Starting phenix.real_space_refine on Sun Aug 24 20:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.map" model { file = "/net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9car_45401/08_2025/9car_45401.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12280 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 7866 2.51 5 N 1990 2.21 5 O 2392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12300 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5971 Classifications: {'peptide': 729} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 701} Chain: "B" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5971 Classifications: {'peptide': 729} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 701} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "B" 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 Time building chain proxies: 2.86, per 1000 atoms: 0.23 Number of scatterers: 12300 At special positions: 0 Unit cell: (100.58, 140.17, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2392 8.00 N 1990 7.00 C 7866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.02 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 762 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.02 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 762 " 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 C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 801 " - " ASN A 150 " " NAG A 802 " - " ASN A 92 " " NAG B 801 " - " ASN B 150 " " NAG B 802 " - " ASN B 92 " " NAG C 1 " - " ASN A 229 " " NAG D 1 " - " ASN A 281 " " NAG E 1 " - " ASN A 219 " " NAG F 1 " - " ASN A 321 " " NAG G 1 " - " ASN A 85 " " NAG H 1 " - " ASN B 229 " " NAG I 1 " - " ASN B 281 " " NAG J 1 " - " ASN B 219 " " NAG K 1 " - " ASN B 321 " " NAG L 1 " - " ASN B 85 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 372.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 24 sheets defined 21.9% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.853A pdb=" N ASN A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.576A pdb=" N TYR A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 600 through 615 Processing helix chain 'A' and resid 631 through 641 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.612A pdb=" N TYR A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 687 through 698 removed outlier: 4.704A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.183A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 763 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 91 through 99 removed outlier: 4.715A pdb=" N GLU B 97 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY B 99 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 497 through 507 removed outlier: 3.872A pdb=" N ASN B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 570 removed outlier: 3.551A pdb=" N TYR B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 600 through 615 Processing helix chain 'B' and resid 631 through 641 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.637A pdb=" N TYR B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 686 Processing helix chain 'B' and resid 687 through 698 removed outlier: 4.707A pdb=" N GLU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 4.131A pdb=" N SER B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 removed outlier: 6.657A pdb=" N ILE A 76 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.572A pdb=" N ASP A 104 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 115 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A 135 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU A 117 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASP A 133 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 119 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 131 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 305 removed outlier: 5.418A pdb=" N LEU A 300 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 302 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 305 removed outlier: 5.418A pdb=" N LEU A 300 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 302 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.932A pdb=" N GLN A 388 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP A 393 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 410 removed outlier: 6.607A pdb=" N TYR A 416 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 410 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 454 through 461 removed outlier: 7.007A pdb=" N GLY A 474 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR A 457 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 472 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 459 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 470 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 461 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A 468 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 