Starting phenix.real_space_refine on Wed Jun 11 23:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sil_25143/06_2025/7sil_25143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sil_25143/06_2025/7sil_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_25143/06_2025/7sil_25143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sil_25143/06_2025/7sil_25143.map" model { file = "/net/cci-nas-00/data/ceres_data/7sil_25143/06_2025/7sil_25143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sil_25143/06_2025/7sil_25143.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.07, per 1000 atoms: 0.62 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: 3.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.66 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: 4.38 Time building geometry restraints manager: 4.20 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: 0.00 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: 0.280 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.770 ------------------------------------------------------------------------------- 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 : 6.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.028 0.002 TRP A 742 HIS 0.003 0.001 HIS A 463 PHE 0.019 0.001 PHE A 619 TYR 0.025 0.001 TYR A 425 ARG 0.003 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 10) link_NAG-ASN : angle 2.80411 ( 30) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 1.60347 ( 12) hydrogen bonds : bond 0.13424 ( 628) hydrogen bonds : angle 5.46683 ( 1794) SS BOND : bond 0.00251 ( 18) SS BOND : angle 1.51168 ( 36) covalent geometry : bond 0.00414 (13256) covalent geometry : angle 0.69823 (18032) *********************** 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 : 1.516 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: 1.1293 time to fit residues: 283.4384 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 : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 253 GLN B 338 HIS B 466 HIS B 802 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154663 restraints weight = 17411.009| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.48 r_work: 0.3614 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13288 Z= 0.132 Angle : 0.576 10.334 18110 Z= 0.297 Chirality : 0.043 0.306 2066 Planarity : 0.004 0.053 2212 Dihedral : 8.470 59.671 2514 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 8.70 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1546 helix: 1.54 (0.19), residues: 722 sheet: -0.64 (0.34), residues: 228 loop : 0.02 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 742 HIS 0.003 0.001 HIS B 463 PHE 0.022 0.001 PHE A 789 TYR 0.020 0.001 TYR A 425 ARG 0.002 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 10) link_NAG-ASN : angle 2.48952 ( 30) link_BETA1-4 : bond 0.00244 ( 4) link_BETA1-4 : angle 1.23565 ( 12) hydrogen bonds : bond 0.05137 ( 628) hydrogen bonds : angle 4.58543 ( 1794) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.62428 ( 36) covalent geometry : bond 0.00284 (13256) covalent geometry : angle 0.56247 (18032) *********************** 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 226 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8337 (tt0) cc_final: 0.8083 (mt0) REVERT: A 52 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: A 285 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7944 (ttp80) REVERT: A 811 MET cc_start: 0.7819 (mmm) cc_final: 0.7545 (mmm) REVERT: B 27 GLN cc_start: 0.8351 (tt0) cc_final: 0.8107 (mt0) REVERT: B 285 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7889 (ttp80) outliers start: 19 outliers final: 3 residues processed: 213 average time/residue: 1.5563 time to fit residues: 365.8235 Evaluate side-chains 196 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 619 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 0.0050 chunk 146 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 98 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.6096 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156108 restraints weight = 17790.372| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.41 r_work: 0.3614 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13288 Z= 0.136 Angle : 0.548 8.578 18110 Z= 0.285 Chirality : 0.042 0.314 2066 Planarity : 0.004 0.046 2212 Dihedral : 7.899 59.896 2514 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.84 % Allowed : 10.32 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1546 helix: 1.50 (0.19), residues: 736 sheet: -0.76 (0.34), residues: 226 loop : -0.04 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 742 HIS 0.006 0.001 HIS A 312 PHE 0.015 0.001 PHE B 226 TYR 0.016 0.001 TYR A 425 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 10) link_NAG-ASN : angle 2.43238 ( 30) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.27494 ( 12) hydrogen bonds : bond 0.05009 ( 628) hydrogen bonds : angle 4.37160 ( 1794) SS BOND : bond 0.00506 ( 18) SS BOND : angle 1.38471 ( 36) covalent geometry : bond 0.00301 (13256) covalent geometry : angle 0.53563 (18032) *********************** 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 229 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8353 (tt0) cc_final: 0.8088 (mt0) REVERT: A 285 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7938 (ttp80) REVERT: B 27 GLN cc_start: 0.8358 (tt0) cc_final: 0.8101 (mt0) REVERT: B 250 GLU cc_start: 0.7497 (tp30) cc_final: 0.6984 (mp0) REVERT: B 605 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7003 (p90) REVERT: B 743 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6534 (mp) outliers start: 25 outliers final: 5 residues processed: 210 average time/residue: 1.1319 time to fit residues: 262.4780 Evaluate side-chains 200 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154714 restraints weight = 17308.349| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.47 r_work: 0.3610 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13288 Z= 0.130 Angle : 0.538 8.301 18110 Z= 0.281 Chirality : 0.042 0.305 2066 Planarity : 0.004 0.045 2212 Dihedral : 7.673 57.643 2514 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.99 % Allowed : 12.83 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1546 helix: 1.51 (0.19), residues: 736 sheet: -0.89 (0.34), residues: 226 loop : -0.03 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 742 HIS 0.003 0.001 HIS B 463 PHE 0.023 0.001 PHE A 789 TYR 0.013 0.001 TYR A 425 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 10) link_NAG-ASN : angle 2.09196 ( 30) link_BETA1-4 : bond 0.00278 ( 4) link_BETA1-4 : angle 1.23906 ( 12) hydrogen bonds : bond 0.04855 ( 628) hydrogen bonds : angle 4.25383 ( 1794) SS BOND : bond 0.00388 ( 18) SS BOND : angle 1.22587 ( 36) covalent geometry : bond 0.00291 (13256) covalent geometry : angle 0.52848 (18032) *********************** 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 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8339 (tt0) cc_final: 0.8066 (mt0) REVERT: A 257 GLU cc_start: 0.7762 (tt0) cc_final: 0.7522 (tt0) REVERT: A 285 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7963 (ttp80) REVERT: A 473 MET cc_start: 0.7651 (mtp) cc_final: 0.7439 (mtp) REVERT: A 764 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6986 (p) REVERT: B 27 GLN cc_start: 0.8350 (tt0) cc_final: 0.8087 (mt0) REVERT: B 605 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7069 (p90) REVERT: B 743 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6503 (mp) REVERT: B 771 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6959 (pmt) outliers start: 27 outliers final: 8 residues processed: 208 average time/residue: 1.0990 time to fit residues: 252.6082 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 251 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152961 restraints weight = 17511.058| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.47 r_work: 0.3586 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13288 Z= 0.173 Angle : 0.572 7.817 18110 Z= 0.299 Chirality : 0.043 0.221 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.481 57.534 2514 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.43 % Allowed : 13.86 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1546 helix: 1.63 (0.19), residues: 722 sheet: -1.07 (0.33), residues: 228 loop : -0.04 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 742 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 469 TYR 0.014 0.002 TYR A 421 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 10) link_NAG-ASN : angle 2.40529 ( 30) link_BETA1-4 : bond 0.00197 ( 4) link_BETA1-4 : angle 1.30637 ( 12) hydrogen bonds : bond 0.05189 ( 628) hydrogen bonds : angle 4.32523 ( 1794) SS BOND : bond 0.00493 ( 18) SS BOND : angle 1.49561 ( 36) covalent geometry : bond 0.00393 (13256) covalent geometry : angle 0.55999 (18032) *********************** 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 233 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8373 (tt0) cc_final: 0.8138 (mt0) REVERT: A 285 