Starting phenix.real_space_refine on Fri Jul 3 09:18:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.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/7sil_25143/07_2026/7sil_25143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.map" model { file = "/net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sil_25143/07_2026/7sil_25143.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.060 sd= 0.251 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 70 5.16 5 Cl 2 4.86 5 C 8454 2.51 5 N 2036 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "C" 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 chiralities: 2 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 142 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 142 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 3.38, per 1000 atoms: 0.26 Number of scatterers: 12924 At special positions: 0 Unit cell: (98.77, 97.11, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 Cl 2 17.00 S 70 16.00 P 2 15.00 O 2352 8.00 N 2036 7.00 C 8454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG A 903 " - " ASN A 468 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 480.8 milliseconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.737A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.638A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.703A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.545A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.540A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.845A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 680 through 703 removed outlier: 3.594A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 Processing helix chain 'A' and resid 769 through 794 Processing helix chain 'A' and resid 802 through 821 removed outlier: 4.264A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 831 through 861 removed outlier: 3.969A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.732A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.618A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.723A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.516A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.689A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 669 removed outlier: 3.754A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 680 through 703 removed outlier: 3.625A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.514A pdb=" N ALA B 746 " --> pdb=" O TRP B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.513A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 4.107A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 831 through 861 removed outlier: 4.010A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.160A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.967A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.148A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.963A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AB2, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB3, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB4, first strand: chain 'B' and resid 602 through 604 628 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.32 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: 3957 1.34 - 1.46: 3211 1.46 - 1.58: 6002 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 13256 Sorted by residual: bond pdb=" CG TCR A 904 " pdb=" CD1 TCR A 904 " ideal model delta sigma weight residual 1.364 1.477 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" CG TCR B 904 " pdb=" CD1 TCR B 904 " ideal model delta sigma weight residual 1.364 1.476 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TCR A 904 " pdb=" CE2 TCR A 904 " ideal model delta sigma weight residual 1.416 1.479 -0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" CD2 TCR B 904 " pdb=" CE2 TCR B 904 " ideal model delta sigma weight residual 1.416 1.478 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.25e+00 ... (remaining 13251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 17440 1.67 - 3.34: 463 3.34 - 5.01: 87 5.01 - 6.68: 27 6.68 - 8.35: 15 Bond angle restraints: 18032 Sorted by residual: