Starting phenix.real_space_refine on Wed Mar 4 11:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sil_25143/03_2026/7sil_25143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sil_25143/03_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_25143/03_2026/7sil_25143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sil_25143/03_2026/7sil_25143.map" model { file = "/net/cci-nas-00/data/ceres_data/7sil_25143/03_2026/7sil_25143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sil_25143/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 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: 2.89, per 1000 atoms: 0.22 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: 0.94 Conformation dependent library (CDL) restraints added in 427.4 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: 0.49 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: 2.37 Time building geometry restraints manager: 1.27 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: 7559 17.77 - 35.53: 643 35.53 - 53.30: 112 53.30 - 71.06: 36 71.06 - 88.83: 12 Dihedral angle restraints: 8362 sinusoidal: 3816 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 8359 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: 0.01 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 13.548 86.088 5368 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 covalent geometry : bond 0.00414 (13256) covalent geometry : angle 0.69823 (18032) SS BOND : bond 0.00251 ( 18) SS BOND : angle 1.51168 ( 36) hydrogen bonds : bond 0.13424 ( 628) hydrogen bonds : angle 5.46683 ( 1794) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 1.60347 ( 12) link_NAG-ASN : bond 0.00507 ( 10) link_NAG-ASN : angle 2.80411 ( 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 : 0.457 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: 0.5129 time to fit residues: 127.8936 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 : 0.454 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.173368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151003 restraints weight = 17348.625| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.52 r_work: 0.3556 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1217 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= 0.238 Angle : 0.661 10.421 18110 Z= 0.343 Chirality : 0.046 0.328 2066 Planarity : 0.005 0.053 2212 Dihedral : 8.664 58.628 2514 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 8.63 % Favored : 89.01 % 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: 0.68 (0.21), residues: 1546 helix: 1.51 (0.19), residues: 704 sheet: -0.91 (0.33), residues: 228 loop : -0.13 (0.24), residues: 614 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 0.020 0.002 PHE A 789 TRP 0.035 0.002 TRP A 742 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00545 (13256) covalent geometry : angle 0.64430 (18032) SS BOND : bond 0.00671 ( 18) SS BOND : angle 2.10666 ( 36) hydrogen bonds : bond 0.05918 ( 628) hydrogen bonds : angle 4.80478 ( 1794) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 1.41890 ( 12) link_NAG-ASN : bond 0.00686 ( 10) link_NAG-ASN : angle 2.81810 ( 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 242 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7811 (ttp80) REVERT: A 696 LEU cc_start: 0.6749 (tp) cc_final: 0.6463 (tt) REVERT: B 285 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7863 (ttp80) REVERT: B 738 ILE cc_start: 0.7724 (mm) cc_final: 0.7474 (mm) outliers start: 32 outliers final: 13 residues processed: 218 average time/residue: 0.4993 time to fit residues: 119.6696 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 66 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 overall best weight: 0.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4144 r_free = 0.4144 target = 0.177042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155018 restraints weight = 17648.415| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.45 r_work: 0.3621 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13288 Z= 0.114 Angle : 0.537 8.668 18110 Z= 0.280 Chirality : 0.042 0.227 2066 Planarity : 0.004 0.045 2212 Dihedral : 8.035 59.629 2514 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.70 % Allowed : 11.73 % Favored : 86.58 % 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: 0.64 (0.21), residues: 1546 helix: 1.39 (0.19), residues: 736 sheet: -0.94 (0.34), residues: 226 loop : -0.12 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.015 0.001 TYR B 573 PHE 0.024 0.001 PHE B 789 TRP 0.024 0.001 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00241 (13256) covalent geometry : angle 0.52772 (18032) SS BOND : bond 0.00447 ( 18) SS BOND : angle 1.21312 ( 36) hydrogen bonds : bond 0.04842 ( 628) hydrogen bonds : angle 4.37337 ( 1794) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.30752 ( 12) link_NAG-ASN : bond 0.00504 ( 10) link_NAG-ASN : angle 