILE B 293 " pdb=" C ILE B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 8241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1386 0.039 - 0.079: 373 0.079 - 0.118: 184 0.118 - 0.157: 19 0.157 - 0.196: 6 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA ALA B 517 " pdb=" N ALA B 517 " pdb=" C ALA B 517 " pdb=" CB ALA B 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA ALA A 517 " pdb=" N ALA A 517 " pdb=" C ALA A 517 " pdb=" CB ALA A 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ALA C 517 " pdb=" N ALA C 517 " pdb=" C ALA C 517 " pdb=" CB ALA C 517 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1965 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 34 " 0.023 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP B 34 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 34 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 34 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 34 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 34 " -0.022 2.00e-02 2.50e+03 1.78e-02 7.90e+00 pdb=" CG TRP C 34 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 34 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 34 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " -0.022 2.00e-02 2.50e+03 1.78e-02 7.90e+00 pdb=" CG TRP A 34 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " -0.013 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3583 2.82 - 3.34: 11821 3.34 - 3.86: 21064 3.86 - 4.38: 24387 4.38 - 4.90: 42932 Nonbonded interactions: 103787 Sorted by model distance: nonbonded pdb=" OH TYR C 492 " pdb=" OD2 ASP C 500 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 492 " pdb=" OD2 ASP B 500 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 492 " pdb=" OD2 ASP A 500 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR C 265 " pdb=" OE2 GLU C 311 " model vdw 2.375 3.040 nonbonded pdb=" OG1 THR A 265 " pdb=" OE2 GLU A 311 " model vdw 2.375 3.040 ... (remaining 103782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.680 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13260 Z= 0.185 Angle : 0.662 10.654 18012 Z= 0.339 Chirality : 0.044 0.196 1968 Planarity : 0.004 0.041 2304 Dihedral : 12.578 79.181 5202 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1560 helix: 1.25 (0.21), residues: 681 sheet: 1.62 (0.32), residues: 279 loop : 0.24 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 34 HIS 0.008 0.001 HIS A 17 PHE 0.019 0.001 PHE B 33 TYR 0.009 0.001 TYR A 136 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 15) link_NAG-ASN : angle 2.35435 ( 45) link_BETA1-4 : bond 0.00793 ( 6) link_BETA1-4 : angle 1.77118 ( 18) hydrogen bonds : bond 0.17501 ( 649) hydrogen bonds : angle 6.64732 ( 1893) SS BOND : bond 0.00283 ( 24) SS BOND : angle 1.17169 ( 48) covalent geometry : bond 0.00348 (13215) covalent geometry : angle 0.64824 (17901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.7265 (t0) cc_final: 0.7000 (m-40) REVERT: A 33 PHE cc_start: 0.6618 (t80) cc_final: 0.6403 (t80) REVERT: A 54 GLN cc_start: 0.7473 (tt0) cc_final: 0.7272 (tt0) REVERT: A 100 ASP cc_start: 0.7206 (t0) cc_final: 0.6501 (t0) REVERT: A 101 ASP cc_start: 0.7859 (t0) cc_final: 0.7569 (t0) REVERT: A 108 ASN cc_start: 0.8048 (m-40) cc_final: 0.7826 (m110) REVERT: A 111 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 129 PHE cc_start: 0.7559 (t80) cc_final: 0.7149 (t80) REVERT: A 136 TYR cc_start: 0.7159 (m-80) cc_final: 0.6815 (m-10) REVERT: A 138 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 166 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 178 ARG cc_start: 0.7447 (mtp85) cc_final: 0.6777 (mtp85) REVERT: A 186 TYR cc_start: 0.8039 (m-80) cc_final: 0.7339 (m-80) REVERT: A 200 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7882 (ttpt) REVERT: A 211 LEU cc_start: 0.7156 (mt) cc_final: 0.6905 (mt) REVERT: A 216 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 217 ASN cc_start: 0.8142 (m-40) cc_final: 0.7860 (m-40) REVERT: A 235 GLU cc_start: 0.7900 (tt0) cc_final: 0.7353 (tt0) REVERT: A 269 PHE cc_start: 0.8359 (m-80) cc_final: 0.7818 (m-80) REVERT: A 274 ASP cc_start: 0.8117 (m-30) cc_final: 0.7781 (m-30) REVERT: A 288 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7494 (mtp85) REVERT: A 301 SER cc_start: 0.7761 (t) cc_final: 0.7530 (p) REVERT: A 335 ASP cc_start: 0.7561 (t0) cc_final: 0.7257 (t0) REVERT: A 350 CYS cc_start: 0.6513 (m) cc_final: 0.6306 (m) REVERT: A 352 ASP cc_start: 0.7498 (t0) cc_final: 0.7273 (t0) REVERT: A 354 ASP cc_start: 0.7850 (t0) cc_final: 0.7365 (t0) REVERT: A 361 MET cc_start: 0.7187 (mtp) cc_final: 0.6880 (mtm) REVERT: A 362 PHE cc_start: 0.7641 (m-80) cc_final: 0.7413 (m-80) REVERT: A 373 MET cc_start: 0.7008 (mmt) cc_final: 0.6750 (mmm) REVERT: A 380 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6992 (mtmt) REVERT: A 388 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6864 (ttpp) REVERT: A 391 LYS cc_start: 0.7769 (mttt) cc_final: 0.7535 (mttt) REVERT: A 427 ASP cc_start: 0.7696 (m-30) cc_final: 0.7402 (m-30) REVERT: A 437 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 449 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7438 (mm-40) REVERT: A 485 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7326 (ttpp) REVERT: A 491 ASP cc_start: 0.7828 (t70) cc_final: 0.7494 (t0) REVERT: A 493 THR cc_start: 0.7507 (p) cc_final: 0.7240 (p) REVERT: A 496 GLN cc_start: 0.7312 (mt0) cc_final: 0.6609 (mt0) REVERT: A 500 ASP cc_start: 0.7190 (m-30) cc_final: 0.6599 (m-30) REVERT: B 24 ASN cc_start: 0.7321 (t0) cc_final: 0.7050 (t0) REVERT: B 51 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 54 GLN cc_start: 0.7499 (tt0) cc_final: 0.7240 (tt0) REVERT: B 108 ASN cc_start: 0.8059 (m-40) cc_final: 0.7739 (m110) REVERT: B 129 PHE cc_start: 0.7608 (t80) cc_final: 0.7367 (t80) REVERT: B 131 ASN cc_start: 0.7668 (m-40) cc_final: 0.7398 (m110) REVERT: B 136 TYR cc_start: 0.7196 (m-80) cc_final: 0.6159 (m-80) REVERT: B 138 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6800 (mt-10) REVERT: B 