482 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 493 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N SER A 484 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 491 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 511 through 519 removed outlier: 3.569A pdb=" N VAL A 575 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A 578 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR A 540 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ALA A 625 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 542 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TRP A 627 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 544 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TRP A 629 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS A 649 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 624 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE A 651 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 626 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 628 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 630 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLY A 705 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR A 700 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N MET A 733 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 702 " --> pdb=" O MET A 733 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N TYR A 735 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N HIS A 704 " --> pdb=" O TYR A 735 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.654A pdb=" N ILE B 76 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.587A pdb=" N ASP B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 115 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 135 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU B 117 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP B 133 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN B 119 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER B 131 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 154 through 157 Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AC1, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.450A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.450A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 363 through 364 removed outlier: 4.946A pdb=" N GLN B 388 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 393 " --> pdb=" O GLN B 388 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 410 removed outlier: 6.612A pdb=" N TYR B 416 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 410 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 454 through 461 removed outlier: 7.004A pdb=" N GLY B 474 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR B 457 " --> pdb=" O CYS B 472 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 472 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 459 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 470 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE B 461 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR B 468 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 482 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B 493 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER B 484 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 491 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 511 through 519 removed outlier: 3.598A pdb=" N VAL B 575 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE B 578 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR B 540 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ALA B 625 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 542 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N TRP B 627 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B 544 " --> pdb=" O TRP B 627 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 629 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS B 649 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 624 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE B 651 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 626 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL B 653 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 628 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER B 630 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLY B 705 " --> pdb=" O ALA B 654 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B 700 " --> pdb=" O GLN B 731 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N MET B 733 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 702 " --> pdb=" O MET B 733 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR B 735 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS B 704 " --> pdb=" O TYR B 735 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1125 