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7956 (ttp80) REVERT: B 27 GLN cc_start: 0.8379 (tt0) cc_final: 0.8119 (mt0) REVERT: B 743 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6657 (mp) REVERT: B 771 MET cc_start: 0.7307 (tmt) cc_final: 0.6826 (pmt) outliers start: 33 outliers final: 13 residues processed: 213 average time/residue: 1.0878 time to fit residues: 257.1953 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 556 GLU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 197 MET 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 619 PHE Chi-restraints excluded: chain B residue 696 LEU 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 90 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 338 HIS B 466 HIS B 493 ASN B 766 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150988 restraints weight = 17588.246| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.48 r_work: 0.3557 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13288 Z= 0.239 Angle : 0.644 10.393 18110 Z= 0.335 Chirality : 0.046 0.207 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.652 57.090 2514 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.88 % Allowed : 14.23 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1546 helix: 1.60 (0.19), residues: 708 sheet: -1.30 (0.31), residues: 228 loop : -0.20 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 742 HIS 0.008 0.001 HIS B 766 PHE 0.020 0.002 PHE A 789 TYR 0.017 0.002 TYR B 425 ARG 0.003 0.001 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 10) link_NAG-ASN : angle 2.70143 ( 30) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.46767 ( 12) hydrogen bonds : bond 0.05689 ( 628) hydrogen bonds : angle 4.52073 ( 1794) SS BOND : bond 0.00632 ( 18) SS BOND : angle 1.84759 ( 36) covalent geometry : bond 0.00551 (13256) covalent geometry : angle 0.62945 (18032) *********************** 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 237 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: A 409 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7988 (tp) REVERT: A 516 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7729 (ptmm) REVERT: B 270 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 743 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6712 (mp) REVERT: B 771 MET cc_start: 0.7389 (tmt) cc_final: 0.6820 (pmt) REVERT: B 776 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7504 (tp) outliers start: 39 outliers final: 18 residues processed: 215 average time/residue: 1.3816 time to fit residues: 328.3866 Evaluate side-chains 216 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 409 ILE Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 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 31 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 493 ASN B 27 GLN B 338 HIS B 466 HIS B 493 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151409 restraints weight = 17346.030| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.46 r_work: 0.3562 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13288 Z= 0.207 Angle : 0.641 12.137 18110 Z= 0.329 Chirality : 0.044 0.215 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.762 58.461 2514 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.36 % Allowed : 15.41 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1546 helix: 1.59 (0.19), residues: 710 sheet: -1.39 (0.31), residues: 228 loop : -0.17 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 742 HIS 0.004 0.001 HIS A 338 PHE 0.029 0.002 PHE B 789 TYR 0.014 0.002 TYR B 425 ARG 0.002 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 10) link_NAG-ASN : angle 4.21834 ( 30) link_BETA1-4 : bond 0.00173 ( 4) link_BETA1-4 : angle 1.37900 ( 12) hydrogen bonds : bond 0.05485 ( 628) hydrogen bonds : angle 4.45670 ( 1794) SS BOND : bond 0.00546 ( 18) SS BOND : angle 1.70633 ( 36) covalent geometry : bond 0.00474 (13256) covalent geometry : angle 0.61342 (18032) *********************** 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 228 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: A 285 ARG cc_start: 0.8227 (ttp80) cc_final: 0.8006 (ttp80) REVERT: B 270 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: B 743 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6705 (mp) REVERT: B 771 MET cc_start: 0.7357 (tmt) cc_final: 0.6809 (pmt) REVERT: B 776 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7458 (tp) REVERT: B 805 LYS cc_start: 0.8124 (pttm) cc_final: 0.7869 (pttm) outliers start: 32 outliers final: 17 residues processed: 210 average