144 PHE cc_start: 0.8362 (m-80) cc_final: 0.7755 (m-80) REVERT: B 166 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 178 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6557 (mtp85) REVERT: B 186 TYR cc_start: 0.8087 (m-80) cc_final: 0.7808 (m-80) REVERT: B 235 GLU cc_start: 0.7981 (tt0) cc_final: 0.7738 (tt0) REVERT: B 249 VAL cc_start: 0.7532 (t) cc_final: 0.7276 (m) REVERT: B 269 PHE cc_start: 0.8470 (m-80) cc_final: 0.8135 (m-80) REVERT: B 273 TYR cc_start: 0.8513 (m-80) cc_final: 0.8115 (m-80) REVERT: B 274 ASP cc_start: 0.8167 (m-30) cc_final: 0.7714 (m-30) REVERT: B 340 LYS cc_start: 0.7959 (tppp) cc_final: 0.7579 (tppp) REVERT: B 354 ASP cc_start: 0.7795 (t0) cc_final: 0.7470 (t0) REVERT: B 373 MET cc_start: 0.7060 (mmt) cc_final: 0.6715 (mmm) REVERT: B 388 LYS cc_start: 0.7152 (ttpp) cc_final: 0.6878 (ttpp) REVERT: B 407 GLU cc_start: 0.7756 (tt0) cc_final: 0.7450 (tt0) REVERT: B 425 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 438 LYS cc_start: 0.8229 (mttt) cc_final: 0.8016 (mttt) REVERT: B 492 TYR cc_start: 0.8089 (t80) cc_final: 0.7878 (t80) REVERT: B 493 THR cc_start: 0.7434 (p) cc_final: 0.7078 (t) REVERT: C 31 ARG cc_start: 0.6587 (ttm170) cc_final: 0.6017 (ttm170) REVERT: C 100 ASP cc_start: 0.7177 (t0) cc_final: 0.6578 (t0) REVERT: C 111 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 129 PHE cc_start: 0.7345 (t80) cc_final: 0.6890 (t80) REVERT: C 131 ASN cc_start: 0.7847 (m-40) cc_final: 0.7645 (m110) REVERT: C 136 TYR cc_start: 0.7004 (m-80) cc_final: 0.6350 (m-80) REVERT: C 138 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 142 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6597 (mm-30) REVERT: C 177 HIS cc_start: 0.7100 (m-70) cc_final: 0.6777 (m-70) REVERT: C 186 TYR cc_start: 0.8033 (m-80) cc_final: 0.7739 (m-80) REVERT: C 200 LYS cc_start: 0.8270 (ttpt) cc_final: 0.8025 (ttpt) REVERT: C 235 GLU cc_start: 0.8043 (tt0) cc_final: 0.7740 (tt0) REVERT: C 237 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7347 (mtp-110) REVERT: C 269 PHE cc_start: 0.8382 (m-80) cc_final: 0.8161 (m-80) REVERT: C 274 ASP cc_start: 0.8204 (m-30) cc_final: 0.7815 (m-30) REVERT: C 301 SER cc_start: 0.7965 (t) cc_final: 0.7694 (p) REVERT: C 333 CYS cc_start: 0.4950 (p) cc_final: 0.3713 (p) REVERT: C 354 ASP cc_start: 0.7647 (t0) cc_final: 0.7227 (t0) REVERT: C 361 MET cc_start: 0.6966 (mtp) cc_final: 0.6758 (mtm) REVERT: C 391 LYS cc_start: 0.7563 (mttt) cc_final: 0.7146 (mttt) REVERT: C 396 MET cc_start: 0.7444 (mmm) cc_final: 0.7104 (mmm) REVERT: C 399 CYS cc_start: 0.6487 (m) cc_final: 0.6224 (m) REVERT: C 407 GLU cc_start: 0.7576 (tt0) cc_final: 0.7275 (tt0) REVERT: C 425 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 449 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7636 (mm110) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 1.4918 time to fit residues: 776.2416 Evaluate side-chains 387 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 106 ASN A 141 GLN A 319 GLN A 355 ASN A 495 ASN B 48 GLN B 141 GLN B 173 HIS B 217 ASN B 355 ASN C 48 GLN C 141 GLN C 164 GLN C 217 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116066 restraints weight = 17617.428| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.86 r_work: 0.3436 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13260 Z= 0.196 Angle : 0.637 14.174 18012 Z= 0.323 Chirality : 0.045 0.313 1968 Planarity : 0.005 0.050 2304 Dihedral : 5.606 53.793 2157 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.66 % Allowed : 11.78 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1560 helix: 1.51 (0.20), residues: 690 sheet: 1.40 (0.30), residues: 279 loop : 0.14 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 34 HIS 0.005 0.001 HIS C 173 PHE 0.024 0.002 PHE A 356 TYR 0.012 0.001 TYR A 414 ARG 0.006 0.001 ARG C 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 15) link_NAG-ASN : angle 2.13225 ( 45) link_BETA1-4 : bond 0.00840 ( 6) link_BETA1-4 : angle 1.40623 ( 18) hydrogen bonds : bond 0.05175 ( 649) hydrogen bonds : angle 4.96142 ( 1893) SS BOND : bond 0.00479 ( 24) SS BOND : angle 2.75728 ( 48) covalent geometry : bond 0.00455 (13215) covalent geometry : angle 0.61227 (17901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 393 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7987 (t0) cc_final: 0.7621 (t0) REVERT: A 129 PHE cc_start: 0.8344 (t80) cc_final: 0.8068 (t80) REVERT: A 136 TYR cc_start: 0.8000 (m-80) cc_final: 0.7798 (m-80) REVERT: A 142 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 164 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 186 TYR cc_start: 0.8601 (m-80) cc_final: 0.8176 (m-80) REVERT: A 217 ASN cc_start: 0.8471 (m-40) cc_final: 0.8214 (m-40) REVERT: A 235 GLU cc_start: 0.8270 (tt0) cc_final: 0.8044 (tt0) REVERT: A 269 PHE cc_start: 0.8456 (m-80) cc_final: 0.8055 (m-80) REVERT: A 274 ASP cc_start: 0.7478 (m-30) cc_final: 0.7256 (m-30) REVERT: A 289 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: A 354 ASP cc_start: 0.8105 (t0) cc_final: 0.7746 (t0) REVERT: A 361 MET cc_start: 0.8078 (mtp) cc_final: 0.7810 (mtm) REVERT: A 391 LYS cc_start: 0.8295 (mttt) cc_final: 0.8054 (mttt) REVERT: A 449 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7856 (mm110) REVERT: B 24 ASN cc_start: 0.7948 (t0) cc_final: 0.7694 (t0) REVERT: B 47 LEU cc_start: 0.8049 (mt) cc_final: 0.7844 (mp) REVERT: B 129 PHE cc_start: 0.8507 (t80) cc_final: 0.8241 (t80) REVERT: B 131 ASN cc_start: 0.8483 (m-40) cc_final: 0.8258 (m110) REVERT: B 138 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 142 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 144 PHE cc_start: 0.8851 (m-80) cc_final: 0.8438 (m-80) REVERT: B 164 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: B 178 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7432 (mtp85) REVERT: B 249 VAL cc_start: 0.8333 (t) cc_final: 0.8005 (m) REVERT: B 273 TYR cc_start: 0.8695 (m-80) cc_final: 0.8238 (m-80) REVERT: B 288 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (mtp-110) REVERT: B 