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: 2.03 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2359 1.33 - 1.45: 3515 1.45 - 1.57: 6690 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 12644 Sorted by residual: bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.52e+01 bond pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.44e+01 bond pdb=" N VAL B 698 " pdb=" CA VAL B 698 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N VAL A 698 " pdb=" CA VAL A 698 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL B 459 " pdb=" CA VAL B 459 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.09e+01 ... (remaining 12639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 10550 1.17 - 2.34: 4872 2.34 - 3.51: 1552 3.51 - 4.68: 200 4.68 - 5.85: 22 Bond angle restraints: 17196 Sorted by residual: angle pdb=" CA GLY B 355 " pdb=" C GLY B 355 " pdb=" O GLY B 355 " ideal model delta sigma weight residual 122.24 118.05 4.19 8.70e-01 1.32e+00 2.32e+01 angle pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" O GLY A 355 " ideal model delta sigma weight residual 122.24 118.08 4.16 8.70e-01 1.32e+00 2.28e+01 angle pdb=" C SER B 242 " pdb=" CA SER B 242 " pdb=" CB SER B 242 " ideal model delta sigma weight residual 116.54 111.15 5.39 1.15e+00 7.56e-01 2.20e+01 angle pdb=" N GLN A 455 " pdb=" CA GLN A 455 " pdb=" C GLN A 455 " ideal model delta sigma weight residual 114.56 108.71 5.85 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N GLN B 455 " pdb=" CA GLN B 455 " pdb=" C GLN B 455 " ideal model delta sigma weight residual 114.56 108.74 5.82 1.27e+00 6.20e-01 2.10e+01 ... (remaining 17191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 7085 21.00 - 42.01: 508 42.01 - 63.01: 98 63.01 - 84.01: 21 84.01 - 105.02: 8 Dihedral angle restraints: 7720 sinusoidal: 3396 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS B 385 " pdb=" SG CYS B 385 " pdb=" SG CYS B 394 " pdb=" CB CYS B 394 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual -86.00 -162.22 76.22 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CD ARG A 658 " pdb=" NE ARG A 658 " pdb=" CZ ARG A 658 " pdb=" NH1 ARG A 658 " ideal model delta sinusoidal sigma weight residual 0.00 44.11 -44.11 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 950 0.081 - 0.162: 766 0.162 - 0.243: 166 0.243 - 0.324: 6 0.324 - 0.405: 2 Chirality restraints: 1890 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.83e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.18e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.18e+01 ... (remaining 1887 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 658 " 0.745 9.50e-02 1.11e+02 3.34e-01 6.80e+01 pdb=" NE ARG A 658 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 658 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 658 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 658 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 54 " -0.738 9.50e-02 1.11e+02 3.31e-01 6.67e+01 pdb=" NE ARG B 54 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 54 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 54 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 54 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 54 " 0.731 9.50e-02 1.11e+02 3.28e-01 6.55e+01 pdb=" NE ARG A 54 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 54 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 54 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 54 " 0.021 2.00e-02 2.50e+03 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4584 2.86 - 3.37: 10995 3.37 - 3.88: 22753 3.88 - 4.39: 26431 4.39 - 4.90: 42759 Nonbonded interactions: 107522 Sorted by model distance: nonbonded pdb=" O PRO A 149 " pdb=" OG1 THR A 152 " model vdw 2.350 3.040 nonbonded pdb=" O PRO B 149 " pdb=" OG1 THR B 152 " model vdw 2.361 3.040 nonbonded pdb=" O GLY A 672 " pdb=" OH TYR A 683 " model vdw 2.399 3.040 nonbonded pdb=" O GLY B 672 " pdb=" OH TYR B 683 " model vdw 2.401 3.040 nonbonded pdb=" OD1 ASP B 171 " pdb=" OG1 THR B 186 " model vdw 2.420 3.040 ... (remaining 107517 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 'H' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.012 0.039 12676 Z= 0.917 Angle : 1.393 7.261 17286 Z= 1.061 Chirality : 0.100 0.405 1890 Planarity : 0.023 0.334 2152 Dihedral : 14.967 105.018 4946 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.52 % Allowed : 6.19 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.19), residues: 1454 helix: 0.51 (0.32), residues: 226 sheet: -0.60 (0.23), residues: 434 loop : -1.30 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 492 TYR 0.018 0.002 TYR A 241 PHE 0.016 0.001 PHE B 387 TRP 0.020 0.002 TRP B 157 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.01212 (12644) covalent geometry : angle 1.39092 (17196) SS BOND : bond 0.00588 ( 6) SS BOND : angle 1.16903 ( 12) hydrogen bonds : bond 0.18871 ( 409) hydrogen