angle pdb=" C PHE B 762 " pdb=" N ILE B 763 " pdb=" CA ILE B 763 " ideal model delta sigma weight residual 122.43 118.02 4.41 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C ASN B 468 " pdb=" N PHE B 469 " pdb=" CA PHE B 469 " ideal model delta sigma weight residual 122.21 116.69 5.52 1.62e+00 3.81e-01 1.16e+01 angle pdb=" C ASN A 468 " pdb=" N PHE A 469 " pdb=" CA PHE A 469 " ideal model delta sigma weight residual 121.75 115.99 5.76 1.73e+00 3.34e-01 1.11e+01 angle pdb=" C GLU B 604 " pdb=" N PHE B 605 " pdb=" CA PHE B 605 " ideal model delta sigma weight residual 122.32 127.79 -5.47 1.76e+00 3.23e-01 9.67e+00 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.47 110.41 3.06 1.01e+00 9.80e-01 9.16e+00 ... (remaining 18027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6878 17.77 - 35.53: 597 35.53 - 53.30: 97 53.30 - 71.06: 24 71.06 - 88.83: 12 Dihedral angle restraints: 7608 sinusoidal: 3062 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual 93.00 -179.25 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 101 " pdb=" CB CYS B 101 " ideal model delta sinusoidal sigma weight residual -86.00 -23.86 -62.14 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1944 0.097 - 0.194: 100 0.194 - 0.291: 13 0.291 - 0.388: 8 0.388 - 0.485: 1 Chirality restraints: 2066 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 261 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C14 CLR B 913 " pdb=" C13 CLR B 913 " pdb=" C15 CLR B 913 " pdb=" C8 CLR B 913 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C14 CLR A 912 " pdb=" C13 CLR A 912 " pdb=" C15 CLR A 912 " pdb=" C8 CLR A 912 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2063 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 746 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO B 747 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 438 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 439 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 438 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 439 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.26: 13040 3.26 - 3.80: 21747 3.80 - 4.35: 28134 4.35 - 4.90: 45612 Nonbonded interactions: 108809 Sorted by model distance: nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.160 3.040 nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.173 3.040 nonbonded pdb=" OE2 GLU B 232 " pdb=" NH1 ARG B 233 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 175 " pdb=" NH2 ARG B 185 " model vdw 2.249 3.120 ... (remaining 108804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.004 0.113 13288 Z= 0.207 Angle : 0.710 8.346 18110 Z= 0.355 Chirality : 0.053 0.485 2066 Planarity : 0.004 0.082 2212 Dihedral : 13.658 86.088 4614 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.15 % Allowed : 0.07 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1546 helix: 1.27 (0.19), residues: 716 sheet: -0.67 (0.36), residues: 198 loop : -0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 227 TYR 0.025 0.001 TYR A 425 PHE 0.019 0.001 PHE A 619 TRP 0.028 0.002 TRP A 742 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (13256) covalent geometry : angle 0.69823 / 0.35 (18032) SS BOND : bond 0.00251 / 0.19 ( 18) SS BOND : angle 1.51168 / 1.13 ( 36) hydrogen bonds : bond 0.13424 / 8.51 ( 628) hydrogen bonds : angle 5.46683 / 4.11 ( 1794) link_BETA1-4 : bond 0.00450 / 0.25 ( 4) link_BETA1-4 : angle 1.60347 / 1.17 ( 12) link_NAG-ASN : bond 0.00507 / 0.34 ( 10) link_NAG-ASN : angle 2.80411 / 1.62 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.509 Fit side-chains REVERT: A 285 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7409 (ttp80) REVERT: B 285 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7376 (ttp80) REVERT: B 536 GLU cc_start: 0.6952 (pm20) cc_final: 0.6697 (pm20) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.5279 time to fit residues: 132.4360 Evaluate side-chains 205 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 253 GLN B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151001 restraints weight = 17351.096| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.52 r_work: 0.3554 