354 ASP cc_start: 0.7996 (t0) cc_final: 0.7668 (t0) REVERT: B 388 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7854 (ttmm) REVERT: B 396 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7841 (mmt) REVERT: B 425 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 493 THR cc_start: 0.8611 (p) cc_final: 0.8319 (t) REVERT: C 21 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7589 (mmtp) REVERT: C 31 ARG cc_start: 0.7580 (ttm170) cc_final: 0.6931 (mtt90) REVERT: C 84 ASN cc_start: 0.8269 (p0) cc_final: 0.8055 (p0) REVERT: C 100 ASP cc_start: 0.8215 (t0) cc_final: 0.7834 (t0) REVERT: C 129 PHE cc_start: 0.8420 (t80) cc_final: 0.7940 (t80) REVERT: C 131 ASN cc_start: 0.8589 (m-40) cc_final: 0.8358 (m110) REVERT: C 177 HIS cc_start: 0.7576 (m-70) cc_final: 0.7361 (m-70) REVERT: C 274 ASP cc_start: 0.7410 (m-30) cc_final: 0.7206 (m-30) REVERT: C 301 SER cc_start: 0.8565 (t) cc_final: 0.8324 (p) REVERT: C 303 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8484 (ptmm) REVERT: C 354 ASP cc_start: 0.8035 (t0) cc_final: 0.7637 (t0) REVERT: C 386 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8250 (mttt) REVERT: C 387 SER cc_start: 0.8435 (t) cc_final: 0.8219 (m) REVERT: C 388 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8198 (ttmm) outliers start: 37 outliers final: 10 residues processed: 408 average time/residue: 1.4556 time to fit residues: 637.3553 Evaluate side-chains 387 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 372 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 516 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 243 HIS A 319 GLN A 355 ASN A 495 ASN A 496 GLN B 48 GLN B 108 ASN B 173 HIS B 217 ASN C 24 ASN C 48 GLN C 164 GLN C 173 HIS C 355 ASN C 370 GLN C 449 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113820 restraints weight = 17709.678| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.88 r_work: 0.3407 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13260 Z= 0.234 Angle : 0.630 7.905 18012 Z= 0.320 Chirality : 0.046 0.305 1968 Planarity : 0.005 0.050 2304 Dihedral : 5.607 53.750 2157 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.16 % Allowed : 15.01 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1560 helix: 1.42 (0.20), residues: 690 sheet: 1.20 (0.30), residues: 270 loop : 0.06 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 349 HIS 0.006 0.001 HIS C 325 PHE 0.023 0.002 PHE B 33 TYR 0.021 0.001 TYR A 132 ARG 0.008 0.001 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 15) link_NAG-ASN : angle 2.51398 ( 45) link_BETA1-4 : bond 0.00583 ( 6) link_BETA1-4 : angle 1.46689 ( 18) hydrogen bonds : bond 0.05097 ( 649) hydrogen bonds : angle 4.60736 ( 1893) SS BOND : bond 0.00397 ( 24) SS BOND : angle 2.24002 ( 48) covalent geometry : bond 0.00557 (13215) covalent geometry : angle 0.60683 (17901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7666 (mmm) cc_final: 0.7403 (mmm) REVERT: A 101 ASP cc_start: 0.7888 (t0) cc_final: 0.7517 (t0) REVERT: A 129 PHE cc_start: 0.8363 (t80) cc_final: 0.8118 (t80) REVERT: A 136 TYR cc_start: 0.8084 (m-80) cc_final: 0.7786 (m-10) REVERT: A 142 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 144 PHE cc_start: 0.8620 (m-80) cc_final: 0.8286 (m-80) REVERT: A 186 TYR cc_start: 0.8603 (m-80) cc_final: 0.8170 (m-80) REVERT: A 217 ASN cc_start: 0.8530 (m-40) cc_final: 0.8230 (m-40) REVERT: A 235 GLU cc_start: 0.8296 (tt0) cc_final: 0.8075 (tt0) REVERT: A 269 PHE cc_start: 0.8512 (m-80) cc_final: 0.8132 (m-80) REVERT: A 289 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8117 (ttm-80) REVERT: A 354 ASP cc_start: 0.8099 (t0) cc_final: 0.7711 (t0) REVERT: A 361 MET cc_start: 0.8056 (mtp) cc_final: 0.7823 (mtm) REVERT: A 388 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8079 (ttpp) REVERT: A 391 LYS cc_start: 0.8261 (mttt) cc_final: 0.8013 (mttt) REVERT: A 396 MET cc_start: 0.7906 (mmp) cc_final: 0.7687 (mpp) REVERT: A 425 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 24 ASN cc_start: 0.8010 (t0) cc_final: 0.7700 (t0) REVERT: B 47 LEU cc_start: 0.8161 (mt) cc_final: 0.7960 (mp) REVERT: B 99 GLU cc_start: 0.8015 (tt0) cc_final: 0.7755 (tt0) REVERT: B 129 PHE cc_start: 0.8501 (t80) cc_final: 0.8234 (t80) REVERT: B 131 ASN cc_start: 0.8464 (m-40) cc_final: 0.8229 (m110) REVERT: B 138 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 142 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 144 PHE cc_start: 0.8824 (m-80) cc_final: 0.8428 (m-80) REVERT: B 164 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: B 171 ASN cc_start: 0.7755 (t0) cc_final: 0.7215 (m-40) REVERT: B 178 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7400 (mtp85) REVERT: B 249 VAL cc_start: 0.8450 (t) cc_final: 0.8107 (m) REVERT: B 273 TYR cc_start: 0.8719 (m-80) cc_final: 0.8336 (m-80) REVERT: B 288 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8001 (mtp180) REVERT: B 354 ASP cc_start: 0.8041 (t0) cc_final: 0.7717 (t0) REVERT: B 388 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7890 (ttmm) REVERT: B 396 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: B 432 ASP cc_start: 0.8235 (t70) cc_final: 0.7973 (t0) REVERT: B 437 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7119 (tp30) REVERT: B 463 ASN cc_start: 0.8601 (t0) cc_final: 0.8384 (t0) REVERT: B 493 THR cc_start: 0.8608 (p) cc_final: 0.8304 (t) REVERT: C 129 PHE cc_start: 0.8476 (t80) cc_final: 0.8001 (t80) REVERT: C 303 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8462 (ptmm) REVERT: C 354 ASP cc_start: 0.8037 (t0) cc_final: 0.7742 (t70) REVERT: C 387 SER cc_start: 0.8460 (t) cc_final: 0.8247 (m) REVERT: C 388 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8255 (ttmm) REVERT: C 424 TYR cc_start: 0.8655 (p90) cc_final: 0.8393 (p90) REVERT: C 507 LEU cc_start: 0.8840 (tm) cc_final: 0.8633 (tp) outliers start: 44 outliers final: 19 residues processed: 402 average time/residue: 1.4596 time to fit residues: 628.8826 Evaluate side-chains 395 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 373 