bonds : angle 8.31708 ( 1125) link_BETA1-4 : bond 0.00236 ( 12) link_BETA1-4 : angle 0.92229 ( 36) link_NAG-ASN : bond 0.00507 ( 14) link_NAG-ASN : angle 2.32548 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 755 MET cc_start: 0.8883 (mtp) cc_final: 0.8629 (mtp) REVERT: B 293 MET cc_start: 0.8836 (mmp) cc_final: 0.8610 (mmt) outliers start: 46 outliers final: 5 residues processed: 266 average time/residue: 0.1357 time to fit residues: 47.1716 Evaluate side-chains 82 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 170 ASN A 314 GLN B 153 GLN B 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074576 restraints weight = 24342.149| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.92 r_work: 0.2912 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12676 Z= 0.140 Angle : 0.559 5.503 17286 Z= 0.303 Chirality : 0.044 0.167 1890 Planarity : 0.004 0.045 2152 Dihedral : 7.283 62.146 2175 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.45 % Allowed : 9.86 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1454 helix: 1.36 (0.36), residues: 226 sheet: -0.56 (0.22), residues: 494 loop : -0.91 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 658 TYR 0.021 0.001 TYR B 118 PHE 0.026 0.002 PHE B 387 TRP 0.014 0.001 TRP A 216 HIS 0.005 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00315 (12644) covalent geometry : angle 0.54890 (17196) SS BOND : bond 0.00328 ( 6) SS BOND : angle 1.38607 ( 12) hydrogen bonds : bond 0.04602 ( 409) hydrogen bonds : angle 5.96370 ( 1125) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.45080 ( 36) link_NAG-ASN : bond 0.00257 ( 14) link_NAG-ASN : angle 1.76587 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 243 ASP cc_start: 0.7708 (p0) cc_final: 0.7423 (p0) REVERT: A 245 SER cc_start: 0.9435 (m) cc_final: 0.8980 (p) REVERT: A 250 LYS cc_start: 0.8297 (tttt) cc_final: 0.8075 (ttpp) REVERT: A 755 MET cc_start: 0.8748 (mtp) cc_final: 0.8397 (mtp) REVERT: B 250 LYS cc_start: 0.8661 (tttt) cc_final: 0.8418 (ttpp) REVERT: B 755 MET cc_start: 0.8712 (mtp) cc_final: 0.8408 (mtp) outliers start: 32 outliers final: 15 residues processed: 115 average time/residue: 0.0992 time to fit residues: 16.6202 Evaluate side-chains 82 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 677 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070236 restraints weight = 24802.043| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.80 r_work: 0.2839 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12676 Z= 0.167 Angle : 0.526 6.052 17286 Z= 0.282 Chirality : 0.044 0.162 1890 Planarity : 0.004 0.040 2152 Dihedral : 5.723 58.524 2173 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.14 % Allowed : 10.09 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.21), residues: 1454 helix: 1.49 (0.36), residues: 226 sheet: -0.37 (0.23), residues: 476 loop : -0.81 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 669 TYR 0.014 0.002 TYR A 752 PHE 0.022 0.002 PHE B 387 TRP 0.012 0.001 TRP B 216 HIS 0.006 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00388 (12644) covalent geometry : angle 0.51697 (17196) SS BOND : bond 0.00507 ( 6) SS BOND : angle 1.20398 ( 12) hydrogen bonds : bond 0.04164 ( 409) hydrogen bonds : angle 5.50343 ( 1125) link_BETA1-4 : bond 0.00315 ( 12) link_BETA1-4 : angle 1.42892 ( 36) link_NAG-ASN : bond 0.00155 ( 14) link_NAG-ASN : angle 1.53652 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8072 (p0) cc_final: 0.7775 (p0) REVERT: A 245 SER cc_start: 0.9397 (m) cc_final: 0.8963 (p) REVERT: A 250 LYS cc_start: 0.8337 (tttt) cc_final: 0.8101 (ttpp) REVERT: A 253 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8666 (ptp-110) REVERT: A 325 MET cc_start: 0.8279 (ttm) cc_final: 0.7932 (ttm) REVERT: A 530 LEU cc_start: 0.8980 (mt) cc_final: 0.8675 (mm) REVERT: A 755 MET cc_start: 0.8809 (mtp) cc_final: 0.8547 (mtp) REVERT: B 243 ASP cc_start: 0.8164 (p0) cc_final: 0.7697 (p0) REVERT: B 245 SER cc_start: 0.9431 (m) cc_final: 0.9005 (p) REVERT: B 530 LEU cc_start: 0.8943 (mt) cc_final: 0.8648 (mm) outliers start: 28 outliers final: 21 residues processed: 94 average time/residue: 0.0894 time to fit residues: 12.7013 Evaluate side-chains 89 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 677 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.066003 restraints weight = 25253.428| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.80 r_work: 0.2760 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12676 Z= 0.295 Angle : 0.591 6.198 17286 Z= 0.315 Chirality : 0.047 0.160 1890 Planarity : 0.004 0.044 2152 Dihedral : 5.672 53.357 2173 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 11.62 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.21), residues: 1454 helix: 1.30 (0.36), residues: 230 sheet: -0.52 (0.23), residues: 480 loop : -0.84 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 623 TYR 0.016 