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13288 Z= 0.237 Angle : 0.661 10.400 18110 Z= 0.343 Chirality : 0.046 0.313 2066 Planarity : 0.005 0.052 2212 Dihedral : 6.824 59.626 1760 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 8.70 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1546 helix: 1.48 (0.19), residues: 706 sheet: -0.91 (0.33), residues: 228 loop : -0.11 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 185 TYR 0.025 0.002 TYR A 425 PHE 0.021 0.002 PHE A 789 TRP 0.035 0.002 TRP A 742 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (13256) covalent geometry : angle 0.64640 / 0.34 (18032) SS BOND : bond 0.00535 / 0.39 ( 18) SS BOND : angle 2.08795 / 1.50 ( 36) hydrogen bonds : bond 0.05878 / 4.07 ( 628) hydrogen bonds : angle 4.80135 / 3.52 ( 1794) link_BETA1-4 : bond 0.00278 / 0.17 ( 4) link_BETA1-4 : angle 1.36304 / 0.97 ( 12) link_NAG-ASN : bond 0.00710 / 0.46 ( 10) link_NAG-ASN : angle 2.58704 / 1.50 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 516 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7340 (pttp) REVERT: A 696 LEU cc_start: 0.7071 (tp) cc_final: 0.6577 (tt) REVERT: A 811 MET cc_start: 0.7911 (mmm) cc_final: 0.7678 (mmm) REVERT: B 285 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7985 (ttp80) REVERT: B 738 ILE cc_start: 0.7809 (mm) cc_final: 0.7557 (mm) outliers start: 32 outliers final: 13 residues processed: 217 average time/residue: 0.5056 time to fit residues: 120.9443 Evaluate side-chains 205 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 179 GLN A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153796 restraints weight = 17628.378| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.45 r_work: 0.3601 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13288 Z= 0.131 Angle : 0.552 8.826 18110 Z= 0.287 Chirality : 0.042 0.269 2066 Planarity : 0.004 0.046 2212 Dihedral : 6.415 59.376 1760 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.77 % Allowed : 11.58 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1546 helix: 1.54 (0.19), residues: 722 sheet: -0.97 (0.34), residues: 226 loop : -0.02 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.015 0.001 TYR B 573 PHE 0.024 0.001 PHE B 789 TRP 0.026 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13256) covalent geometry : angle 0.54171 / 0.28 (18032) SS BOND : bond 0.00418 / 0.29 ( 18) SS BOND : angle 1.41186 / 0.99 ( 36) hydrogen bonds : bond 0.05056 / 3.50 ( 628) hydrogen bonds : angle 4.44824 / 3.26 ( 1794) link_BETA1-4 : bond 0.00238 / 0.14 ( 4) link_BETA1-4 : angle 1.25058 / 0.94 ( 12) link_NAG-ASN : bond 0.00471 / 0.30 ( 10) link_NAG-ASN : angle 2.10797 / 1.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7836 (ttp80) REVERT: A 516 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7538 (ptmm) REVERT: A 696 LEU cc_start: 0.6785 (tp) cc_final: 0.6349 (tt) REVERT: B 250 GLU cc_start: 0.7420 (tp30) cc_final: 0.6901 (mp0) REVERT: B 287 ASN cc_start: 0.8043 (t0) cc_final: 0.7831 (t0) REVERT: B 605 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7058 (p90) REVERT: B 738 ILE cc_start: 0.7771 (mm) cc_final: 0.7519 (mm) REVERT: B 743 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6629 (mp) outliers start: 24 outliers final: 7 residues processed: 216 average time/residue: 0.5133 time to fit residues: 122.2580 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS B 493 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151502 restraints weight = 17373.505| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.51 r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13288 Z= 0.279 Angle : 0.685 9.331 18110 Z= 0.356 Chirality : 0.047 0.186 2066 Planarity : 0.005 0.047 2212 Dihedral : 6.855 59.702 1760 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.32 % Allowed : 12.76 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1546 helix: 1.46 (0.19), residues: 706 sheet: -1.35 (0.31), residues: 228 loop : -0.