1.99485 ( 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 231 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8353 (tt0) cc_final: 0.8053 (mt0) REVERT: A 257 GLU cc_start: 0.7704 (tt0) cc_final: 0.7419 (tt0) REVERT: A 261 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7517 (t0) REVERT: A 285 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7826 (ttp80) REVERT: A 811 MET cc_start: 0.7731 (mmm) cc_final: 0.7477 (mmm) REVERT: B 27 GLN cc_start: 0.8335 (tt0) cc_final: 0.8025 (mt0) REVERT: B 250 GLU cc_start: 0.7427 (tp30) cc_final: 0.6903 (mp0) REVERT: B 287 ASN cc_start: 0.8034 (t0) cc_final: 0.7828 (t0) REVERT: B 516 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7625 (ptmm) REVERT: B 605 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7071 (p90) REVERT: B 696 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6137 (tp) outliers start: 23 outliers final: 7 residues processed: 216 average time/residue: 0.5159 time to fit residues: 122.0104 Evaluate side-chains 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 603 ILE 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 696 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 493 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150492 restraints weight = 17394.108| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.45 r_work: 0.3544 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13288 Z= 0.270 Angle : 0.663 8.473 18110 Z= 0.346 Chirality : 0.047 0.188 2066 Planarity : 0.005 0.046 2212 Dihedral : 8.034 56.028 2514 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.88 % Allowed : 13.35 % Favored : 83.78 % 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: 0.51 (0.21), residues: 1546 helix: 1.47 (0.19), residues: 708 sheet: -1.25 (0.32), residues: 228 loop : -0.24 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 185 TYR 0.020 0.002 TYR A 421 PHE 0.020 0.002 PHE B 469 TRP 0.034 0.002 TRP A 742 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00626 (13256) covalent geometry : angle 0.64787 (18032) SS BOND : bond 0.00720 ( 18) SS BOND : angle 2.10408 ( 36) hydrogen bonds : bond 0.05948 ( 628) hydrogen bonds : angle 4.65900 ( 1794) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.51311 ( 12) link_NAG-ASN : bond 0.00506 ( 10) link_NAG-ASN : angle 2.65216 ( 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 243 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8382 (tt0) cc_final: 0.8070 (mt0) REVERT: A 257 GLU cc_start: 0.7712 (tt0) cc_final: 0.7425 (tt0) REVERT: A 270 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: A 409 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 526 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7234 (mp0) REVERT: A 544 ARG cc_start: 0.6978 (mmt180) cc_final: 0.6687 (mmt180) REVERT: A 811 MET cc_start: 0.8044 (mmm) cc_final: 0.7678 (mmm) REVERT: B 27 GLN cc_start: 0.8364 (tt0) cc_final: 0.8046 (mt0) REVERT: B 249 GLU cc_start: 0.7314 (mp0) cc_final: 0.6986 (mm-30) REVERT: B 250 GLU cc_start: 0.7499 (tp30) cc_final: 0.6889 (mp0) REVERT: B 270 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: B 743 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6697 (mp) REVERT: B 771 MET cc_start: 0.7029 (pmt) cc_final: 0.6596 (tmt) REVERT: B 776 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7523 (tp) REVERT: B 802 ASN cc_start: 0.7045 (t0) cc_final: 0.6841 (t0) outliers start: 39 outliers final: 15 residues processed: 220 average time/residue: 0.4848 time to fit residues: 117.6889 Evaluate side-chains 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 738 ILE 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 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 743 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: 10.0000 chunk 112 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN ** B 189 ASN ** 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 = 0.4110 r_free = 0.4110 target = 0.174322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152078 restraints weight = 17440.190| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.48 r_work: 0.3573 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13288 Z= 0.173 Angle : 0.584 7.861 18110 Z= 0.305 Chirality : 0.043 0.259 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.783 58.573 2514 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 14.38 % Favored : 82.82 % 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: 0.61 (0.21), residues: 1546 helix: 1.55 (0.19), residues: 710 sheet: -1.30 (0.32), residues: 228 loop : -0.16 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 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 0.007 0.001 HIS B 766 Details of bonding type rmsd covalent geometry : bond 0.00394 (13256) covalent geometry : angle 0.57085 (18032) SS BOND : bond 0.00487 ( 18) SS BOND : angle 1.58038 ( 36) hydrogen bonds : bond 0.05292 ( 628) hydrogen bonds : angle 