0.002 TYR A 752 PHE 0.021 0.002 PHE B 387 TRP 0.014 0.002 TRP B 216 HIS 0.007 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00694 (12644) covalent geometry : angle 0.58152 (17196) SS BOND : bond 0.00718 ( 6) SS BOND : angle 1.37767 ( 12) hydrogen bonds : bond 0.04553 ( 409) hydrogen bonds : angle 5.57239 ( 1125) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.52953 ( 36) link_NAG-ASN : bond 0.00308 ( 14) link_NAG-ASN : angle 1.72338 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8213 (p0) cc_final: 0.7884 (p0) REVERT: A 245 SER cc_start: 0.9377 (m) cc_final: 0.8983 (p) REVERT: A 250 LYS cc_start: 0.8269 (tttt) cc_final: 0.8036 (ttpp) REVERT: A 253 ARG cc_start: 0.9069 (mtm110) cc_final: 0.8650 (ptp-110) REVERT: B 245 SER cc_start: 0.9405 (m) cc_final: 0.9055 (p) REVERT: B 361 GLU cc_start: 0.7742 (pm20) cc_final: 0.7536 (pm20) outliers start: 32 outliers final: 26 residues processed: 93 average time/residue: 0.0864 time to fit residues: 12.2447 Evaluate side-chains 85 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068862 restraints weight = 25045.656| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.82 r_work: 0.2815 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12676 Z= 0.122 Angle : 0.483 5.074 17286 Z= 0.260 Chirality : 0.043 0.167 1890 Planarity : 0.003 0.042 2152 Dihedral : 5.415 54.778 2172 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.06 % Allowed : 11.77 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1454 helix: 1.30 (0.35), residues: 230 sheet: -0.40 (0.23), residues: 476 loop : -0.83 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 597 TYR 0.013 0.001 TYR B 661 PHE 0.019 0.001 PHE B 387 TRP 0.012 0.001 TRP A 124 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00276 (12644) covalent geometry : angle 0.47381 (17196) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.03138 ( 12) hydrogen bonds : bond 0.03664 ( 409) hydrogen bonds : angle 5.27085 ( 1125) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.35363 ( 36) link_NAG-ASN : bond 0.00183 ( 14) link_NAG-ASN : angle 1.47267 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8358 (p0) cc_final: 0.8091 (p0) REVERT: A 245 SER cc_start: 0.9372 (m) cc_final: 0.8904 (p) REVERT: A 250 LYS cc_start: 0.8179 (tttt) cc_final: 0.7953 (ttpp) REVERT: A 253 ARG cc_start: 0.9058 (mtm110) cc_final: 0.8631 (ptp-110) REVERT: A 452 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8911 (pt0) REVERT: A 536 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8076 (ttpp) REVERT: B 98 PHE cc_start: 0.6155 (t80) cc_final: 0.5828 (t80) REVERT: B 153 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: B 245 SER cc_start: 0.9394 (m) cc_final: 0.9170 (p) REVERT: B 361 GLU cc_start: 0.7681 (pm20) cc_final: 0.7457 (pm20) REVERT: B 530 LEU cc_start: 0.8866 (mt) cc_final: 0.8665 (mt) REVERT: B 536 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8132 (ttpp) REVERT: B 673 LEU cc_start: 0.8961 (mt) cc_final: 0.8689 (mm) outliers start: 27 outliers final: 19 residues processed: 91 average time/residue: 0.0839 time to fit residues: 11.8494 Evaluate side-chains 87 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 79 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068422 restraints weight = 24829.074| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.78 r_work: 0.2808 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12676 Z= 0.149 Angle : 0.487 5.350 17286 Z= 0.262 Chirality : 0.043 0.161 1890 Planarity : 0.003 0.042 2152 Dihedral : 5.368 53.705 2172 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.99 % Allowed : 12.31 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.21), residues: 1454 helix: 1.43 (0.35), residues: 228 sheet: -0.41 (0.23), residues: 472 loop : -0.81 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.013 0.001 TYR B 661 PHE 0.017 0.001 PHE B 387 TRP 0.011 0.001 TRP A 157 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00346 (12644) covalent geometry : angle 0.47763 (17196) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.05698 ( 12) hydrogen bonds : bond 0.03670 ( 409) hydrogen bonds : angle 5.19661 ( 1125) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.35348 ( 36) link_NAG-ASN : bond 0.00153 ( 14) link_NAG-ASN : angle 1.48867 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8398 (p0) cc_final: 0.8134 (p0) REVERT: A 245 SER cc_start: 0.9347 (m) cc_final: 0.8873 (p) REVERT: A 250 LYS cc_start: 0.8170 (tttt) cc_final: 0.7940 (ttpp) REVERT: A 253 ARG cc_start: 0.9082 (mtm110) cc_final: 0.8654 (ptp-110) REVERT: A 361 GLU cc_start: 0.7718 (pm20) cc_final: 0.7514 (pm20) REVERT: A 452 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8883 (pt0) REVERT: A 536 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8106 (ttpp) REVERT: B 153 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: B 245 SER cc_start: 0.9403 (m) cc_final: 0.9144 (p) REVERT: B 361 GLU cc_start: 0.7695 (pm20) cc_final: 0.7464 (pm20) REVERT: B 452 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8859 (pt0) REVERT: B 530 LEU cc_start: 0.8881 (mt) cc_final: 0.8675 (mt) REVERT: B 536 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8163 (ttpp) REVERT: B 673 LEU cc_start: 0.8981 (mt) cc_final: 0.8705 (mm) REVERT: B 715 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8276 (mt0) outliers start: 26 outliers final: 17 residues processed: 89 average time/residue: 0.0891 time to fit residues: 12.3278 Evaluate side-chains 84 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069697 restraints weight = 24662.549| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.78 r_work: 0.2837 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12676 Z= 0.109 Angle : 0.457 5.458 17286 Z= 0.247 Chirality : 0.042 0.166 1890 Planarity : 0.003 0.041 2152 Dihedral : 5.263 53.852 2172 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.61 % Allowed : 12.39 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.21), residues: 1454 helix: 1.47 (0.35), residues: 228 sheet: -0.38 (0.23), residues: 474 loop : -0.75 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 597 TYR 0.012 0.001 TYR B 752 PHE 0.024 0.001 PHE A 98 TRP 0.011 0.001 TRP B 315 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00247 (12644) covalent geometry : angle 0.44862 (17196) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.92580 ( 12) hydrogen bonds : bond 0.03376 ( 409) hydrogen bonds : angle 5.10805 ( 1125) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.28226 ( 36) link_NAG-ASN : bond 0.00155 ( 14) link_NAG-ASN : angle 1.40005 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8416 (p0) cc_final: 0.8166 (p0) REVERT: A 245 SER cc_start: 0.9345 (m) cc_final: 0.8896 (p) REVERT: A 250 LYS cc_start: 0.8159 (tttt) cc_final: 0.7917 (ttpp) REVERT: A 253 ARG cc_start: 0.9092 (mtm110) cc_final: 0.8655 (ptp-110) REVERT: A 361 GLU cc_start: 0.7727 (pm20) cc_final: 0.7526 (pm20) REVERT: A 536 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8112 (ttpp) REVERT: B 91 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8223 (tp30) REVERT: B 98 PHE cc_start: 0.6051 (t80) cc_final: 0.5728 (t80) REVERT: B 153 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: B 245 SER cc_start: 0.9390 (m) cc_final: 0.9115 (p) REVERT: B 361 GLU cc_start: 0.7727 (pm20) cc_final: 0.7492 (pm20) REVERT: B 536 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8162 (ttpp) REVERT: B 673 LEU cc_start: 0.8993 (mt) cc_final: 0.8723 (mm) REVERT: B 715 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8227 (mt0) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.0889 time to fit residues: 12.0450 Evaluate side-chains 82 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.069709 restraints weight = 24699.362| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.79 r_work: 0.2837 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12676 Z= 0.110 Angle : 0.456 5.632 17286 Z= 0.245 Chirality : 0.042 0.162 1890 Planarity : 0.003 0.040 2152 Dihedral : 5.223 53.666 2172 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 12.84 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1454 helix: 1.54 (0.35), residues: 228 sheet: -0.41 (0.23), residues: 476 loop : -0.68 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 597 TYR 0.012 0.001 TYR B 752 PHE 0.016 0.001 PHE A 387 TRP 0.010 0.001 TRP B 157 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00248 (12644) covalent geometry : angle 0.44740 (17196) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.92709 ( 12) hydrogen bonds : bond 0.03326 ( 409) hydrogen bonds : angle 5.03634 ( 1125) link_BETA1-4 : bond 0.00366 ( 12) link_BETA1-4 : angle 1.27424 ( 36) link_NAG-ASN : bond 0.00137 ( 14) link_NAG-ASN : angle 1.39810 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8415 (p0) cc_final: 0.8173 (p0) REVERT: A 245 SER cc_start: 0.9333 (m) cc_final: 0.8883 (p) REVERT: A 250 LYS cc_start: 0.8121 (tttt) cc_final: 0.7877 (ttpp) REVERT: A 253 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8629 (ptp-110) REVERT: B 91 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8217 (tp30) REVERT: B 98 PHE cc_start: 0.6099 (t80) cc_final: 0.5868 (t80) REVERT: B 153 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: B 245 SER cc_start: 0.9383 (m) cc_final: 0.9114 (p) REVERT: B 361 GLU cc_start: 0.7803 (pm20) cc_final: 0.7585 (pm20) REVERT: B 536 LYS cc_start: 0.8630 (ptpt) cc_final: 0.8164 (ttpp) REVERT: B 673 LEU cc_start: 0.8996 (mt) cc_final: 0.8718 (mm) REVERT: B 715 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8237 (mt0) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.0831 time to fit residues: 11.1794 Evaluate side-chains 83 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 chunk 93 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.070965 