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 185 TYR 0.019 0.002 TYR B 425 PHE 0.021 0.002 PHE B 469 TRP 0.036 0.002 TRP A 742 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (13256) covalent geometry : angle 0.66905 / 0.35 (18032) SS BOND : bond 0.00746 / 0.52 ( 18) SS BOND : angle 2.18987 / 1.64 ( 36) hydrogen bonds : bond 0.06051 / 4.19 ( 628) hydrogen bonds : angle 4.74581 / 3.45 ( 1794) link_BETA1-4 : bond 0.00406 / 0.25 ( 4) link_BETA1-4 : angle 1.48069 / 1.03 ( 12) link_NAG-ASN : bond 0.00503 / 0.35 ( 10) link_NAG-ASN : angle 2.78137 / 1.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 270 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 516 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7646 (ptmm) REVERT: A 526 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7322 (mp0) REVERT: A 696 LEU cc_start: 0.6940 (tp) cc_final: 0.6490 (tt) REVERT: A 811 MET cc_start: 0.7940 (mmm) cc_final: 0.7583 (mmm) REVERT: B 224 GLU cc_start: 0.8174 (tp30) cc_final: 0.7967 (tp30) REVERT: B 270 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 691 CYS cc_start: 0.7694 (p) cc_final: 0.7490 (m) REVERT: B 738 ILE cc_start: 0.7875 (mm) cc_final: 0.7607 (mm) REVERT: B 776 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7539 (tp) outliers start: 45 outliers final: 18 residues processed: 219 average time/residue: 0.4706 time to fit residues: 113.9305 Evaluate side-chains 218 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS B 493 ASN B 766 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.173999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151801 restraints weight = 17468.018| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.46 r_work: 0.3572 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13288 Z= 0.173 Angle : 0.595 7.893 18110 Z= 0.310 Chirality : 0.043 0.178 2066 Planarity : 0.004 0.043 2212 Dihedral : 6.663 59.104 1760 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.88 % Allowed : 14.53 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1546 helix: 1.52 (0.19), residues: 710 sheet: -1.39 (0.31), residues: 228 loop : -0.21 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.012 0.002 TYR A 425 PHE 0.017 0.001 PHE B 469 TRP 0.028 0.002 TRP A 742 HIS 0.008 0.001 HIS B 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (13256) covalent geometry : angle 0.58354 / 0.31 (18032) SS BOND : bond 0.00484 / 0.34 ( 18) SS BOND : angle 1.55980 / 1.16 ( 36) hydrogen bonds : bond 0.05328 / 3.69 ( 628) hydrogen bonds : angle 4.48789 / 3.26 ( 1794) link_BETA1-4 : bond 0.00264 / 0.16 ( 4) link_BETA1-4 : angle 1.31235 / 0.95 ( 12) link_NAG-ASN : bond 0.00687 / 0.52 ( 10) link_NAG-ASN : angle 2.29392 / 1.32 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7642 (t0) REVERT: A 270 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: A 285 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7966 (ttp80) REVERT: A 516 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7718 (ptmm) REVERT: A 526 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7331 (mp0) REVERT: A 696 LEU cc_start: 0.6915 (tp) cc_final: 0.6357 (tt) REVERT: A 811 MET cc_start: 0.7894 (mmm) cc_final: 0.7653 (mmm) REVERT: B 28 LYS cc_start: 0.8424 (tttt) cc_final: 0.8011 (ttpp) REVERT: B 224 GLU cc_start: 0.8150 (tp30) cc_final: 0.7949 (tp30) REVERT: B 270 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: B 738 ILE cc_start: 0.7859 (mm) cc_final: 0.7572 (mm) REVERT: B 743 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6775 (mp) REVERT: B 776 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7532 (tp) REVERT: B 805 LYS cc_start: 0.8070 (pttm) cc_final: 0.7823 (pttm) outliers start: 39 outliers final: 19 residues processed: 221 average time/residue: 0.5343 time to fit residues: 130.0212 Evaluate side-chains 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 802 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150413 restraints weight = 17334.094| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.46 r_work: 0.3547 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13288 Z= 0.243 Angle : 0.651 9.627 18110 Z= 0.339 Chirality : 0.045 0.169 2066 Planarity : 0.004 0.044 2212 Dihedral : 6.782 59.190 1760 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.61 % Allowed : 14.45 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1546 