4.45549 ( 1794) link_BETA1-4 : bond 0.00136 ( 4) link_BETA1-4 : angle 1.35741 ( 12) link_NAG-ASN : bond 0.00809 ( 10) link_NAG-ASN : angle 2.48469 ( 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 241 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: A 285 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7932 (ttp80) REVERT: A 544 ARG cc_start: 0.6969 (mmt180) cc_final: 0.6658 (mmt180) REVERT: B 224 GLU cc_start: 0.8164 (tp30) cc_final: 0.7960 (tp30) REVERT: B 250 GLU cc_start: 0.7527 (tp30) cc_final: 0.6952 (mp0) REVERT: B 270 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: B 743 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6702 (mp) outliers start: 38 outliers final: 18 residues processed: 219 average time/residue: 0.5220 time to fit residues: 125.8153 Evaluate side-chains 215 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 270 PHE Chi-restraints excluded: chain A residue 412 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 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 696 LEU Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 253 GLN A 338 HIS A 466 HIS B 27 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151122 restraints weight = 17344.175| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.50 r_work: 0.3558 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13288 Z= 0.217 Angle : 0.632 9.381 18110 Z= 0.328 Chirality : 0.045 0.422 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.771 59.860 2514 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.10 % Allowed : 14.60 % Favored : 82.30 % 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: 0.50 (0.21), residues: 1546 helix: 1.50 (0.19), residues: 710 sheet: -1.40 (0.32), residues: 228 loop : -0.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.015 0.002 TYR B 425 PHE 0.027 0.002 PHE B 789 TRP 0.030 0.002 TRP A 742 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00501 (13256) covalent geometry : angle 0.61649 (18032) SS BOND : bond 0.00602 ( 18) SS BOND : angle 1.76479 ( 36) hydrogen bonds : bond 0.05568 ( 628) hydrogen bonds : angle 4.52382 ( 1794) link_BETA1-4 : bond 0.00218 ( 4) link_BETA1-4 : angle 1.42486 ( 12) link_NAG-ASN : bond 0.00446 ( 10) link_NAG-ASN : angle 2.86563 ( 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 242 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8354 (tt0) cc_final: 0.8116 (mt0) REVERT: A 270 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: A 285 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7897 (ttp80) REVERT: A 544 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6708 (mmt180) REVERT: A 811 MET cc_start: 0.7921 (mmm) cc_final: 0.7627 (mmm) REVERT: B 27 GLN cc_start: 0.8317 (tt0) cc_final: 0.8080 (mt0) REVERT: B 224 GLU cc_start: 0.8149 (tp30) cc_final: 0.7943 (tp30) REVERT: B 249 GLU cc_start: 0.7351 (mp0) cc_final: 0.7091 (mm-30) REVERT: B 250 GLU cc_start: 0.7532 (tp30) cc_final: 0.6968 (mp0) REVERT: B 270 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: B 409 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8013 (tp) REVERT: B 743 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6720 (mp) REVERT: B 776 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (tp) REVERT: B 805 LYS cc_start: 0.8106 (pttm) cc_final: 0.7873 (pttm) REVERT: B 811 MET cc_start: 0.7918 (mmm) cc_final: 0.7699 (mmt) outliers start: 42 outliers final: 23 residues processed: 222 average time/residue: 0.5054 time to fit residues: 124.0419 Evaluate side-chains 223 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 270 PHE Chi-restraints excluded: chain A residue 412 THR 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 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 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 696 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 802 ASN ** B 189 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.174882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152555 restraints weight = 17298.491| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.51 r_work: 0.3585 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13288 Z= 0.144 Angle : 0.567 7.577 18110 Z= 0.296 Chirality : 0.042 0.275 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.511 60.403 2514 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.36 % Allowed : 16.08 % Favored : 81.56 % 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: 1.63 (0.19), residues: 710 sheet: -1.36 (0.32), residues: 228 loop : -0.12 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.018 0.002 TYR A 573 PHE 0.014 0.001 PHE B 469 TRP 0.023 0.002 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00320 (13256) covalent geometry : angle 0.55566 (18032) SS BOND : bond 0.00407 ( 18) SS BOND : angle 1.32349 ( 36) hydrogen bonds : bond 0.05040 ( 628) hydrogen bonds : angle 4.33721 ( 1794) link_BETA1-4 : bond 0.00172 ( 4) link_BETA1-4 : angle 