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 319 GLN A 495 ASN A 496 GLN B 217 ASN B 355 ASN C 24 ASN C 131 ASN C 173 HIS C 217 ASN C 355 ASN C 370 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115002 restraints weight = 17535.994| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.87 r_work: 0.3427 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13260 Z= 0.134 Angle : 0.576 8.411 18012 Z= 0.288 Chirality : 0.042 0.203 1968 Planarity : 0.004 0.046 2304 Dihedral : 5.405 53.403 2157 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.09 % Allowed : 15.73 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1560 helix: 1.56 (0.20), residues: 690 sheet: 1.05 (0.30), residues: 279 loop : 0.16 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.005 0.001 HIS C 173 PHE 0.021 0.001 PHE C 33 TYR 0.020 0.001 TYR A 132 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 15) link_NAG-ASN : angle 2.23957 ( 45) link_BETA1-4 : bond 0.00583 ( 6) link_BETA1-4 : angle 1.22330 ( 18) hydrogen bonds : bond 0.04269 ( 649) hydrogen bonds : angle 4.40771 ( 1893) SS BOND : bond 0.00393 ( 24) SS BOND : angle 1.73652 ( 48) covalent geometry : bond 0.00306 (13215) covalent geometry : angle 0.55867 (17901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7672 (mmm) cc_final: 0.7422 (mmm) REVERT: A 82 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8128 (mtt) REVERT: A 101 ASP cc_start: 0.7886 (t0) cc_final: 0.7528 (t0) REVERT: A 129 PHE cc_start: 0.8270 (t80) cc_final: 0.7930 (t80) REVERT: A 186 TYR cc_start: 0.8631 (m-80) cc_final: 0.8231 (m-80) REVERT: A 217 ASN cc_start: 0.8555 (m-40) cc_final: 0.8255 (m-40) REVERT: A 235 GLU cc_start: 0.8292 (tt0) cc_final: 0.8062 (tt0) REVERT: A 269 PHE cc_start: 0.8475 (m-80) cc_final: 0.8073 (m-80) REVERT: A 289 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8129 (ttm-80) REVERT: A 352 ASP cc_start: 0.8248 (t0) cc_final: 0.8047 (t0) REVERT: A 354 ASP cc_start: 0.8086 (t0) cc_final: 0.7486 (t0) REVERT: A 388 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8024 (ttpp) REVERT: A 391 LYS cc_start: 0.8230 (mttt) cc_final: 0.7936 (mttt) REVERT: A 396 MET cc_start: 0.7954 (mmp) cc_final: 0.7603 (mpp) REVERT: A 425 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 491 ASP cc_start: 0.8082 (t70) cc_final: 0.7777 (t0) REVERT: B 24 ASN cc_start: 0.8024 (t0) cc_final: 0.7720 (t0) REVERT: B 129 PHE cc_start: 0.8508 (t80) cc_final: 0.8206 (t80) REVERT: B 131 ASN cc_start: 0.8452 (m-40) cc_final: 0.8136 (m110) REVERT: B 138 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 142 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 144 PHE cc_start: 0.8795 (m-80) cc_final: 0.8396 (m-80) REVERT: B 164 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: B 171 ASN cc_start: 0.7747 (t0) cc_final: 0.7262 (m-40) REVERT: B 178 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7334 (mtp85) REVERT: B 223 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8118 (mt) REVERT: B 237 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (ptp-110) REVERT: B 249 VAL cc_start: 0.8415 (t) cc_final: 0.8069 (m) REVERT: B 273 TYR cc_start: 0.8728 (m-80) cc_final: 0.8268 (m-80) REVERT: B 274 ASP cc_start: 0.7470 (m-30) cc_final: 0.7252 (m-30) REVERT: B 347 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 354 ASP cc_start: 0.8021 (t0) cc_final: 0.7695 (t0) REVERT: B 383 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7974 (ttm-80) REVERT: B 388 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7890 (ttmm) REVERT: B 432 ASP cc_start: 0.8226 (t70) cc_final: 0.7970 (t0) REVERT: B 437 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7120 (tp30) REVERT: B 493 THR cc_start: 0.8564 (p) cc_final: 0.8281 (t) REVERT: C 16 MET cc_start: 0.8083 (mmm) cc_final: 0.7815 (mtp) REVERT: C 21 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7960 (mmtm) REVERT: C 24 ASN cc_start: 0.7957 (t0) cc_final: 0.7662 (t0) REVERT: C 47 LEU cc_start: 0.8197 (mt) cc_final: 0.7981 (mp) REVERT: C 129 PHE cc_start: 0.8534 (t80) cc_final: 0.8130 (t80) REVERT: C 142 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7715 (mm-30) REVERT: C 303 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8422 (ptmm) REVERT: C 354 ASP cc_start: 0.7996 (t0) cc_final: 0.7708 (t70) REVERT: C 387 SER cc_start: 0.8440 (t) cc_final: 0.8232 (m) REVERT: C 388 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8225 (ttmm) REVERT: C 468 MET cc_start: 0.8863 (mmm) cc_final: 0.8654 (mmm) outliers start: 43 outliers final: 16 residues processed: 403 average time/residue: 1.4473 time to fit residues: 625.5098 Evaluate side-chains 388 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 366 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 142 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 495 ASN A 496 GLN B 108 ASN B 217 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115165 restraints weight = 17695.163| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.88 r_work: 0.3432 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13260 Z= 0.124 Angle : 0.561 9.054 18012 Z= 0.278 Chirality : 0.042 0.200 1968 Planarity : 0.004 0.047 2304 Dihedral : 5.213 53.299 2157 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 16.67 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1560 helix: 1.47 (0.20), residues: 708 sheet: 1.03 (0.30), residues: 264 loop : 0.