helix: 1.47 (0.19), residues: 706 sheet: -1.48 (0.31), residues: 228 loop : -0.34 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 185 TYR 0.017 0.002 TYR B 425 PHE 0.026 0.002 PHE B 789 TRP 0.032 0.002 TRP A 742 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (13256) covalent geometry : angle 0.63695 / 0.33 (18032) SS BOND : bond 0.00680 / 0.48 ( 18) SS BOND : angle 1.89410 / 1.43 ( 36) hydrogen bonds : bond 0.05759 / 4.00 ( 628) hydrogen bonds : angle 4.60401 / 3.34 ( 1794) link_BETA1-4 : bond 0.00261 / 0.15 ( 4) link_BETA1-4 : angle 1.41971 / 0.98 ( 12) link_NAG-ASN : bond 0.00526 / 0.39 ( 10) link_NAG-ASN : angle 2.56427 / 1.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8380 (tttt) cc_final: 0.7887 (ttpp) REVERT: A 261 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 270 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 285 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7904 (ttp80) REVERT: A 409 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 516 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7710 (ptmm) REVERT: A 526 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7262 (mp0) REVERT: A 696 LEU cc_start: 0.6870 (tp) cc_final: 0.6334 (tt) REVERT: A 805 LYS cc_start: 0.8242 (pttm) cc_final: 0.8014 (pttm) REVERT: B 28 LYS cc_start: 0.8379 (tttt) cc_final: 0.7898 (ttpp) REVERT: B 224 GLU cc_start: 0.8127 (tp30) cc_final: 0.7911 (tp30) REVERT: B 270 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 409 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8012 (tp) REVERT: B 691 CYS cc_start: 0.7828 (p) cc_final: 0.7575 (m) REVERT: B 738 ILE cc_start: 0.7932 (mm) cc_final: 0.7640 (mm) REVERT: B 743 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 776 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7464 (tp) REVERT: B 805 LYS cc_start: 0.8135 (pttm) cc_final: 0.7826 (pttm) REVERT: B 811 MET cc_start: 0.7915 (mmm) cc_final: 0.7710 (mmt) outliers start: 49 outliers final: 32 residues processed: 227 average time/residue: 0.4864 time to fit residues: 122.0313 Evaluate side-chains 235 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.173941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151717 restraints weight = 17282.876| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.49 r_work: 0.3567 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13288 Z= 0.174 Angle : 0.601 8.860 18110 Z= 0.312 Chirality : 0.043 0.164 2066 Planarity : 0.004 0.044 2212 Dihedral : 6.585 58.215 1760 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.17 % Allowed : 15.34 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1546 helix: 1.55 (0.19), residues: 708 sheet: -1.47 (0.31), residues: 228 loop : -0.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.018 0.002 TYR A 573 PHE 0.016 0.001 PHE B 469 TRP 0.026 0.002 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (13256) covalent geometry : angle 0.59004 / 0.31 (18032) SS BOND : bond 0.00488 / 0.34 ( 18) SS BOND : angle 1.53341 / 1.15 ( 36) hydrogen bonds : bond 0.05301 / 3.67 ( 628) hydrogen bonds : angle 4.45863 / 3.24 ( 1794) link_BETA1-4 : bond 0.00183 / 0.10 ( 4) link_BETA1-4 : angle 1.28694 / 0.91 ( 12) link_NAG-ASN : bond 0.01020 / 0.81 ( 10) link_NAG-ASN : angle 2.27958 / 1.30 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8427 (tttt) cc_final: 0.7944 (ttpp) REVERT: A 270 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: A 285 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7948 (ttp80) REVERT: A 516 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7713 (ptmm) REVERT: A 696 LEU cc_start: 0.6728 (tp) cc_final: 0.6209 (tt) REVERT: A 811 MET cc_start: 0.7941 (mmm) cc_final: 0.7617 (mmm) REVERT: B 28 LYS cc_start: 0.8391 (tttt) cc_final: 0.7919 (ttpp) REVERT: B 224 GLU cc_start: 0.8113 (tp30) cc_final: 0.7901 (tp30) REVERT: B 270 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 350 GLU cc_start: 0.7832 (tt0) cc_final: 0.7608 (tt0) REVERT: B 738 ILE cc_start: 0.7915 (mm) cc_final: 0.7620 (mm) REVERT: B 743 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6759 (mp) REVERT: B 776 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7451 (tp) outliers start: 43 outliers final: 25 residues processed: 223 average time/residue: 0.4805 time to fit residues: 118.0783 Evaluate side-chains 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.173997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151731 restraints weight = 17343.555| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.47 r_work: 0.3571 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13288 Z= 0.177 Angle : 0.634 14.388 18110 Z= 0.322 Chirality : 0.044 0.295 2066 Planarity : 0.004 0.043 2212 Dihedral : 6.557 57.814 1760 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.10 % Allowed : 15.78 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1546 helix: 1.57 (0.19), residues: 708 sheet: -1.48 (0.31), residues: 228 loop : -0.24 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.022 0.002 TYR A 573 PHE 0.025 0.001 PHE A 789 TRP 0.025 0.002 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (13256) covalent geometry : angle 0.60273 / 0.31 (18032) SS BOND : bond 0.00515 / 0.36 ( 18) SS BOND : angle 1.48194 / 1.13 ( 36) hydrogen bonds : bond 0.05311 / 3.67 ( 628) hydrogen bonds : angle 4.43786 / 3.23 ( 1794) link_BETA1-4 : bond 0.00216 / 0.13 ( 4) link_BETA1-4 : angle 1.30191 / 0.93 ( 12) link_NAG-ASN : bond 0.00474 / 0.35 ( 10) link_NAG-ASN : angle 4.58816 / 3.09 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8434 (tttt) cc_final: 0.8027 (ttpp) REVERT: A 270 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: A 285 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7960 (ttp80) REVERT: A 516 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7753 (ptmm) REVERT: A 573 TYR cc_start: 0.8133 (p90) cc_final: 0.7825 (p90) REVERT: A 696 LEU cc_start: 0.6811 (tp) cc_final: 0.6224 (tt) REVERT: A 771 MET cc_start: 0.7114 (pmt) cc_final: 0.6830 (tmt) REVERT: A 811 MET cc_start: 0.7931 (mmm) cc_final: 0.7576 (mmm) REVERT: B 28 LYS cc_start: 0.8405 (tttt) cc_final: 0.8019 (ttpp) REVERT: B 224 GLU cc_start: 0.8145 (tp30) cc_final: 0.7939 (tp30) REVERT: B 270 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 350 GLU cc_start: 0.7834 (tt0) cc_final: 0.7618 (tt0) REVERT: B 409 ILE cc_start: 0.8272 (mm) cc_final: 0.8063 (tp) REVERT: B 738 ILE cc_start: 0.7920 (mm) cc_final: 0.7635 (mm) REVERT: B 743 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6766 (mp) REVERT: B 776 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7480 (tp) outliers start: 42 outliers final: 28 residues processed: 226 average time/residue: 0.5004 time to fit residues: 124.5397 Evaluate side-chains 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.173971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151673 restraints weight = 17467.611| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.49 r_work: 0.3569 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13288 Z= 0.184 Angle : 0.630 11.070 18110 Z= 0.324 Chirality : 0.044 0.175 2066 Planarity : 0.004 0.044 2212 Dihedral : 6.504 57.637 1760 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.10 % Allowed : 15.86 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1546 helix: 1.57 (0.19), residues: 708 sheet: -1.47 (0.31), residues: 228 loop : -0.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.020 0.002 TYR A 573 PHE 0.017 0.001 PHE B 469 TRP 0.026 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (13256) covalent geometry : angle 0.60691 / 0.32 (18032) SS BOND : bond 0.00520 / 0.36 ( 18) SS BOND : angle 1.48965 / 1.15 ( 36) hydrogen bonds : bond 0.05358 / 3.72 ( 628) hydrogen bonds : angle 4.44044 / 3.24 ( 1794) link_BETA1-4 : bond 0.00220 / 0.13 ( 4) link_BETA1-4 : angle 1.31652 / 0.92 ( 12) link_NAG-ASN : bond 0.00728 / 0.46 ( 10) link_NAG-ASN : angle 3.86436 / 2.