1.28511 ( 12) link_NAG-ASN : bond 0.01228 ( 10) link_NAG-ASN : angle 2.33908 ( 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 231 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8356 (tt0) cc_final: 0.8079 (mt0) REVERT: A 270 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: A 811 MET cc_start: 0.7964 (mmm) cc_final: 0.7715 (mmm) REVERT: B 27 GLN cc_start: 0.8345 (tt0) cc_final: 0.8067 (mt0) REVERT: B 224 GLU cc_start: 0.8104 (tp30) cc_final: 0.7904 (tp30) REVERT: B 249 GLU cc_start: 0.7249 (mp0) cc_final: 0.6949 (mm-30) REVERT: B 250 GLU cc_start: 0.7487 (tp30) cc_final: 0.6906 (mp0) REVERT: B 270 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: B 743 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6766 (mp) REVERT: B 776 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7411 (tp) REVERT: B 805 LYS cc_start: 0.8056 (pttm) cc_final: 0.7785 (pttm) outliers start: 32 outliers final: 18 residues processed: 216 average time/residue: 0.5258 time to fit residues: 124.8419 Evaluate side-chains 213 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 270 PHE Chi-restraints excluded: chain A residue 412 THR 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 197 MET Chi-restraints excluded: chain B residue 270 PHE 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 603 ILE Chi-restraints excluded: chain B residue 605 PHE 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 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: 3.9990 chunk 104 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 253 GLN A 338 HIS A 466 HIS ** B 189 ASN ** 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 = 0.4109 r_free = 0.4109 target = 0.174390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152054 restraints weight = 17336.945| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.52 r_work: 0.3579 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13288 Z= 0.163 Angle : 0.605 14.238 18110 Z= 0.310 Chirality : 0.043 0.239 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.447 60.722 2514 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.88 % Allowed : 16.00 % 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: 0.65 (0.21), residues: 1546 helix: 1.62 (0.19), residues: 710 sheet: -1.38 (0.32), residues: 228 loop : -0.14 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.012 0.002 TYR A 573 PHE 0.023 0.001 PHE A 789 TRP 0.024 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00371 (13256) covalent geometry : angle 0.57612 (18032) SS BOND : bond 0.00463 ( 18) SS BOND : angle 1.41295 ( 36) hydrogen bonds : bond 0.05177 ( 628) hydrogen bonds : angle 4.34761 ( 1794) link_BETA1-4 : bond 0.00172 ( 4) link_BETA1-4 : angle 1.30484 ( 12) link_NAG-ASN : bond 0.00332 ( 10) link_NAG-ASN : angle 4.32840 ( 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 239 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8379 (tt0) cc_final: 0.8121 (mt0) REVERT: A 270 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: A 811 MET cc_start: 0.7903 (mmm) cc_final: 0.7693 (mmm) REVERT: B 27 GLN cc_start: 0.8345 (tt0) cc_final: 0.8082 (mt0) REVERT: B 270 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 350 GLU cc_start: 0.7820 (tt0) cc_final: 0.7580 (tt0) REVERT: B 409 ILE cc_start: 0.8250 (mm) cc_final: 0.8026 (tp) REVERT: B 743 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 776 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7431 (tp) outliers start: 39 outliers final: 23 residues processed: 223 average time/residue: 0.5180 time to fit residues: 126.7948 Evaluate side-chains 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 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 689 VAL Chi-restraints excluded: chain B residue 696 LEU 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: 4.9990 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS 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 = 0.4115 r_free = 0.4115 target = 0.174900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152578 restraints weight = 17513.668| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.51 r_work: 0.3587 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13288 Z= 0.148 Angle : 0.578 10.293 18110 Z= 0.301 Chirality : 0.042 0.205 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.343 61.271 2514 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.43 % Allowed : 16.67 % Favored : 80.90 % 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: 0.71 (0.21), residues: 1546 helix: 1.66 (0.19), residues: 710 sheet: -1.37 (0.32), residues: 228 loop : -0.09 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 285 TYR 0.015 0.002 TYR B 573 PHE 0.015 0.001 PHE B 469 TRP 0.023 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00335 (13256) covalent geometry : angle 0.56011 (18032) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.29239 ( 36) hydrogen bonds : bond 0.05046 ( 