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.002 0.001 HIS B 325 PHE 0.022 0.001 PHE C 33 TYR 0.023 0.001 TYR C 132 ARG 0.007 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 15) link_NAG-ASN : angle 2.03175 ( 45) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 1.13726 ( 18) hydrogen bonds : bond 0.03978 ( 649) hydrogen bonds : angle 4.31053 ( 1893) SS BOND : bond 0.00433 ( 24) SS BOND : angle 1.49713 ( 48) covalent geometry : bond 0.00285 (13215) covalent geometry : angle 0.54629 (17901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 374 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7705 (mmm) cc_final: 0.7480 (mmm) REVERT: A 49 MET cc_start: 0.8109 (tpp) cc_final: 0.7704 (mmm) REVERT: A 82 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: A 101 ASP cc_start: 0.7869 (t0) cc_final: 0.7493 (t0) REVERT: A 116 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7884 (mtm-85) REVERT: A 129 PHE cc_start: 0.8244 (t80) cc_final: 0.7819 (t80) REVERT: A 186 TYR cc_start: 0.8634 (m-80) cc_final: 0.8205 (m-80) REVERT: A 217 ASN cc_start: 0.8534 (m-40) cc_final: 0.8233 (m-40) REVERT: A 235 GLU cc_start: 0.8268 (tt0) cc_final: 0.8043 (tt0) REVERT: A 269 PHE cc_start: 0.8455 (m-80) cc_final: 0.8099 (m-80) REVERT: A 289 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: A 354 ASP cc_start: 0.8066 (t0) cc_final: 0.7644 (t0) REVERT: A 373 MET cc_start: 0.8005 (mmm) cc_final: 0.7802 (mmp) REVERT: A 388 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8017 (ttpp) REVERT: B 24 ASN cc_start: 0.8031 (t0) cc_final: 0.7726 (t0) REVERT: B 129 PHE cc_start: 0.8488 (t80) cc_final: 0.8192 (t80) REVERT: B 131 ASN cc_start: 0.8423 (m-40) cc_final: 0.8186 (m110) REVERT: B 138 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7278 (mt-10) REVERT: B 142 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 144 PHE cc_start: 0.8764 (m-80) cc_final: 0.8317 (m-80) REVERT: B 164 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: B 171 ASN cc_start: 0.7747 (t0) cc_final: 0.7258 (m-40) REVERT: B 178 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7265 (mtp85) REVERT: B 223 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 238 MET cc_start: 0.8855 (mtp) cc_final: 0.8279 (mtp) REVERT: B 249 VAL cc_start: 0.8399 (t) cc_final: 0.8056 (m) REVERT: B 273 TYR cc_start: 0.8744 (m-80) cc_final: 0.8289 (m-80) REVERT: B 274 ASP cc_start: 0.7465 (m-30) cc_final: 0.7243 (m-30) REVERT: B 289 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8199 (ttm110) REVERT: B 347 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8273 (tt) REVERT: B 354 ASP cc_start: 0.8006 (t0) cc_final: 0.7685 (t0) REVERT: B 383 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7922 (ttm-80) REVERT: B 388 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7941 (ttmm) REVERT: B 432 ASP cc_start: 0.8208 (t70) cc_final: 0.7958 (t0) REVERT: B 437 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7037 (tp30) REVERT: B 493 THR cc_start: 0.8544 (p) cc_final: 0.8280 (t) REVERT: C 16 MET cc_start: 0.8055 (mmm) cc_final: 0.7755 (mtp) REVERT: C 21 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: C 47 LEU cc_start: 0.8184 (mt) cc_final: 0.7976 (mp) REVERT: C 129 PHE cc_start: 0.8514 (t80) cc_final: 0.8175 (t80) REVERT: C 354 ASP cc_start: 0.7980 (t0) cc_final: 0.7616 (t0) REVERT: C 373 MET cc_start: 0.8064 (mmm) cc_final: 0.7767 (mmt) REVERT: C 387 SER cc_start: 0.8438 (t) cc_final: 0.8230 (m) REVERT: C 388 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8257 (ttmm) REVERT: C 424 TYR cc_start: 0.8616 (p90) cc_final: 0.8310 (p90) REVERT: C 485 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8428 (ttpt) REVERT: C 507 LEU cc_start: 0.8724 (tm) cc_final: 0.8521 (tp) outliers start: 41 outliers final: 15 residues processed: 389 average time/residue: 1.4547 time to fit residues: 606.8346 Evaluate side-chains 392 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 370 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 485 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 319 GLN A 495 ASN A 496 GLN B 108 ASN B 217 ASN B 344 GLN C 24 ASN C 217 ASN C 355 ASN C 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115685 restraints weight = 17814.582| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.89 r_work: 0.3425 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13260 Z= 0.131 Angle : 0.571 10.281 18012 Z= 0.281 Chirality : 0.042 0.210 1968 Planarity : 0.004 0.047 2304 Dihedral : 5.184 53.270 2157 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 17.46 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1560 helix: 1.49 (0.20), residues: 711 sheet: 1.03 (0.30), residues: 264 loop : 0.10 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.003 0.001 HIS B 325 PHE 0.022 0.001 PHE C 33 TYR 0.017 0.001 TYR C 132 ARG 0.006 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 15) link_NAG-ASN : angle 1.95242 ( 45) link_BETA1-4 : bond 0.00560 ( 6) link_BETA1-4 : angle 1.16551 ( 18) hydrogen bonds : bond 0.03923 ( 649) hydrogen bonds : angle 4.30459 ( 1893) SS BOND : bond 0.00426 ( 24) SS BOND : angle 1.65647 ( 48) covalent geometry : bond 0.00304 (13215) covalent geometry : angle 0.55672 (17901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7690 (mmm) cc_final: 0.7488 (mmm) REVERT: A 101 ASP cc_start: 0.7861 (t0) cc_final: 0.7485 (t0) REVERT: A 129 PHE cc_start: 0.8239 (t80) cc_final: 0.7806 (t80) REVERT: A 186 TYR cc_start: 0.8635 (m-80) cc_final: 0.8201 (m-80) REVERT: A 217 ASN cc_start: 0.8527 (m-40) cc_final: 0.8226 (m-40) REVERT: A 223 LEU cc_start: 0.8415 (mt) cc_final: 0.8213 (mt) REVERT: A 235 GLU cc_start: 0.8232 (tt0) cc_final: 0.8011 (tt0) REVERT: A 269 PHE cc_start: 0.8478 (m-80) cc_final: 0.8117 (m-80) REVERT: A 289 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8151 (ttm-80) REVERT: A 354 ASP cc_start: 0.8046 (t0) cc_final: 0.7619 (t0) REVERT: A 373 MET cc_start: 0.7903 (mmm) cc_final: 0.7688 (mmp) REVERT: A 388 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8037 (ttpp) REVERT: B 24 ASN cc_start: 0.8112 (t0) cc_final: 0.7792 (t0) REVERT: B 119 MET cc_start: 0.8895 (mmt) cc_final: 0.8667 (mmp) REVERT: B 129 PHE cc_start: 0.8465 (t80) cc_final: 0.8175 (t80) REVERT: B 131 ASN cc_start: 0.8450 (m-40) cc_final: 0.8184 (m110) REVERT: B 138 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 142 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 164 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: B 171 ASN cc_start: 0.7785 (t0) cc_final: 0.7296 (m-40) REVERT: B 178 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7278 (mtp85) REVERT: B 223 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 238 