restraints weight = 24577.513| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.77 r_work: 0.2859 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12676 Z= 0.095 Angle : 0.452 7.782 17286 Z= 0.243 Chirality : 0.042 0.164 1890 Planarity : 0.003 0.040 2152 Dihedral : 5.155 53.809 2172 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.45 % Allowed : 12.84 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.22), residues: 1454 helix: 1.61 (0.35), residues: 228 sheet: -0.37 (0.23), residues: 476 loop : -0.64 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 597 TYR 0.011 0.001 TYR B 752 PHE 0.026 0.001 PHE A 98 TRP 0.012 0.001 TRP B 315 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00213 (12644) covalent geometry : angle 0.44425 (17196) SS BOND : bond 0.00282 ( 6) SS BOND : angle 0.85498 ( 12) hydrogen bonds : bond 0.03163 ( 409) hydrogen bonds : angle 4.96125 ( 1125) link_BETA1-4 : bond 0.00384 ( 12) link_BETA1-4 : angle 1.22909 ( 36) link_NAG-ASN : bond 0.00163 ( 14) link_NAG-ASN : angle 1.34514 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9195 (pp) REVERT: A 243 ASP cc_start: 0.8418 (p0) cc_final: 0.8189 (p0) REVERT: A 245 SER cc_start: 0.9309 (m) cc_final: 0.8831 (p) REVERT: A 250 LYS cc_start: 0.8145 (tttt) cc_final: 0.7860 (ttpp) REVERT: A 253 ARG cc_start: 0.9095 (mtm110) cc_final: 0.8636 (ptp-110) REVERT: B 74 ASN cc_start: 0.8839 (m-40) cc_final: 0.8618 (m110) REVERT: B 98 PHE cc_start: 0.6068 (t80) cc_final: 0.5852 (t80) REVERT: B 153 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: B 245 SER cc_start: 0.9360 (m) cc_final: 0.9066 (p) REVERT: B 673 LEU cc_start: 0.8999 (mt) cc_final: 0.8724 (mm) REVERT: B 715 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8185 (mt0) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.0844 time to fit residues: 11.4461 Evaluate side-chains 82 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070834 restraints weight = 24777.917| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.82 r_work: 0.2865 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12676 Z= 0.121 Angle : 0.471 8.338 17286 Z= 0.251 Chirality : 0.042 0.160 1890 Planarity : 0.003 0.040 2152 Dihedral : 5.175 53.467 2172 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.45 % Allowed : 12.84 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.22), residues: 1454 helix: 1.64 (0.35), residues: 228 sheet: -0.38 (0.23), residues: 476 loop : -0.62 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 597 TYR 0.021 0.001 TYR B 58 PHE 0.015 0.001 PHE A 387 TRP 0.011 0.001 TRP A 157 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00279 (12644) covalent geometry : angle 0.46318 (17196) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.93345 ( 12) hydrogen bonds : bond 0.03295 ( 409) hydrogen bonds : angle 4.96665 ( 1125) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.26127 ( 36) link_NAG-ASN : bond 0.00125 ( 14) link_NAG-ASN : angle 1.38305 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9222 (pp) REVERT: A 243 ASP cc_start: 0.8426 (p0) cc_final: 0.8186 (p0) REVERT: A 245 SER cc_start: 0.9299 (m) cc_final: 0.8837 (p) REVERT: A 250 LYS cc_start: 0.8137 (tttt) cc_final: 0.7840 (ttpp) REVERT: A 253 ARG cc_start: 0.9114 (mtm110) cc_final: 0.8640 (ptp-110) REVERT: B 153 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: B 245 SER cc_start: 0.9341 (m) cc_final: 0.9050 (p) REVERT: B 673 LEU cc_start: 0.8994 (mt) cc_final: 0.8709 (mm) REVERT: B 715 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8216 (mt0) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.0851 time to fit residues: 11.0075 Evaluate side-chains 80 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.068323 restraints weight = 24896.836| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.81 r_work: 0.2806 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12676 Z= 0.234 Angle : 0.559 8.284 17286 Z= 0.296 Chirality : 0.045 0.195 1890 Planarity : 0.004 0.041 2152 Dihedral : 5.492 53.254 2172 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.53 % Allowed : 13.15 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.22), residues: 1454 helix: 1.61 (0.36), residues: 228 sheet: -0.48 (0.23), residues: 476 loop : -0.73 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 669 TYR 0.018 0.002 TYR B 58 PHE 0.028 0.002 PHE A 98 TRP 0.010 0.001 TRP A 157 HIS 0.007 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00547 (12644) covalent geometry : angle 0.54911 (17196) SS BOND : bond 0.00647 ( 6) SS BOND : angle 1.12696 ( 12) hydrogen bonds : bond 0.03971 ( 409) hydrogen bonds : angle 5.18300 ( 1125) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 1.44249 ( 36) link_NAG-ASN : bond 0.00271 ( 14) link_NAG-ASN : angle 1.74240 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.72 seconds wall clock time: 33 minutes 26.18 seconds (2006.18 seconds total)