628) hydrogen bonds : angle 4.28345 ( 1794) link_BETA1-4 : bond 0.00237 ( 4) link_BETA1-4 : angle 1.27750 ( 12) link_NAG-ASN : bond 0.00370 ( 10) link_NAG-ASN : angle 3.28119 ( 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 229 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8364 (tt0) cc_final: 0.8113 (mt0) REVERT: A 270 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: A 350 GLU cc_start: 0.7879 (tt0) cc_final: 0.7648 (tt0) REVERT: B 27 GLN cc_start: 0.8343 (tt0) cc_final: 0.8089 (mt0) REVERT: B 270 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: B 743 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6828 (mp) REVERT: B 776 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7447 (tp) outliers start: 33 outliers final: 21 residues processed: 217 average time/residue: 0.5138 time to fit residues: 122.7391 Evaluate side-chains 221 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 789 PHE 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 197 MET Chi-restraints excluded: chain B residue 270 PHE 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 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: 2.9990 chunk 142 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS 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 = 0.4123 r_free = 0.4123 target = 0.175621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153429 restraints weight = 17536.365| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.51 r_work: 0.3598 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13288 Z= 0.136 Angle : 0.592 9.098 18110 Z= 0.304 Chirality : 0.042 0.195 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.295 61.450 2514 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.77 % Allowed : 17.48 % Favored : 80.75 % 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: 0.62 (0.21), residues: 1546 helix: 1.58 (0.19), residues: 722 sheet: -1.47 (0.31), residues: 240 loop : -0.09 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 285 TYR 0.022 0.001 TYR A 573 PHE 0.014 0.001 PHE B 469 TRP 0.020 0.001 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00303 (13256) covalent geometry : angle 0.57498 (18032) SS BOND : bond 0.00376 ( 18) SS BOND : angle 1.14967 ( 36) hydrogen bonds : bond 0.04944 ( 628) hydrogen bonds : angle 4.25682 ( 1794) link_BETA1-4 : bond 0.00238 ( 4) link_BETA1-4 : angle 1.21645 ( 12) link_NAG-ASN : bond 0.01097 ( 10) link_NAG-ASN : angle 3.24388 ( 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 225 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8361 (tt0) cc_final: 0.8105 (mt0) REVERT: A 270 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: A 350 GLU cc_start: 0.7848 (tt0) cc_final: 0.7528 (tt0) REVERT: B 27 GLN cc_start: 0.8330 (tt0) cc_final: 0.8073 (mt0) REVERT: B 270 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: B 605 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7210 (p90) REVERT: B 743 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 776 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7442 (tp) REVERT: B 811 MET cc_start: 0.7744 (mmm) cc_final: 0.7466 (mmm) outliers start: 24 outliers final: 16 residues processed: 217 average time/residue: 0.5214 time to fit residues: 124.3072 Evaluate side-chains 217 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE 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 743 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 149 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS 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 = 0.4090 r_free = 0.4090 target = 0.172931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150449 restraints weight = 17384.039| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.50 r_work: 0.3550 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13288 Z= 0.235 Angle : 0.661 9.842 18110 Z= 0.343 Chirality : 0.045 0.205 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.504 61.289 2514 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.99 % Allowed : 17.40 % Favored : 80.60 % 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: 0.49 (0.21), residues: 1546 helix: 1.50 (0.19), residues: 708 sheet: -1.42 (0.32), residues: 228 loop : -0.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 285 TYR 0.018 0.002 TYR B 425 PHE 0.021 0.002 PHE B 469 TRP 0.034 0.002 TRP A 742 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00540 (13256) covalent geometry : angle 0.64074 (18032) SS BOND : bond 0.00615 ( 18) SS BOND : angle 1.76124 ( 36) hydrogen bonds : bond 0.05652 ( 628) hydrogen bonds : angle 4.50931 ( 1794) link_BETA1-4 : bond 0.00289 ( 4) link_BETA1-4 : angle 1.40357 ( 12) link_NAG-ASN : bond 0.00874 ( 10) link_NAG-ASN : angle 3.53557 ( 30) =============================================================================== Job complete usr+sys time: 4955.71 seconds wall clock time: 84 minutes 59.71 seconds (5099.71 seconds total)