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: B 249 VAL cc_start: 0.8398 (t) cc_final: 0.8049 (m) REVERT: B 273 TYR cc_start: 0.8740 (m-80) cc_final: 0.8268 (m-80) REVERT: B 274 ASP cc_start: 0.7470 (m-30) cc_final: 0.7245 (m-30) REVERT: B 347 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 354 ASP cc_start: 0.8011 (t0) cc_final: 0.7691 (t0) REVERT: B 388 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7967 (ttmm) REVERT: B 396 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: B 432 ASP cc_start: 0.8207 (t70) cc_final: 0.7955 (t0) REVERT: B 437 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7037 (tp30) REVERT: B 493 THR cc_start: 0.8544 (p) cc_final: 0.8276 (t) REVERT: C 16 MET cc_start: 0.7985 (mmm) cc_final: 0.7673 (mtp) REVERT: C 21 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7991 (mmtm) REVERT: C 47 LEU cc_start: 0.8191 (mt) cc_final: 0.7985 (mp) REVERT: C 129 PHE cc_start: 0.8498 (t80) cc_final: 0.8086 (t80) REVERT: C 354 ASP cc_start: 0.7978 (t0) cc_final: 0.7618 (t0) REVERT: C 387 SER cc_start: 0.8450 (t) cc_final: 0.8241 (m) REVERT: C 424 TYR cc_start: 0.8662 (p90) cc_final: 0.8395 (p90) REVERT: C 485 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (ttpt) REVERT: C 507 LEU cc_start: 0.8783 (tm) cc_final: 0.8583 (tp) outliers start: 35 outliers final: 21 residues processed: 387 average time/residue: 1.4260 time to fit residues: 593.2713 Evaluate side-chains 390 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 121 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A 495 ASN A 496 GLN B 48 GLN B 108 ASN B 217 ASN B 377 ASN C 217 ASN C 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114153 restraints weight = 17606.382| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.88 r_work: 0.3402 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13260 Z= 0.202 Angle : 0.600 8.629 18012 Z= 0.301 Chirality : 0.044 0.223 1968 Planarity : 0.004 0.053 2304 Dihedral : 5.264 53.745 2157 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.02 % Allowed : 18.03 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1560 helix: 1.40 (0.20), residues: 714 sheet: 0.91 (0.30), residues: 267 loop : -0.12 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 508 HIS 0.005 0.001 HIS B 325 PHE 0.023 0.002 PHE C 33 TYR 0.018 0.001 TYR C 132 ARG 0.013 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 15) link_NAG-ASN : angle 1.99242 ( 45) link_BETA1-4 : bond 0.00441 ( 6) link_BETA1-4 : angle 1.26363 ( 18) hydrogen bonds : bond 0.04453 ( 649) hydrogen bonds : angle 4.33908 ( 1893) SS BOND : bond 0.00416 ( 24) SS BOND : angle 1.84759 ( 48) covalent geometry : bond 0.00482 (13215) covalent geometry : angle 0.58398 (17901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 383 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7873 (t0) cc_final: 0.7509 (t0) REVERT: A 129 PHE cc_start: 0.8256 (t80) cc_final: 0.7855 (t80) REVERT: A 144 PHE cc_start: 0.8586 (m-80) cc_final: 0.8265 (m-80) REVERT: A 186 TYR cc_start: 0.8662 (m-80) cc_final: 0.8238 (m-80) REVERT: A 217 ASN cc_start: 0.8555 (m-40) cc_final: 0.8242 (m-40) REVERT: A 235 GLU cc_start: 0.8302 (tt0) cc_final: 0.8074 (tt0) REVERT: A 238 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7666 (mtt) REVERT: A 269 PHE cc_start: 0.8487 (m-80) cc_final: 0.8046 (m-80) REVERT: A 373 MET cc_start: 0.7888 (mmm) cc_final: 0.7656 (mmp) REVERT: B 24 ASN cc_start: 0.8174 (t0) cc_final: 0.7900 (t0) REVERT: B 44 MET cc_start: 0.7761 (mmm) cc_final: 0.7514 (mmm) REVERT: B 47 LEU cc_start: 0.8161 (mt) cc_final: 0.7955 (mp) REVERT: B 129 PHE cc_start: 0.8481 (t80) cc_final: 0.8207 (t80) REVERT: B 131 ASN cc_start: 0.8499 (m-40) cc_final: 0.8239 (m110) REVERT: B 136 TYR cc_start: 0.8006 (m-80) cc_final: 0.7715 (m-80) REVERT: B 142 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 164 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: B 171 ASN cc_start: 0.7794 (t0) cc_final: 0.7385 (m-40) REVERT: B 238 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: B 249 VAL cc_start: 0.8472 (t) cc_final: 0.8128 (m) REVERT: B 273 TYR cc_start: 0.8754 (m-80) cc_final: 0.8396 (m-80) REVERT: B 274 ASP cc_start: 0.7453 (m-30) cc_final: 0.7231 (m-30) REVERT: B 347 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8425 (tt) REVERT: B 354 ASP cc_start: 0.8047 (t0) cc_final: 0.7718 (t0) REVERT: B 388 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7961 (ttmm) REVERT: B 396 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: B 432 ASP cc_start: 0.8192 (t70) cc_final: 0.7969 (t0) REVERT: B 437 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7445 (tp30) REVERT: B 493 THR cc_start: 0.8558 (p) cc_final: 0.8282 (t) REVERT: C 16 MET cc_start: 0.7957 (mmm) cc_final: 0.7701 (mtp) REVERT: C 21 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8014 (mmtp) REVERT: C 129 PHE cc_start: 0.8531 (t80) cc_final: 0.8046 (t80) REVERT: C 354 ASP cc_start: 0.8008 (t0) cc_final: 0.7641 (t0) REVERT: C 481 SER cc_start: 0.8388 (t) cc_final: 0.8146 (m) REVERT: C 507 LEU cc_start: 0.8808 (tm) cc_final: 0.8596 (tp) outliers start: 42 outliers final: 22 residues processed: 401 average time/residue: 1.4555 time to fit residues: 625.7075 Evaluate side-chains 398 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 370 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 495 ASN B 48 GLN B 108 ASN B 217 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114515 restraints weight = 17758.850| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.89 r_work: 0.3410 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13260 Z= 0.171 Angle : 0.616 9.203 18012 Z= 0.306 Chirality : 0.043 0.195 1968 Planarity : 0.004 0.058 2304 Dihedral : 5.289 53.318 2157 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.51 % Allowed : 18.89 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1560 helix: 1.36 (0.20), residues: 717 sheet: 0.90 (0.30), residues: 267 loop : -0.11 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 34 HIS 0.004 0.001 HIS B 325 PHE 0.023 0.001 PHE C 33 TYR 0.022 0.001 