time/residue: 1.3418 time to fit residues: 313.6929 Evaluate side-chains 214 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 794 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 802 ASN 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 = 0.4116 r_free = 0.4116 target = 0.174960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152604 restraints weight = 17526.934| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.48 r_work: 0.3589 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13288 Z= 0.143 Angle : 0.576 9.626 18110 Z= 0.300 Chirality : 0.042 0.186 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.463 59.612 2514 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.43 % Allowed : 16.15 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1546 helix: 1.66 (0.19), residues: 722 sheet: -1.37 (0.31), residues: 228 loop : -0.11 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 PHE 0.025 0.001 PHE A 789 TYR 0.016 0.002 TYR A 573 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.01093 ( 10) link_NAG-ASN : angle 2.84515 ( 30) link_BETA1-4 : bond 0.00177 ( 4) link_BETA1-4 : angle 1.26869 ( 12) hydrogen bonds : bond 0.05019 ( 628) hydrogen bonds : angle 4.30307 ( 1794) SS BOND : bond 0.00403 ( 18) SS BOND : angle 1.31644 ( 36) covalent geometry : bond 0.00318 (13256) covalent geometry : angle 0.56177 (18032) *********************** 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 231 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8418 (tttt) cc_final: 0.7956 (ttpp) REVERT: A 270 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 285 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7984 (ttp80) REVERT: B 28 LYS cc_start: 0.8415 (tttt) cc_final: 0.7967 (ttpp) REVERT: B 270 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: B 350 GLU cc_start: 0.7903 (tt0) cc_final: 0.7702 (tt0) REVERT: B 516 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7170 (mppt) REVERT: B 605 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7447 (p90) REVERT: B 743 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6818 (mp) REVERT: B 771 MET cc_start: 0.7309 (tmt) cc_final: 0.6801 (pmt) REVERT: B 776 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7467 (tp) REVERT: B 805 LYS cc_start: 0.8053 (pttm) cc_final: 0.7810 (pttm) outliers start: 33 outliers final: 13 residues processed: 214 average time/residue: 1.5459 time to fit residues: 366.5471 Evaluate side-chains 210 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 689 VAL Chi-restraints excluded: chain A residue 794 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 121 optimal weight: 0.0470 chunk 119 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 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 = 0.4138 r_free = 0.4138 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154670 restraints weight = 17591.707| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.49 r_work: 0.3616 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13288 Z= 0.119 Angle : 0.585 14.099 18110 Z= 0.301 Chirality : 0.042 0.382 2066 Planarity : 0.004 0.041 2212 Dihedral : 7.472 60.133 2514 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.70 % Allowed : 17.11 % Favored : 81.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1546 helix: 1.72 (0.19), residues: 722 sheet: -1.40 (0.31), residues: 240 loop : -0.02 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 742 HIS 0.005 0.000 HIS B 463 PHE 0.011 0.001 PHE A 688 TYR 0.019 0.001 TYR A 573 ARG 0.007 0.000 ARG B 285 Details of bonding type rmsd link_NAG-ASN : bond 0.01962 ( 10) link_NAG-ASN : angle 2.57871 ( 30) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 1.15998 ( 12) hydrogen bonds : bond 0.04674 ( 628) hydrogen bonds : angle 4.15165 ( 1794) SS BOND : bond 0.00295 ( 18) SS BOND : angle 0.98360 ( 36) covalent geometry : bond 0.00250 (13256) covalent geometry : angle 0.57439 (18032) *********************** 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 223 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8434 (tttt) cc_final: 0.7977 (ttpp) REVERT: A 270 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: A 516 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7714 (pttp) REVERT: B 28 LYS cc_start: 0.8424 (tttt) cc_final: 0.7973 (ttpp) REVERT: B 250 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6912 (mp0) REVERT: B 270 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: B 350 GLU cc_start: 0.7795 (tt0) cc_final: 0.7587 (tt0) REVERT: B 516 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7115 (mppt) REVERT: B 605 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7203 (p90) REVERT: B 743 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6751 (mp) REVERT: B 771 MET cc_start: 0.7318 (tmt) cc_final: 0.6850 (pmt) REVERT: B 805 LYS cc_start: 0.8042 (pttm) cc_final: 0.7785 (pttm) REVERT: B 811 MET cc_start: 0.7741 (mmm) cc_final: 0.7462 (mmm) outliers start: 23 outliers final: 11 residues processed: 214 average time/residue: 1.1715 time to fit residues: 277.6640 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 794 SER 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 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 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 = 0.4120 r_free = 0.4120 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153139 restraints weight = 17478.472| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.47 r_work: 0.3595 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13288 Z= 0.159 Angle : 0.598 13.092 18110 Z= 0.309 Chirality : 0.043 0.302 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.640 60.468 2514 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.25 % Allowed : 17.48 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1546 helix: 1.72 (0.19), residues: 722 sheet: -1.38 (0.31), residues: 240 loop : -0.07 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 742 HIS 0.003 0.001 HIS B 463 PHE 0.028 0.001 PHE A 789 TYR 0.015 0.002 TYR A 573 ARG 0.006 0.000 ARG B 285 Details of bonding type rmsd link_NAG-ASN : bond 0.01520 ( 10) link_NAG-ASN : angle 2.43687 ( 30) link_BETA1-4 : bond 0.00208 ( 4) link_BETA1-4 : angle 1.25366 ( 12) hydrogen bonds : bond 0.05024 ( 628) hydrogen bonds : angle 4.22251 ( 1794) SS BOND : bond 0.00416 ( 18) SS BOND : angle 1.28330 ( 36) covalent geometry : bond 0.00359 (13256) covalent geometry : angle 0.58745 (18032) ********************** 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 211 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8423 (tttt) cc_final: 0.8033 (ttpp) REVERT: A 270 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: A 516 LYS cc_start: 0.7956 (ptmm) cc_final: 0.7717 (pttp) REVERT: B 28 LYS cc_start: 0.8414 (tttt) cc_final: 0.8025 (ttpp) REVERT: B 270 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: B 350 GLU cc_start: 0.7854 (tt0) cc_final: 0.7525 (tt0) REVERT: B 516 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7198 (mppt) REVERT: B 526 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 743 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6782 (mp) REVERT: B 771 MET cc_start: 0.7315 (tmt) cc_final: 0.6848 (pmt) REVERT: B 811 MET cc_start: 0.7701 (mmm) cc_final: 0.7440 (mmm) outliers start: 17 outliers final: 10 residues processed: 205 average time/residue: 1.1767 time to fit residues: 265.1754 Evaluate side-chains 203 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 775 PHE 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 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 127 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 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 = 0.4137 r_free = 0.4137 target = 0.176522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.154529 restraints weight = 17541.422| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.56 r_work: 0.3614 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1953 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= 0.116 Angle : 0.555 11.461 18110 Z= 0.286 Chirality : 0.041 0.274 2066 Planarity : 0.004 0.041 2212 Dihedral : 7.636 64.646 2514 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.55 % Allowed : 17.48 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1546 helix: 1.77 (0.19), residues: 722 sheet: -1.33 (0.31), residues: 240 loop : 0.01 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 742 HIS 0.005 0.001 HIS A 312 PHE 0.011 0.001 PHE B 469 TYR 0.018 0.001 TYR B 573 ARG 0.007 0.000 ARG B 285 Details of bonding type rmsd link_NAG-ASN : bond 0.01047 ( 10) link_NAG-ASN : angle 1.88577 ( 30) link_BETA1-4 : bond 0.00244 ( 4) link_BETA1-4 : angle 1.20567 ( 12) hydrogen bonds : bond 0.04584 ( 628) hydrogen bonds : angle 4.07962 ( 1794) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.94917 ( 36) covalent geometry : bond 0.00250 (13256) covalent geometry : angle 0.54807 (18032) =============================================================================== Job complete usr+sys time: 11503.46 seconds wall clock time: 202 minutes 58.05 seconds (12178.05 seconds total)