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8443 (tttt) cc_final: 0.8039 (ttpp) REVERT: A 270 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 285 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7965 (ttp80) REVERT: A 573 TYR cc_start: 0.8150 (p90) cc_final: 0.7811 (p90) REVERT: A 696 LEU cc_start: 0.6817 (tp) cc_final: 0.6283 (tt) REVERT: A 771 MET cc_start: 0.7113 (pmt) cc_final: 0.6819 (tmt) REVERT: A 811 MET cc_start: 0.7916 (mmm) cc_final: 0.7562 (mmm) REVERT: B 28 LYS cc_start: 0.8422 (tttt) cc_final: 0.8034 (ttpp) REVERT: B 224 GLU cc_start: 0.8155 (tp30) cc_final: 0.7950 (tp30) REVERT: B 270 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 350 GLU cc_start: 0.7837 (tt0) cc_final: 0.7606 (tt0) REVERT: B 738 ILE cc_start: 0.7920 (mm) cc_final: 0.7642 (mm) REVERT: B 743 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6774 (mp) REVERT: B 776 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7483 (tp) outliers start: 42 outliers final: 30 residues processed: 224 average time/residue: 0.5389 time to fit residues: 133.0334 Evaluate side-chains 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151243 restraints weight = 17430.002| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.49 r_work: 0.3566 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13288 Z= 0.187 Angle : 0.631 10.357 18110 Z= 0.325 Chirality : 0.044 0.168 2066 Planarity : 0.004 0.044 2212 Dihedral : 6.476 57.399 1760 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.65 % Allowed : 16.15 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1546 helix: 1.55 (0.19), residues: 708 sheet: -1.50 (0.31), residues: 228 loop : -0.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 285 TYR 0.020 0.002 TYR A 573 PHE 0.026 0.002 PHE A 789 TRP 0.026 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (13256) covalent geometry : angle 0.61033 / 0.32 (18032) SS BOND : bond 0.00521 / 0.37 ( 18) SS BOND : angle 1.51801 / 1.16 ( 36) hydrogen bonds : bond 0.05375 / 3.73 ( 628) hydrogen bonds : angle 4.45421 / 3.24 ( 1794) link_BETA1-4 : bond 0.00173 / 0.10 ( 4) link_BETA1-4 : angle 1.31780 / 0.92 ( 12) link_NAG-ASN : bond 0.00755 / 0.48 ( 10) link_NAG-ASN : angle 3.55762 / 2.31 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8249 (tttt) cc_final: 0.7881 (ttpp) REVERT: A 270 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: A 285 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A 516 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7731 (pttp) REVERT: A 573 TYR cc_start: 0.7923 (p90) cc_final: 0.7655 (p90) REVERT: A 696 LEU cc_start: 0.6447 (tp) cc_final: 0.6190 (tt) REVERT: A 811 MET cc_start: 0.7666 (mmm) cc_final: 0.7353 (mmm) REVERT: B 28 LYS cc_start: 0.8227 (tttt) cc_final: 0.7892 (ttpp) REVERT: B 270 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 738 ILE cc_start: 0.7841 (mm) cc_final: 0.7563 (mm) REVERT: B 743 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6698 (mp) REVERT: B 776 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7364 (tp) outliers start: 36 outliers final: 28 residues processed: 220 average time/residue: 0.4905 time to fit residues: 119.3987 Evaluate side-chains 226 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.171662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149239 restraints weight = 17356.748| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.47 r_work: 0.3534 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13288 Z= 0.281 Angle : 0.708 9.954 18110 Z= 0.366 Chirality : 0.047 0.192 2066 Planarity : 0.005 0.071 2212 Dihedral : 6.743 58.175 1760 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 16.37 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1546 helix: 1.38 (0.19), residues: 706 sheet: -1.58 (0.31), residues: 228 loop : -0.41 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.019 0.003 TYR B 425 PHE 0.023 0.002 PHE B 469 TRP 0.035 0.002 TRP A 742 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (13256) covalent geometry : angle 0.68618 / 0.36 (18032) SS BOND : bond 0.00743 / 0.52 ( 18) SS BOND : angle 2.01374 / 1.54 ( 36) hydrogen bonds : bond 0.05986 / 4.16 ( 628) hydrogen bonds : angle 4.69615 / 3.41 ( 1794) link_BETA1-4 : bond 0.00292 / 0.19 ( 4) link_BETA1-4 : angle 1.52800 / 1.03 ( 12) link_NAG-ASN : bond 0.00804 / 0.52 ( 10) link_NAG-ASN : angle 3.71700 / 2.38 ( 30) =============================================================================== Job complete usr+sys time: 4776.83 seconds wall clock time: 82 minutes 6.26 seconds (4926.26 seconds total)