TYR A 136 ARG 0.014 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 15) link_NAG-ASN : angle 1.96610 ( 45) link_BETA1-4 : bond 0.00509 ( 6) link_BETA1-4 : angle 1.23377 ( 18) hydrogen bonds : bond 0.04246 ( 649) hydrogen bonds : angle 4.34422 ( 1893) SS BOND : bond 0.00446 ( 24) SS BOND : angle 2.45377 ( 48) covalent geometry : bond 0.00406 (13215) covalent geometry : angle 0.59569 (17901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7878 (t0) cc_final: 0.7518 (t0) REVERT: A 129 PHE cc_start: 0.8249 (t80) cc_final: 0.7848 (t80) REVERT: A 144 PHE cc_start: 0.8578 (m-80) cc_final: 0.8207 (m-80) REVERT: A 186 TYR cc_start: 0.8655 (m-80) cc_final: 0.8242 (m-80) REVERT: A 217 ASN cc_start: 0.8548 (m-40) cc_final: 0.8249 (m-40) REVERT: A 235 GLU cc_start: 0.8295 (tt0) cc_final: 0.8084 (tt0) REVERT: A 269 PHE cc_start: 0.8457 (m-80) cc_final: 0.8048 (m-80) REVERT: A 373 MET cc_start: 0.7934 (mmm) cc_final: 0.7720 (mmp) REVERT: A 388 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8100 (ttpp) REVERT: B 24 ASN cc_start: 0.8154 (t0) cc_final: 0.7875 (t0) REVERT: B 129 PHE cc_start: 0.8467 (t80) cc_final: 0.8253 (t80) REVERT: B 131 ASN cc_start: 0.8505 (m-40) cc_final: 0.8245 (m110) REVERT: B 136 TYR cc_start: 0.7951 (m-80) cc_final: 0.7611 (m-80) REVERT: B 142 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 164 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: B 171 ASN cc_start: 0.7763 (t0) cc_final: 0.7490 (m-40) REVERT: B 238 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: B 249 VAL cc_start: 0.8475 (t) cc_final: 0.8141 (m) REVERT: B 273 TYR cc_start: 0.8733 (m-80) cc_final: 0.8318 (m-80) REVERT: B 274 ASP cc_start: 0.7460 (m-30) cc_final: 0.7235 (m-30) REVERT: B 347 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 354 ASP cc_start: 0.8056 (t0) cc_final: 0.7715 (t0) REVERT: B 383 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7876 (ttp80) REVERT: B 388 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7947 (ttmm) REVERT: B 396 MET cc_start: 0.8214 (mmm) cc_final: 0.7939 (mmm) REVERT: B 432 ASP cc_start: 0.8191 (t70) cc_final: 0.7977 (t0) REVERT: B 437 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7518 (mm-30) REVERT: B 493 THR cc_start: 0.8562 (p) cc_final: 0.8289 (t) REVERT: C 21 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8079 (mmtp) REVERT: C 31 ARG cc_start: 0.7511 (ttm170) cc_final: 0.7077 (ttm170) REVERT: C 129 PHE cc_start: 0.8525 (t80) cc_final: 0.8066 (t80) REVERT: C 354 ASP cc_start: 0.8004 (t0) cc_final: 0.7632 (t0) REVERT: C 373 MET cc_start: 0.8117 (mmm) cc_final: 0.7761 (mmm) REVERT: C 481 SER cc_start: 0.8379 (t) cc_final: 0.8144 (m) REVERT: C 507 LEU cc_start: 0.8780 (tm) cc_final: 0.8555 (tp) outliers start: 35 outliers final: 23 residues processed: 388 average time/residue: 1.4545 time to fit residues: 605.4287 Evaluate side-chains 392 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 364 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 104 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 495 ASN B 48 GLN B 108 ASN B 217 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116016 restraints weight = 17588.344| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.88 r_work: 0.3434 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13260 Z= 0.122 Angle : 0.618 10.725 18012 Z= 0.302 Chirality : 0.042 0.187 1968 Planarity : 0.004 0.061 2304 Dihedral : 5.172 53.323 2157 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.23 % Allowed : 19.61 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1560 helix: 1.45 (0.20), residues: 717 sheet: 0.90 (0.30), residues: 267 loop : -0.14 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 34 HIS 0.003 0.000 HIS B 325 PHE 0.023 0.001 PHE C 33 TYR 0.027 0.001 TYR A 132 ARG 0.015 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 15) link_NAG-ASN : angle 1.83246 ( 45) link_BETA1-4 : bond 0.00509 ( 6) link_BETA1-4 : angle 1.16113 ( 18) hydrogen bonds : bond 0.03896 ( 649) hydrogen bonds : angle 4.29870 ( 1893) SS BOND : bond 0.00412 ( 24) SS BOND : angle 2.47992 ( 48) covalent geometry : bond 0.00281 (13215) covalent geometry : angle 0.59844 (17901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7870 (t0) cc_final: 0.7516 (t0) REVERT: A 129 PHE cc_start: 0.8233 (t80) cc_final: 0.7831 (t80) REVERT: A 144 PHE cc_start: 0.8572 (m-80) cc_final: 0.8199 (m-80) REVERT: A 186 TYR cc_start: 0.8667 (m-80) cc_final: 0.8280 (m-80) REVERT: A 217 ASN cc_start: 0.8535 (m-40) cc_final: 0.8249 (m-40) REVERT: A 223 LEU cc_start: 0.8416 (mt) cc_final: 0.8201 (mt) REVERT: A 235 GLU cc_start: 0.8270 (tt0) cc_final: 0.8069 (tt0) REVERT: A 269 PHE cc_start: 0.8431 (m-80) cc_final: 0.7910 (m-80) REVERT: A 373 MET cc_start: 0.7804 (mmm) cc_final: 0.7563 (mmp) REVERT: A 388 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8094 (ttpp) REVERT: B 24 ASN cc_start: 0.8127 (t0) cc_final: 0.7837 (t0) REVERT: B 129 PHE cc_start: 0.8419 (t80) cc_final: 0.8113 (t80) REVERT: B 131 ASN cc_start: 0.8491 (m-40) cc_final: 0.8227 (m110) REVERT: B 136 TYR cc_start: 0.7942 (m-80) cc_final: 0.7607 (m-80) REVERT: B 142 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 164 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: B 171 ASN cc_start: 0.7774 (t0) cc_final: 0.7348 (m-40) REVERT: B 249 VAL cc_start: 0.8451 (t) cc_final: 0.8130 (m) REVERT: B 273 TYR cc_start: 0.8726 (m-80) cc_final: 0.8253 (m-80) REVERT: B 274 ASP cc_start: 0.7454 (m-30) cc_final: 0.7215 (m-30) REVERT: B 347 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8291 (tt) REVERT: B 354 ASP cc_start: 0.8043 (t0) cc_final: 0.7715 (t0) REVERT: B 383 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7808 (ttm110) REVERT: B 388 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7924 (ttmm) REVERT: B 396 MET cc_start: 0.8189 (mmm) cc_final: 0.7915 (mmm) REVERT: B 432 ASP cc_start: 0.8199 (t70) cc_final: 0.7973 (t0) REVERT: B 437 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7392 (tp30) REVERT: B 493 THR cc_start: 0.8553 (p) cc_final: 0.8289 (t) REVERT: C 21 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8058 (mmtp) REVERT: C 31 ARG cc_start: 0.7489 (ttm170) cc_final: 0.7052 (ttm170) REVERT: C 129 PHE cc_start: 0.8492 (t80) cc_final: 0.8024 (t80) REVERT: C 354 ASP cc_start: 0.7974 (t0) cc_final: 0.7607 (t0) REVERT: C 373 MET cc_start: 0.8084 (mmm) cc_final: 0.7796 (mmt) REVERT: C 481 SER cc_start: 0.8396 (t) cc_final: 0.8140 (m) REVERT: C 507 LEU cc_start: 0.8736 (tm) cc_final: 0.8523 (tp) outliers start: 31 outliers final: 22 residues processed: 379 average time/residue: 1.4499 time to fit residues: 589.9028 Evaluate side-chains 385 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 359 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 495 ASN B 48 GLN B 108 ASN B 217 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 217 ASN C 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116351 restraints weight = 17574.235| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.89 r_work: 0.3438 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13260 Z= 0.121 Angle : 0.622 11.470 18012 Z= 0.304 Chirality : 0.042 0.188 1968 Planarity : 0.004 0.049 2304 Dihedral : 5.123 53.337 2157 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.65 % Allowed : 20.11 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1560 helix: 1.52 (0.20), residues: 717 sheet: 0.91 (0.31), residues: 267 loop : -0.18 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 34 HIS 0.004 0.000 HIS B 325 PHE 0.023 0.001 PHE C 33 TYR 0.022 0.001 TYR A 132 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 15) link_NAG-ASN : angle 1.75872 ( 45) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 1.10781 ( 18) hydrogen bonds : bond 0.03849 ( 649) hydrogen bonds : angle 4.30335 ( 1893) SS BOND : bond 0.00432 ( 24) SS BOND : angle 2.61018 ( 48) covalent geometry : bond 0.00278 (13215) covalent geometry : angle 0.60124 (17901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 363 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7864 (t0) cc_final: 0.7509 (t0) REVERT: A 129 PHE cc_start: 0.8223 (t80) cc_final: 0.7824 (t80) REVERT: A 144 PHE cc_start: 0.8552 (m-80) cc_final: 0.8201 (m-80) REVERT: A 186 TYR cc_start: 0.8650 (m-80) cc_final: 0.8269 (m-80) REVERT: A 217 ASN cc_start: 0.8523 (m-40) cc_final: 0.8244 (m-40) REVERT: A 235 GLU cc_start: 0.8212 (tt0) cc_final: 0.8012 (tt0) REVERT: A 269 PHE cc_start: 0.8425 (m-80) cc_final: 0.7951 (m-80) REVERT: A 288 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7834 (mtp85) REVERT: A 373 MET cc_start: 0.7801 (mmm) cc_final: 0.7560 (mmp) REVERT: A 380 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7750 (mtmt) REVERT: B 24 ASN cc_start: 0.8152 (t0) cc_final: 0.7852 (t0) REVERT: B 129 PHE cc_start: 0.8396 (t80) cc_final: 0.8141 (t80) REVERT: B 131 ASN cc_start: 0.8476 (m-40) cc_final: 0.8233 (m110) REVERT: B 136 TYR cc_start: 0.7896 (m-80) cc_final: 0.7555 (m-80) REVERT: B 142 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7319 (mm-30) REVERT: B 164 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: B 171 ASN cc_start: 0.7778 (t0) cc_final: 0.7309 (m-40) REVERT: B 178 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7327 (mtp85) REVERT: B 249 VAL cc_start: 0.8430 (t) cc_final: 0.8095 (m) REVERT: B 273 TYR cc_start: 0.8726 (m-80) cc_final: 0.8265 (m-80) REVERT: B 274 ASP cc_start: 0.7476 (m-30) cc_final: 0.7243 (m-30) REVERT: B 347 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 354 ASP cc_start: 0.8004 (t0) cc_final: 0.7673 (t0) REVERT: B 383 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7770 (ttm110) REVERT: B 388 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7941 (ttmm) REVERT: B 396 MET cc_start: 0.8167 (mmm) cc_final: 0.7889 (mmm) REVERT: B 432 ASP cc_start: 0.8195 (t70) cc_final: 0.7973 (t0) REVERT: B 437 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7018 (tp30) REVERT: B 493 THR cc_start: 0.8515 (p) cc_final: 0.8260 (t) REVERT: C 21 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8066 (mmtp) REVERT: C 31 ARG cc_start: 0.7458 (ttm170) cc_final: 0.7095 (ttm170) REVERT: C 129 PHE cc_start: 0.8481 (t80) cc_final: 0.8000 (t80) REVERT: C 200 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8149 (ttmm) REVERT: C 354 ASP cc_start: 0.7924 (t0) cc_final: 0.7556 (t0) REVERT: C 373 MET cc_start: 0.8084 (mmm) cc_final: 0.7788 (mmt) REVERT: C 481 SER cc_start: 0.8382 (t) cc_final: 0.8147 (m) REVERT: C 507 LEU cc_start: 0.8716 (tm) cc_final: 0.8506 (tp) outliers start: 23 outliers final: 19 residues processed: 375 average time/residue: 1.5342 time to fit residues: 622.2972 Evaluate side-chains 382 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 359 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 109 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN B 108 ASN B 217 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114872 restraints weight = 17695.957| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.88 r_work: 0.3429 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13260 Z= 0.139 Angle : 0.621 12.302 18012 Z= 0.305 Chirality : 0.042 0.162 1968 Planarity : 0.004 0.050 2304 Dihedral : 5.119 53.511 2157 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.87 % Allowed : 20.55 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1560 helix: 1.51 (0.20), residues: 717 sheet: 0.92 (0.30), residues: 267 loop : -0.19 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 34 HIS 0.004 0.001 HIS B 325 PHE 0.023 0.001 PHE C 33 TYR 0.021 0.001 TYR A 132 ARG 0.012 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 15) link_NAG-ASN : angle 1.80621 ( 45) link_BETA1-4 : bond 0.00480 ( 6) link_BETA1-4 : angle 1.14548 ( 18) hydrogen bonds : bond 0.03934 ( 649) hydrogen bonds : angle 4.28507 ( 1893) SS BOND : bond 0.00449 ( 24) SS BOND : angle 2.75272 ( 48) covalent geometry : bond 0.00329 (13215) covalent geometry : angle 0.59868 (17901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12392.46 seconds wall clock time: 212 minutes 49.22 seconds (12769.22 seconds total)